diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000002_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000002_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ec7df45c542848dee1d4e0c6bb3beb7952782a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000002_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_02348:0,GCF_005280335_PROKKA_02630:0)n2:0.0233998,(GCF_023573625_PROKKA_01019:5e-09,((GCF_002008305_PROKKA_01387:0,GCF_003691675_PROKKA_00320:0,GCF_003691675_PROKKA_01328:0,GCF_003691675_PROKKA_02266:0)n5:5e-09,((GCF_020097155_PROKKA_00316:0.0567134,(GCF_003691675_PROKKA_00787:5e-09,GCF_003691675_PROKKA_01659:0.0136713)n8:0.00151904)n7:0.00815592,(GCF_003691675_PROKKA_00332:0,GCF_020097155_PROKKA_02231:0)n9:0.0140067)n6:0.00140067)n4:0.00015563)n3:0.0233965)n1:0.0038409,((GCF_002008305_PROKKA_01069:0.0155085,((GCF_003691675_PROKKA_01117:0.0153727,(GCF_020097155_PROKKA_01795:0,GCF_020097155_PROKKA_01837:0,GCF_020097155_PROKKA_02208:0)n14:5e-09)n13:0.00768729,(GCF_005280335_PROKKA_01280:5e-09,(GCF_005280335_PROKKA_01313:0,GCF_005280335_PROKKA_01318:0)n16:0.0075694)n15:0.0469002)n12:5e-09)n11:5e-09,((GCF_005280335_PROKKA_00757:0,GCF_005280335_PROKKA_01303:0,GCF_005280335_PROKKA_02332:0)n18:5e-09,(GCF_023573625_PROKKA_01540:5e-09,((GCF_020097155_PROKKA_00621:0,GCF_020097155_PROKKA_00626:0)n21:0.015475,(GCF_023573625_PROKKA_00113:0,GCF_023573625_PROKKA_01883:0)n22:6e-09)n20:0.00776783)n19:0.00690848)n17:0.000767609)n10:0.0038409)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000019_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000019_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..746d8fa78c5964a884f1cb778fd9dc6300509db6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000019_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01886:0.013508,(((GCF_005280335_PROKKA_02497:0,GCF_005280335_PROKKA_02616:0)n3:5e-09,(GCF_005280335_PROKKA_02275:0.0102694,GCF_005280335_PROKKA_02634:5e-09)n4:0.0102682)n2:0.0226592,((GCF_003691675_PROKKA_00342:0.0961499,GCF_023573625_PROKKA_01543:0.288029)n6:0.0685307,(GCF_023573625_PROKKA_00899:0.0372964,GCF_003691675_PROKKA_01766:0.038296)n7:0.00425511)n5:0.207353)n1:0.0230392)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000030_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000030_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb1b98a897fdf31757dcb204a53bf38bd2515da4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000030_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_02334:5e-09,(GCF_005280335_PROKKA_00171:0.589658,(GCF_005280335_PROKKA_00191:1.12225,GCF_005280335_PROKKA_02217:0.747883)n3:0.326334)n2:0.628863)n1:0.00198673,(GCF_002008305_PROKKA_00169:0.00603084,(GCF_003691675_PROKKA_00360:5e-09,GCF_023573625_PROKKA_02010:0.00199069)n5:0.00400144)n4:0.00198673)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000038_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000038_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31b69784e37e5e1a15b7910eea4b3709db811bca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000038_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01023:0.0453106,((GCF_005280335_PROKKA_01099:0.0624218,(GCF_002008305_PROKKA_01778:0.00213185,(GCF_002008305_PROKKA_00836:0.127971,GCF_002008305_PROKKA_00837:0.0590392)n4:0.474128)n3:0.0526808)n2:0.0456872,(GCF_003691675_PROKKA_01485:0.00975291,GCF_023573625_PROKKA_01707:0.00414833)n5:0.00347634)n1:0.0453106)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000039_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000039_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f955a972da9864e82096e8d4aae1dfe42e1f8095
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000039_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01944:0.302987,((GCF_005280335_PROKKA_02045:0.691889,((GCF_002008305_PROKKA_00894:0.0271898,GCF_003691675_PROKKA_00616:0.0302301)n4:0.644884,(GCF_002008305_PROKKA_00884:0.00825059,GCF_003691675_PROKKA_00606:0.00961045)n5:0.524179)n3:0.0582421)n2:0.561111,GCF_023573625_PROKKA_00845:0.742872)n1:0.0951319)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000055_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000055_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..714469b1fe17eb56e0cafd841f1e3e4c6fbfeda7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000055_tree.txt
@@ -0,0 +1 @@
+(GCF_023573625_PROKKA_00735:0.225294,((GCF_020097155_PROKKA_00792:0.0836997,(GCF_003691675_PROKKA_01696:0.0139572,GCF_005280335_PROKKA_00855:0.00623493)n3:0.122743)n2:0.115924,(GCF_005280335_PROKKA_01010:0.469059,(GCF_020097155_PROKKA_00943:0.492378,GCF_020097155_PROKKA_00870:0.646041)n5:0.0717824)n4:0.0950986)n1:0.0105665)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000073_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000073_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60df2a2a276f279036362d3ecdfad24590624c72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000073_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00079:0.126939,GCF_020097155_PROKKA_00526:0.889959)n1:0.0522248,(GCF_005280335_PROKKA_00111:0.0515937,(GCF_003691675_PROKKA_02272:0.0107424,(GCF_002008305_PROKKA_00258:0.00411397,GCF_023573625_PROKKA_00257:5e-09)n4:0.014808)n3:0.0609834)n2:0.0522248)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000075_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000075_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc88b1cc716e562b4a091b4136d2737c626e4860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000075_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00057:0.26398,GCF_020097155_PROKKA_00450:1.72894)n1:0.0354745,(GCF_005280335_PROKKA_00071:0.0172183,(GCF_003691675_PROKKA_02297:5e-09,(GCF_002008305_PROKKA_00282:0.0100593,GCF_023573625_PROKKA_00281:0.00499956)n4:0.0101127)n3:0.0723531)n2:0.0354745)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000078_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000078_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbfc7612c9579b259e70e758c19d29de3cbeb0c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000078_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00027:0.24417,(GCF_020097155_PROKKA_00654:1.32246,GCF_020097155_PROKKA_00023:0.174907)n2:0.0194342)n1:0.0365071,(GCF_002008305_PROKKA_00310:0.00291069,(GCF_003691675_PROKKA_00025:0.00559649,GCF_023573625_PROKKA_00317:5e-09)n4:0.0112438)n3:0.103671)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000085_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000085_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7924c21315b271936cd01314266829e4d3dd1c47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000085_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02405:0.0525143,((GCF_002008305_PROKKA_00423:0.0165947,(GCF_003691675_PROKKA_00144:0.0118738,GCF_023573625_PROKKA_00426:0.0062224)n3:0.011001)n2:0.0782166,(GCF_005280335_PROKKA_02535:0.101283,GCF_005280335_PROKKA_02534:0.0872366)n4:0.00969295)n1:0.0184057)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000086_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000086_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f00120e07059bb34f5a0d89b5849e53a351fe23a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000086_tree.txt
@@ -0,0 +1 @@
+(((GCF_005280335_PROKKA_02509:0.0347178,(GCF_020097155_PROKKA_00683:0.97028,GCF_020097155_PROKKA_02380:0.0591297)n3:0.00656997)n2:0.0384262,GCF_023573625_PROKKA_00451:0.00232437)n1:2.5e-09,(GCF_002008305_PROKKA_00448:5e-09,GCF_003691675_PROKKA_00169:0.00233114)n4:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000101_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000101_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15fd6e95c63d1fc83bcf90f269bf5f778fce7fa6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000101_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02170:0.0617663,(GCF_005280335_PROKKA_02313:0.0673918,((GCF_003691675_PROKKA_00387:0.007385,GCF_023573625_PROKKA_00620:0.0048582)n3:0.0270805,(GCF_002008305_PROKKA_00841:1.91988,GCF_002008305_PROKKA_00650:0.0148699)n4:0.00165221)n2:0.0393187)n1:0.150212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000102_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000102_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f4dec67179d4ec45b9e1751f30061f4f0f9b7a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000102_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02164:0.122944,((GCF_005280335_PROKKA_00162:1.39379,GCF_005280335_PROKKA_02307:0.0572831)n2:0.0435128,(GCF_003691675_PROKKA_00393:5e-09,(GCF_002008305_PROKKA_00656:5e-09,GCF_023573625_PROKKA_00626:0.00354992)n4:0.00354882)n3:0.0215804)n1:0.122944)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000121_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000121_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bffe64b1f36166790415d034a42e4d4e72322ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000121_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01639:0.0439273,((GCF_002008305_PROKKA_01147:0.00374438,(GCF_003691675_PROKKA_00866:0,GCF_023573625_PROKKA_01097:0)n3:0.00386493)n2:0.0425685,(GCF_005280335_PROKKA_01745:0.0110625,GCF_005280335_PROKKA_00771:1.43435)n4:0.00775569)n1:0.0439273)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000122_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000122_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8349f081091df872c40fb6a23c6349ee034a7622
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000122_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01740:6e-09,(GCF_020097155_PROKKA_01634:0.154248,GCF_020097155_PROKKA_00545:1.33084)n2:0.147871)n1:0.0245682,(GCF_002008305_PROKKA_01152:0.00620805,(GCF_003691675_PROKKA_00871:0,GCF_023573625_PROKKA_01102:0)n4:0.00484693)n3:0.0470658)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000125_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000125_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c27f32503b3300d4faa8debc1348c0f6fda71a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000125_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_00131:1.36414,GCF_020097155_PROKKA_01453:0.1415)n1:0.0629249,(GCF_005280335_PROKKA_01557:0.0475667,((GCF_002008305_PROKKA_01334:0,GCF_023573625_PROKKA_01290:0)n4:5e-09,GCF_003691675_PROKKA_01055:0.0028761)n3:0.0403515)n2:0.0629249)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000127_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000127_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b49fd3aeb5b7aa17d31de735016377cb238ab471
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000127_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01419:0.179044,(GCF_005280335_PROKKA_01524:0.0821859,(GCF_023573625_PROKKA_01324:0.00400482,(GCF_003691675_PROKKA_01089:0.0280004,(GCF_002008305_PROKKA_01953:1.50914,GCF_002008305_PROKKA_01369:0.00817524)n4:0.000908361)n3:0.0114932)n2:0.0343099)n1:0.179044)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000137_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000137_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..768674cc6f2efd81fdd49eeb17d91caed5653184
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000137_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00456:0.0674171,((GCF_005280335_PROKKA_01337:0.0207395,GCF_023573625_PROKKA_01512:0.00693389)n2:5e-09,(GCF_003691675_PROKKA_01296:0.00691918,(GCF_002008305_PROKKA_02251:0.0762475,GCF_002008305_PROKKA_01585:0.00749909)n4:0.000833232)n3:0.00302958)n1:0.709677)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000154_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000154_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9164c8abe8299522ef977567ae5bfe7caff40b64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000154_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00875:0.142041,(GCF_020097155_PROKKA_00810:0.0159145,GCF_020097155_PROKKA_00823:0.177426)n2:0.0197139)n1:0.103096,((GCF_002008305_PROKKA_01983:0,GCF_023573625_PROKKA_01909:0)n4:5e-09,GCF_003691675_PROKKA_01677:0.00624049)n3:0.00917423)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000158_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000158_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c7427f827c04e5a363f22b016adef32014cad4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000158_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00750:0.154272,(((GCF_005280335_PROKKA_00789:0.0273817,GCF_023573625_PROKKA_01966:0.00209429)n3:0.0423828,(GCF_002008305_PROKKA_02031:0.0221068,GCF_002008305_PROKKA_02029:0.0170158)n4:0.00189064)n2:0.11949,GCF_003691675_PROKKA_01738:5e-09)n1:0.154272)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000167_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000167_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8f2da39fa3f5835e4d2da61bb1de0860c59bdf1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000167_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00491:0.0966885,(GCF_005280335_PROKKA_00566:0.0703984,(GCF_003691675_PROKKA_01898:0.00634878,(GCF_023573625_PROKKA_00166:1.46154,(GCF_002008305_PROKKA_02184:5e-09,GCF_023573625_PROKKA_02129:0.00371049)n4:0.00448949)n3:0.000498833)n2:0.0359085)n1:0.0422593)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000172_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000172_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..055b199e4f9d2024d3e27e6e51d11be205a734f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000172_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_00111:0.0984241,((GCF_005280335_PROKKA_01501:0.727312,(GCF_020097155_PROKKA_00694:0.197338,GCF_020097155_PROKKA_00288:0.397796)n4:0.0441996)n3:0.33429,GCF_020097155_PROKKA_00347:0.0722297)n2:0.00802553)n1:0.143819,GCF_003691675_PROKKA_02019:1.11717)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000179_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000179_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..512b8c5e541f94b6636b03cd44b4c826bddcfdfe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000179_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00370:0.0434789,(GCF_005280335_PROKKA_00418:0.0215076,(GCF_003691675_PROKKA_02011:0.00110173,(GCF_002008305_PROKKA_00006:0.00229181,GCF_023573625_PROKKA_00006:5e-09)n3:5e-09)n2:0.0245563)n1:0.0434789)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000182_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000182_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dda05eca8e490c59e8a663f93aeb46fc196d61cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000182_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02181:0.149491,(GCF_005280335_PROKKA_00386:0.0685417,(GCF_023573625_PROKKA_00011:5e-09,(GCF_003691675_PROKKA_02029:0.0115118,GCF_002008305_PROKKA_00011:0.00384383)n3:0.00377888)n2:0.0525377)n1:0.149491)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000194_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000194_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bdacbbd3b1bba63d08c283f6fb0e029593f48e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000194_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00304:0.0664401,(GCF_005280335_PROKKA_00366:0.020539,(GCF_002008305_PROKKA_00032:5e-09,(GCF_003691675_PROKKA_02049:0.0030909,GCF_023573625_PROKKA_00031:0.00615684)n3:0.00306956)n2:0.0112394)n1:0.0664401)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000197_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000197_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a61f0d26290bbd25f865ba93bcda49807780a667
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000197_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00209:0.0101908,(GCF_023573625_PROKKA_00190:0.0059304,(GCF_003691675_PROKKA_02020:1.45261,(GCF_002008305_PROKKA_00190:6e-09,GCF_002008305_PROKKA_00035:0.803399)n3:0.0892666)n2:0.608316)n1:0.0101908)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000198_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000198_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..777139e3a458fd9d05bbf0d0b70685abfee009a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000198_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00302:0.0272878,(GCF_005280335_PROKKA_00361:0.0959516,(GCF_023573625_PROKKA_00034:0.00862329,(GCF_002008305_PROKKA_00039:5e-09,GCF_003691675_PROKKA_02052:0.00423473)n3:5e-09)n2:0.0502468)n1:0.0272878)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000210_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000210_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fefdf2e72974461fe75d11d60a9978570fdfaddc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000210_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00278:0.192732,(GCF_003691675_PROKKA_02070:0.00298778,(GCF_005280335_PROKKA_00338:0.135539,(GCF_002008305_PROKKA_00057:0.0026836,GCF_023573625_PROKKA_00052:0.00267826)n3:5e-09)n2:0.00248432)n1:0.192732)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000211_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000211_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5609116640118e939fdb3ade038aff9d3a05d838
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000211_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00277:0.16741,(GCF_005280335_PROKKA_00337:0.0575252,(GCF_002008305_PROKKA_00058:0.00780026,(GCF_003691675_PROKKA_02071:0.0056242,GCF_023573625_PROKKA_00053:0.00140212)n3:0.00203306)n2:0.0795924)n1:0.16741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000213_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000213_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f60665dbd9eb8cba15aa40667c347bb1fe09d506
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000213_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00275:0.0349221,(GCF_005280335_PROKKA_00334:0.0187596,((GCF_002008305_PROKKA_00061:0,GCF_023573625_PROKKA_00056:0)n3:5e-09,GCF_003691675_PROKKA_02074:0.00932753)n2:0.0292382)n1:0.0349221)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000225_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000225_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c2d905d3e748d19586ce51f6fa9d004484dc559
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000225_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00256:0.181184,(GCF_005280335_PROKKA_00315:0.0720153,(GCF_002008305_PROKKA_00078:0.0161606,(GCF_003691675_PROKKA_02091:0,GCF_023573625_PROKKA_00072:0)n3:0.016553)n2:0.102898)n1:0.181184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000226_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000226_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0dee43d9d7dbed686ac2d0dd0756bcac4ba6a35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000226_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00255:0.194519,(GCF_005280335_PROKKA_00314:0.101092,(GCF_002008305_PROKKA_00079:0.0287554,(GCF_003691675_PROKKA_02092:0,GCF_023573625_PROKKA_00073:0)n3:0.00728075)n2:0.0999786)n1:0.194519)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000243_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000243_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0581e12e633b1fd73aeca969e79da6c2bb2af058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000243_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00238:0.0853837,(GCF_005280335_PROKKA_00293:0.207122,((GCF_002008305_PROKKA_00098:0,GCF_023573625_PROKKA_00093:0)n3:5e-09,GCF_003691675_PROKKA_02111:0.0131183)n2:0.193888)n1:0.0853837)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000245_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000245_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71ad53ff2e981b372803cdd2f41f446c97a61245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000245_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00235:0.192437,(GCF_005280335_PROKKA_00289:5e-09,(GCF_003691675_PROKKA_02114:5e-09,(GCF_002008305_PROKKA_00101:5e-09,GCF_023573625_PROKKA_00096:0.0162854)n3:0.01619)n2:0.0498763)n1:0.192437)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000257_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000257_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6fb9d554015861d71c4d02cea65535c6c4aa551
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000257_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00204:0.0798111,(GCF_005280335_PROKKA_00272:0.0974807,((GCF_002008305_PROKKA_00115:0,GCF_003691675_PROKKA_02128:0)n3:0.00426828,GCF_023573625_PROKKA_00120:0.00400912)n2:0.089999)n1:0.0798111)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000264_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000264_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d7fcdb65d9d950981b1dfc9725812a3cac3c581
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000264_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00193:0.119622,(GCF_005280335_PROKKA_00259:0.0690494,(GCF_002008305_PROKKA_00126:0.008145,(GCF_003691675_PROKKA_02140:0.00306198,GCF_023573625_PROKKA_00134:5e-09)n3:0.0104122)n2:0.0778492)n1:0.119622)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000267_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000267_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c80c19050028c49c73d27944524763398fbc442
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000267_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00188:0.0623438,(GCF_005280335_PROKKA_00252:0.108645,(GCF_023573625_PROKKA_00141:0.0219943,(GCF_002008305_PROKKA_00133:0.0062645,GCF_003691675_PROKKA_02147:0.00188606)n3:0.0122163)n2:0.104837)n1:0.0623438)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000270_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000270_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0abc0f91a52c8f52883d07237550c779b604464f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000270_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00181:0.00929656,((GCF_002008305_PROKKA_00137:0.00372642,GCF_005280335_PROKKA_00247:0.0715891)n2:0.00370741,(GCF_003691675_PROKKA_02151:5e-09,GCF_023573625_PROKKA_00145:0.00370457)n3:5e-09)n1:0.00929656)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000274_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000274_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b03daa099504d57af64f7986c688ee11c132dc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000274_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00177:0.168865,(GCF_005280335_PROKKA_00243:0.107545,(GCF_002008305_PROKKA_00141:0.00311403,(GCF_003691675_PROKKA_02155:0,GCF_023573625_PROKKA_00149:0)n3:0.00515727)n2:0.0764295)n1:0.168865)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000276_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000276_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2c0d46da1a7d8776d17901a37118a7bf6a696ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000276_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00175:0.0371212,(GCF_005280335_PROKKA_00241:0.0865828,(GCF_023573625_PROKKA_00151:0.00593509,(GCF_003691675_PROKKA_02157:0.0130984,GCF_002008305_PROKKA_00143:0.00681703)n3:0.000281041)n2:0.0592956)n1:0.0371212)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000280_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000280_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48b1b00042986eda06cd704ad8f3663f6a24f8d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000280_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00820:0.0609395,((GCF_002008305_PROKKA_00148:0,GCF_003691675_PROKKA_02162:0,GCF_023573625_PROKKA_00156:0)n2:0.00629425,GCF_005280335_PROKKA_00235:0.0140518)n1:0.0609395)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000287_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000287_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6f11d78fb6aab4f4d2a578d766c71dac153d6ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000287_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00169:0.650968,(GCF_005280335_PROKKA_00223:0.0149304,(GCF_003691675_PROKKA_02174:0.0251951,(GCF_002008305_PROKKA_00178:0.00601323,GCF_023573625_PROKKA_00175:0.0510235)n3:0.0144957)n2:0.0428155)n1:0.650968)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000289_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000289_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..837d63b1b8e0178a49b112d038a39b4e0463d169
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000289_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00166:0.052807,(GCF_005280335_PROKKA_00221:0.0202464,(GCF_003691675_PROKKA_02176:0.00269585,(GCF_023573625_PROKKA_00177:0.0054009,GCF_002008305_PROKKA_00180:0.00269069)n3:0.00132241)n2:0.0171959)n1:0.052807)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000298_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000298_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5d328df946f135c439feb46e8bc84d7a062de2d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000298_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00154:2.5e-09,(GCF_005280335_PROKKA_00207:0.0288614,(GCF_002008305_PROKKA_00193:0.00571307,(GCF_003691675_PROKKA_02189:0,GCF_023573625_PROKKA_00193:0)n3:5e-09)n2:0.00569246)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000305_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000305_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3be2081fb172d07534057a79e06db9310f793d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000305_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00140:0.00306697,(GCF_002008305_PROKKA_00204:0.00461133,((GCF_003691675_PROKKA_02199:0,GCF_023573625_PROKKA_00206:0)n3:0.00788612,GCF_005280335_PROKKA_00198:0.21002)n2:0.00453874)n1:0.00306697)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000312_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000312_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..071a4971cfa34fd25d0e7d6a5019dcffe5d2b8b5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000312_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00120:0.128342,(GCF_005280335_PROKKA_00169:0.202063,(GCF_023573625_PROKKA_00214:0.0168546,(GCF_002008305_PROKKA_00214:0.0364367,GCF_003691675_PROKKA_02207:0.0280191)n3:0.0110104)n2:0.0750789)n1:0.128342)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000313_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000313_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..167e90703691b00d0179cecb7d3d28d6883b7713
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000313_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00119:0.605644,(GCF_005280335_PROKKA_00166:0.357479,((GCF_002008305_PROKKA_00215:0,GCF_003691675_PROKKA_02208:0)n3:5e-09,GCF_023573625_PROKKA_00215:0.0202792)n2:0.218365)n1:0.605644)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000321_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000321_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2616a4009d5b35ea79063c8791a77613ae71b73b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000321_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00108:0.0335028,(GCF_005280335_PROKKA_00151:0.135636,(GCF_023573625_PROKKA_00231:0.00229916,(GCF_002008305_PROKKA_00230:0.00195798,GCF_003691675_PROKKA_02243:0.00188003)n3:0.00930367)n2:0.0585)n1:0.0335028)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000323_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000323_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e98f23ed7c4b3ae9912443ecbd73220f84af880c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000323_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00105:0.0563272,(GCF_005280335_PROKKA_00147:0.111509,(GCF_023573625_PROKKA_00233:0.00630314,(GCF_002008305_PROKKA_00232:0.00325259,GCF_003691675_PROKKA_02245:0.0033612)n3:0.0205365)n2:0.160375)n1:0.0563272)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000329_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000329_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f73601a53c6e11b95d4423d95651939ee42e9e3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000329_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00097:0.205511,(GCF_005280335_PROKKA_00132:0.0525527,(GCF_002008305_PROKKA_00239:0.00550086,(GCF_003691675_PROKKA_02252:0,GCF_023573625_PROKKA_00240:0)n3:0.00554103)n2:0.0527197)n1:0.205511)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000333_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000333_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e44984efd0ab916a9aa2fdbd01cf98a4ee96a28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000333_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00092:0.180749,(GCF_005280335_PROKKA_00123:0.0230347,(GCF_023573625_PROKKA_00246:0.00294237,(GCF_002008305_PROKKA_00246:0.0029907,GCF_003691675_PROKKA_02258:5e-09)n3:0.00305186)n2:0.0221317)n1:0.180749)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000346_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000346_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e260a11dc89c9776b13c9594d4536d151da18702
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000346_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00067:0.148862,((GCF_002008305_PROKKA_00267:0,GCF_003691675_PROKKA_02280:0,GCF_023573625_PROKKA_00265:0)n2:0.0493004,GCF_005280335_PROKKA_00096:0.074978)n1:0.148862)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000349_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000349_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f769f4851c8e5a17dab3219a519acb381414dc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000349_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00064:0.0561884,(GCF_005280335_PROKKA_00087:0.0425379,(GCF_002008305_PROKKA_00270:0.00934128,(GCF_003691675_PROKKA_02285:0,GCF_023573625_PROKKA_00268:0)n3:0.00256215)n2:0.018143)n1:0.0561884)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000361_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000361_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5074aadf3e2b8a93d5013dfc57752349665a650c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000361_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00040:0.0406922,((GCF_002008305_PROKKA_00293:0,GCF_003691675_PROKKA_00001:0,GCF_023573625_PROKKA_00300:0)n2:0.0161382,GCF_005280335_PROKKA_00061:0.0303967)n1:0.0406922)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000362_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000362_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..533bb33cb7d26289084b213c4f1e73115610bb7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000362_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00039:0.10969,(GCF_005280335_PROKKA_00060:0.0338653,(GCF_002008305_PROKKA_00294:5e-09,(GCF_003691675_PROKKA_00002:5e-09,GCF_023573625_PROKKA_00301:0.00580708)n3:0.00582184)n2:0.0143945)n1:0.10969)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000364_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000364_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f38e3330fc575fa13fb023380372f4838220e02
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000364_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00034:0.180196,(GCF_002008305_PROKKA_00298:0.165864,(GCF_005280335_PROKKA_00056:0.114154,(GCF_003691675_PROKKA_00006:0.0370136,GCF_023573625_PROKKA_00305:0.00987664)n3:0.0899591)n2:0.0647294)n1:0.180196)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000366_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000366_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1262f2b2f4c546414426298b7d109b1ce2cccde3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000366_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00032:0.0857111,(GCF_005280335_PROKKA_00054:0.0389552,(GCF_003691675_PROKKA_00008:0.00187112,(GCF_002008305_PROKKA_00300:5e-09,GCF_023573625_PROKKA_00307:0.00786961)n3:0.00401763)n2:0.0344207)n1:0.0857111)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000385_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000385_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3c09eb718f1a3fd8f9767f31f0e29d5b0b4fa72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000385_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00008:0.0605653,(GCF_005280335_PROKKA_00012:0.0286617,(GCF_023573625_PROKKA_00332:0.0063449,(GCF_002008305_PROKKA_00325:0.00206731,GCF_003691675_PROKKA_00040:0.00414453)n3:0.00820073)n2:0.0310679)n1:0.0605653)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000391_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000391_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..219a0ffd5b63e3d56242747fcc3dc7f57a4b67c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000391_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02486:0.131123,(GCF_005280335_PROKKA_02674:0.0922283,(GCF_003691675_PROKKA_00054:5e-09,(GCF_002008305_PROKKA_00338:5e-09,GCF_023573625_PROKKA_00345:0.0119535)n3:0.0242347)n2:0.100109)n1:0.131123)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000394_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000394_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed15fa5fa6132ac8a6c31d6c2fb897324ef132d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000394_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02480:0.055091,(GCF_005280335_PROKKA_02628:0.0720711,(GCF_003691675_PROKKA_00057:0.00957004,(GCF_002008305_PROKKA_00341:5e-09,GCF_023573625_PROKKA_00348:0.00671703)n3:0.00385217)n2:0.0718696)n1:0.055091)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000397_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000397_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4da17ecff2c85a225f68c30ec77fad9a7ba81f5f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000397_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02477:0.148937,(GCF_005280335_PROKKA_02625:0.0768538,(GCF_002008305_PROKKA_00344:0.00332907,(GCF_023573625_PROKKA_00351:0.0182897,GCF_003691675_PROKKA_00060:0.00837079)n3:0.00433859)n2:0.0718495)n1:0.148937)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000401_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000401_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6dc5fd545dcad3c8fa14478eb473b99558405f8f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000401_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02469:0.24032,(GCF_005280335_PROKKA_02610:0.0423944,(GCF_023573625_PROKKA_00358:0.00803764,(GCF_002008305_PROKKA_00351:5e-09,GCF_003691675_PROKKA_00067:0.00308335)n3:0.0045546)n2:0.0770851)n1:0.24032)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000406_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000406_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abef95c1871a90ca857239c5203c986d58514fd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000406_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02463:0.0655722,((GCF_002008305_PROKKA_00357:0,GCF_003691675_PROKKA_00073:0,GCF_023573625_PROKKA_00364:0)n2:0.00909932,GCF_005280335_PROKKA_02604:0.0540733)n1:0.0655722)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000407_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000407_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0604b7e288fd5772e620b745d0e911260a8a4916
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000407_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02462:0.148172,(GCF_005280335_PROKKA_02603:0.102292,(GCF_002008305_PROKKA_00358:0.00549518,(GCF_003691675_PROKKA_00074:0.00638675,GCF_023573625_PROKKA_00365:5e-09)n3:0.00899748)n2:0.0576889)n1:0.148172)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000417_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000417_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a2e1ae16d79023fa9c5c2ef8f0e22519a8bcfc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000417_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02449:0.0162452,(GCF_005280335_PROKKA_02590:0.00669202,(GCF_023573625_PROKKA_00379:5e-09,(GCF_003691675_PROKKA_00088:0.0161208,GCF_002008305_PROKKA_00372:0.00312876)n3:0.00318915)n2:0.00615026)n1:0.0162452)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000424_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000424_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b1cb390c52dbab9d08511683df70f857af0acf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000424_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02445:0.001281,(GCF_005280335_PROKKA_02573:0.0024683,(GCF_023573625_PROKKA_00388:0.00281106,(GCF_002008305_PROKKA_00382:0.0129726,GCF_003691675_PROKKA_00106:0.0175481)n3:0.00254892)n2:0.0227846)n1:0.001281)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000439_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000439_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db1cea7bad2c9324a65f8d905e59a14fe113e9f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000439_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02425:0.0524182,(GCF_005280335_PROKKA_02556:0.0132821,(GCF_002008305_PROKKA_00401:0.0121017,(GCF_003691675_PROKKA_00125:5e-09,GCF_023573625_PROKKA_00407:0.00513094)n3:0.0159035)n2:0.0164874)n1:0.0524182)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000443_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000443_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b1493458247955219ed18b6cd5423b3ca8c57e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000443_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02418:0.203135,(GCF_005280335_PROKKA_02550:0.00631582,(GCF_003691675_PROKKA_00129:0.00324505,(GCF_002008305_PROKKA_00406:0.00301972,GCF_023573625_PROKKA_00412:0.00645388)n3:0.0031839)n2:0.00939868)n1:0.203135)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000448_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000448_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e965dd99dfe2951f49ff10bf9d8ffe987b4c3fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000448_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02412:0.115753,(GCF_005280335_PROKKA_02544:0.0268444,((GCF_002008305_PROKKA_00416:0,GCF_003691675_PROKKA_00136:0)n3:5e-09,GCF_023573625_PROKKA_00419:0.0110267)n2:0.0266166)n1:0.115753)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000459_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000459_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4fe05ea91f3ba2d6942d8b6f2716b7f74af7315
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000459_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02398:0.112954,(GCF_005280335_PROKKA_02528:0.136932,(GCF_023573625_PROKKA_00432:5e-09,(GCF_003691675_PROKKA_00150:0.0069044,GCF_002008305_PROKKA_00429:0.0022888)n3:0.00456861)n2:0.233088)n1:0.112954)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000479_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000479_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c86e74adbf4a5179d8d83b147e0ae04614e6ce4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000479_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02377:0.0627156,((GCF_003691675_PROKKA_00172:5e-09,GCF_023573625_PROKKA_00454:0.0021095)n2:0.112731,(GCF_002008305_PROKKA_00451:0.0317413,GCF_005280335_PROKKA_02505:0.0428201)n3:0.0729513)n1:0.0627156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000480_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000480_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0908c28d964fef7900080d445107e3d92493ceb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000480_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02375:0.115935,(GCF_002008305_PROKKA_00456:0.00849902,((GCF_003691675_PROKKA_00174:0,GCF_023573625_PROKKA_00456:0)n3:6e-09,GCF_005280335_PROKKA_02491:0.00698204)n2:0.0431614)n1:0.115935)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000495_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000495_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47decf0ed142dcd147418b960cf1917765836aa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000495_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02359:0.238655,(GCF_005280335_PROKKA_02475:0.0881506,((GCF_002008305_PROKKA_00472:0,GCF_003691675_PROKKA_00190:0)n3:0.0149784,GCF_023573625_PROKKA_00472:5e-09)n2:0.0815079)n1:0.238655)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000496_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000496_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db573f0da99952e8a4646c3f2c47f2d41d8fc225
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000496_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02358:0.0223276,(GCF_005280335_PROKKA_02474:0.0538064,(GCF_002008305_PROKKA_00473:5e-09,(GCF_023573625_PROKKA_00473:0.00568823,GCF_003691675_PROKKA_00191:5e-09)n3:0.00283933)n2:0.00995376)n1:0.0223276)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000497_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000497_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f10a7561386ab6d1c82f50bf26ec01f2a067f1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000497_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02357:0.224872,(GCF_005280335_PROKKA_02473:0.0919029,(GCF_003691675_PROKKA_00192:0.00972038,(GCF_002008305_PROKKA_00474:0.0023867,GCF_023573625_PROKKA_00474:5e-09)n3:0.00477103)n2:0.0485273)n1:0.224872)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000499_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000499_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..493911494c5a81e3500b3f03a7019e9fb3e1f196
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000499_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02354:0.0842668,(GCF_005280335_PROKKA_02470:0.0552353,((GCF_002008305_PROKKA_00477:0,GCF_023573625_PROKKA_00477:0)n3:0.00266435,GCF_003691675_PROKKA_00195:0.00718709)n2:0.0500165)n1:0.0842668)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000502_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000502_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d653f1150f97acef36a9b0b468c449e7042c9e89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000502_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02351:0.134485,(GCF_005280335_PROKKA_02467:0.0761101,(GCF_002008305_PROKKA_00480:0.0112889,(GCF_003691675_PROKKA_00198:0.00571471,GCF_023573625_PROKKA_00480:0.0112251)n3:0.00568941)n2:0.0840493)n1:0.134485)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000508_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000508_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7318213875c9ca258d2d298a8503c31025fb4c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000508_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02344:0.1207,(GCF_005280335_PROKKA_02461:0.053121,(GCF_023573625_PROKKA_00486:0.0173138,(GCF_002008305_PROKKA_00486:0.00824294,GCF_003691675_PROKKA_00205:0.00545542)n3:0.00468639)n2:0.0591335)n1:0.1207)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000514_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000514_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b587f228650fae3904eb819341000d96c756d993
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000514_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02337:0.0713156,(GCF_005280335_PROKKA_02453:0.0169962,(GCF_023573625_PROKKA_00493:0.0065968,(GCF_002008305_PROKKA_00494:0.00992881,GCF_003691675_PROKKA_00215:0.00494082)n3:5e-09)n2:0.0298905)n1:0.0713156)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000515_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000515_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..734d3bdc07707b1590286d02e28b116f64f19791
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000515_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02334:0.0499648,(GCF_005280335_PROKKA_02450:0.0400879,(GCF_002008305_PROKKA_00497:0.0034793,(GCF_003691675_PROKKA_00218:0.0177022,GCF_023573625_PROKKA_00496:0.00191659)n3:0.00236811)n2:0.0529319)n1:0.0499648)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000522_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000522_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afa3f780942c1891b70a41b083214c591a4ea7fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000522_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02327:0.0464284,(GCF_005280335_PROKKA_02443:0.0500262,(GCF_003691675_PROKKA_00227:0.00516578,(GCF_002008305_PROKKA_00507:0.0271539,GCF_023573625_PROKKA_00506:0.00383471)n3:0.00652128)n2:0.133134)n1:0.0464284)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000524_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000524_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..895fb9aad231cc6473b7b40b14d6b643f03cad5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000524_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02323:0.314475,((GCF_002008305_PROKKA_00511:0.0215029,GCF_005280335_PROKKA_02440:0.0202268)n2:0.0140855,(GCF_003691675_PROKKA_00231:0.0401944,GCF_023573625_PROKKA_00510:0.0381348)n3:0.0138874)n1:0.314475)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000536_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000536_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21c674ad0ba5835063ce6b6ad92ea79fb0e20b6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000536_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02297:0.349065,(GCF_005280335_PROKKA_02415:0.296802,(GCF_002008305_PROKKA_00534:0.0114941,(GCF_003691675_PROKKA_00258:0.020296,GCF_023573625_PROKKA_00537:0.0213797)n3:0.0116089)n2:0.0509946)n1:0.349065)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000551_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000551_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..359913c30f04d501d0b4469b5b6367c04c848560
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000551_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02277:0.0872775,(GCF_005280335_PROKKA_02392:0.128947,((GCF_002008305_PROKKA_00553:0,GCF_003691675_PROKKA_00278:0)n3:5e-09,GCF_023573625_PROKKA_00556:0.0323608)n2:0.673542)n1:0.0872775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000553_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000553_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9668ae1ccc728d14305abe1a053aafe6dcf7df3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000553_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02272:0.0769114,(GCF_005280335_PROKKA_02389:0.0328124,(GCF_023573625_PROKKA_00559:0.00825134,(GCF_002008305_PROKKA_00556:0.0110012,GCF_003691675_PROKKA_00281:5e-09)n3:0.00641328)n2:0.0363101)n1:0.0769114)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000556_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000556_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..065277ba2d472a06dd4f31cb87aac62aa86bd938
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000556_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02268:0.054132,(GCF_005280335_PROKKA_02384:0.0916547,(GCF_023573625_PROKKA_00562:0.0142562,(GCF_002008305_PROKKA_00559:5e-09,GCF_003691675_PROKKA_00284:0.0069191)n3:0.00324498)n2:0.114451)n1:0.054132)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000575_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000575_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b5aba4a9858dc6b383bf6cfa431d4d966800625
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000575_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02195:0,(GCF_002008305_PROKKA_00634:0.00404248,(GCF_023573625_PROKKA_00597:0.024634,(GCF_005280335_PROKKA_00406:0,GCF_005280335_PROKKA_00753:1.25722)n3:0.139691)n2:5e-09)n1:5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000579_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000579_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70b93368d5b1a8d91b957dc63f25c2d75f8ee834
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000579_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02183:0.00476878,(GCF_023573625_PROKKA_00612:0.00945536,(GCF_005280335_PROKKA_02320:0.16251,(GCF_002008305_PROKKA_00642:0.00949332,GCF_003691675_PROKKA_00379:5e-09)n3:0.00327429)n2:0.0062793)n1:0.00476878)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000581_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000581_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c815e46b7e9f446b8a4efc5d534b1f8e182e8e30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000581_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02177:0.0965231,(GCF_005280335_PROKKA_02318:0.0696576,(GCF_023573625_PROKKA_00615:0.0160919,(GCF_002008305_PROKKA_00645:5e-09,GCF_003691675_PROKKA_00382:0.00321744)n3:0.0197955)n2:0.00663232)n1:0.0965231)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000584_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000584_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e13ef38d29b79c4efd043a731a5c193b3b23aff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000584_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02169:0.252702,(GCF_005280335_PROKKA_02312:0.219616,(GCF_002008305_PROKKA_00651:0.020471,(GCF_003691675_PROKKA_00388:0.0239831,GCF_023573625_PROKKA_00621:0.0036144)n3:0.0625794)n2:0.261167)n1:0.252702)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000588_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000588_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9a4c9c3859cfab9d2d9e0d64d1ca266591855c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000588_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02165:0.0399987,((GCF_002008305_PROKKA_00655:0,GCF_003691675_PROKKA_00392:0,GCF_023573625_PROKKA_00625:0)n2:0.0347613,GCF_005280335_PROKKA_02308:0.0187484)n1:0.0399987)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000592_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000592_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f8725bf4f1783ac0687ea785d2ec75713c3927a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000592_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02159:0.210765,(GCF_005280335_PROKKA_02303:0.0744604,(GCF_023573625_PROKKA_00630:0.011982,(GCF_002008305_PROKKA_00660:5e-09,GCF_003691675_PROKKA_00397:0.00623085)n3:0.00800552)n2:0.044799)n1:0.210765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000595_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000595_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3907b7bf2a56a17f5d4d6878f8812ab98d21441b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000595_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_01220:1.66797,GCF_005280335_PROKKA_02299:0.0545273)n1:0.0495435,(GCF_002008305_PROKKA_00664:0.0323912,(GCF_003691675_PROKKA_00401:0.00270715,GCF_023573625_PROKKA_00634:5e-09)n3:0.0141268)n2:0.0495435)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000596_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000596_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6794c4ad662eb094d170c06395f824b73aa4d2cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000596_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02156:0.11374,(GCF_005280335_PROKKA_02294:0.0349618,(GCF_023573625_PROKKA_00638:5e-09,(GCF_002008305_PROKKA_00668:0.00794127,GCF_003691675_PROKKA_00405:5e-09)n3:0.00795003)n2:0.0303615)n1:0.11374)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000604_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000604_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31d2146afbe97381a38832d1b973a6ddba3060b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000604_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02148:0.19,(GCF_005280335_PROKKA_02286:0.109663,((GCF_002008305_PROKKA_00676:0,GCF_003691675_PROKKA_00413:0)n3:0.00874382,GCF_023573625_PROKKA_00646:0.00110417)n2:0.117348)n1:0.19)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000609_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000609_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab7554c9af20f9734b656b03f84981fa26af09d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000609_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02142:0.0764047,((GCF_002008305_PROKKA_00682:0,GCF_003691675_PROKKA_00419:0,GCF_023573625_PROKKA_00652:0)n2:0.0943498,GCF_005280335_PROKKA_02281:0.041354)n1:0.0764047)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000611_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000611_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d183d89adad60ce8412dd21b04a63e58d206f75c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000611_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02140:0.093525,(GCF_005280335_PROKKA_02279:0.0780813,((GCF_002008305_PROKKA_00684:0,GCF_003691675_PROKKA_00421:0)n3:0.00291229,GCF_023573625_PROKKA_00654:0.00310559)n2:0.0853633)n1:0.093525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000612_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000612_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9645c2b208bc7b6c945963dbdc52034137d3d13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000612_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02139:0.0924522,(GCF_005280335_PROKKA_02278:0.155944,(GCF_023573625_PROKKA_00655:0.0143501,(GCF_002008305_PROKKA_00685:5e-09,GCF_003691675_PROKKA_00422:0.00348963)n3:0.00322858)n2:0.114694)n1:0.0924522)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000621_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000621_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52abd04fd9a0db8a73fbacc61423ecd8eedbe70e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000621_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02130:0.0994319,(GCF_005280335_PROKKA_02259:0.026782,(GCF_003691675_PROKKA_00432:0.011513,(GCF_002008305_PROKKA_00695:0.00470626,GCF_023573625_PROKKA_00665:0.00674314)n3:0.00833794)n2:0.0626868)n1:0.0994319)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000626_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000626_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ed8b6ec20d41f1196597e7f2f1055680fdcd464
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000626_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02125:0.02703,(GCF_005280335_PROKKA_02253:0.0159012,((GCF_002008305_PROKKA_00704:0,GCF_003691675_PROKKA_00438:0)n3:5e-09,GCF_023573625_PROKKA_00671:0.00276607)n2:0.00754937)n1:0.02703)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000630_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000630_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..afda7dc9ff1794b97195f22793271bedc0b50bf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000630_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02121:0.010341,((GCF_005280335_PROKKA_02249:0.170167,GCF_003691675_PROKKA_00442:5e-09)n2:0.00795707,(GCF_002008305_PROKKA_00708:0.00466342,GCF_023573625_PROKKA_00675:0.0110965)n3:0.00313207)n1:0.010341)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000638_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000638_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6cff8e15495f6ee57ab46af84cd1e1d7f814c6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000638_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02111:0.0243977,(GCF_005280335_PROKKA_02239:0.0186952,((GCF_002008305_PROKKA_00719:0,GCF_003691675_PROKKA_00450:0)n3:5e-09,GCF_023573625_PROKKA_00683:0.00464988)n2:6e-09)n1:0.0243977)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000643_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000643_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c8c059d58ac1044887a67e05ff42837b742d1d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000643_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02106:0.266238,((GCF_002008305_PROKKA_00724:0,GCF_003691675_PROKKA_00455:0,GCF_023573625_PROKKA_00688:0)n2:0.0721221,GCF_005280335_PROKKA_02234:0.10969)n1:0.266238)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000648_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000648_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf7c46fb246a1f04187c134c9b64e4eb1e54835f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000648_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02100:0.111177,(GCF_005280335_PROKKA_02226:0.0816901,((GCF_002008305_PROKKA_00729:0,GCF_023573625_PROKKA_00693:0)n3:0.00703178,GCF_003691675_PROKKA_00460:0.00371442)n2:0.0902465)n1:0.111177)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000649_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000649_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e816d0d4bb40ba420dce343d9cc920cbcb83dd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000649_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02099:0.138518,(GCF_005280335_PROKKA_02223:0.221053,(GCF_002008305_PROKKA_00730:0.00570315,(GCF_003691675_PROKKA_00461:0.0158347,GCF_023573625_PROKKA_00694:5e-09)n3:0.00479722)n2:0.141776)n1:0.138518)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000654_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000654_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..189f3fb2c119e4286e6db2731ede63c25c0c8393
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000654_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02093:0.20756,(GCF_005280335_PROKKA_02194:0.154551,(GCF_003691675_PROKKA_00467:0.040841,(GCF_002008305_PROKKA_00736:0.00848616,GCF_023573625_PROKKA_00700:0.0206679)n3:5e-09)n2:0.0278567)n1:0.20756)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000655_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000655_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7da5f672bbd92dcfe70aa00c80b4bc96b4c23e10
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000655_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02092:0.27512,(GCF_005280335_PROKKA_02193:0.162965,((GCF_002008305_PROKKA_00737:0,GCF_003691675_PROKKA_00468:0)n3:5e-09,GCF_023573625_PROKKA_00701:0.0203828)n2:0.16499)n1:0.27512)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000656_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000656_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12f5967362dd3aa818de0041f44684b358801a76
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000656_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02091:0.303333,(GCF_005280335_PROKKA_02192:0.143467,(GCF_023573625_PROKKA_00702:0.0135311,(GCF_002008305_PROKKA_00738:5e-09,GCF_003691675_PROKKA_00469:0.00637017)n3:0.0253731)n2:0.149576)n1:0.303333)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000664_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000664_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7690be2dd9e6560baef88385a481521e0e10b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000664_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02074:0.0791474,(GCF_005280335_PROKKA_02179:0.0454018,(GCF_023573625_PROKKA_00715:0.00249526,(GCF_002008305_PROKKA_00751:0.00789332,GCF_003691675_PROKKA_00481:0.00535432)n3:0.00295687)n2:0.0143166)n1:0.0791474)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000669_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000669_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ac6a15a344b984b67cf7e8fd33bbddefd670740
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000669_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02069:0.0790851,(GCF_005280335_PROKKA_02174:0.0450384,(GCF_003691675_PROKKA_00486:0.00287507,(GCF_023573625_PROKKA_00720:0.0117922,GCF_002008305_PROKKA_00756:0.00788024)n3:0.00381726)n2:0.0197933)n1:0.0790851)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000670_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000670_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c763fe2cf39bac64b490323804df95259df0c319
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000670_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02068:0.106037,(GCF_005280335_PROKKA_02173:0.0506272,(GCF_023573625_PROKKA_00721:0.00603728,(GCF_002008305_PROKKA_00757:0.00394396,GCF_003691675_PROKKA_00487:0.00196835)n3:0.00184504)n2:0.0538167)n1:0.106037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000676_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000676_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d57291b54e19b1baf71506504488e4c73e7cc89
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000676_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02061:0.162184,(GCF_005280335_PROKKA_02165:0.0364387,(GCF_002008305_PROKKA_00764:0.00780641,(GCF_003691675_PROKKA_00494:5e-09,GCF_023573625_PROKKA_00728:0.0080587)n3:0.00563488)n2:0.122899)n1:0.162184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000704_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000704_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6ebd9cf7b747f49141b7e03aa2c141cd511c5e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000704_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02028:0.0366805,(GCF_005280335_PROKKA_02135:0.0154795,((GCF_002008305_PROKKA_00796:0,GCF_003691675_PROKKA_00527:0)n3:5e-09,GCF_023573625_PROKKA_00763:0.00320484)n2:0.0287085)n1:0.0366805)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000708_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000708_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f3dfc29e6a11528edc2543b64117c2ecf3620df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000708_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02023:0.0337844,(GCF_005280335_PROKKA_02130:0.0657254,((GCF_002008305_PROKKA_00800:0,GCF_003691675_PROKKA_00531:0)n3:5e-09,GCF_023573625_PROKKA_00767:0.00430919)n2:0.0322294)n1:0.0337844)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000709_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000709_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fac5917fb98f4d2e6cfc694047843fdd1cad6c7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000709_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02022:0.0391943,(GCF_005280335_PROKKA_02129:0.0485996,(GCF_023573625_PROKKA_00768:0.00869902,(GCF_002008305_PROKKA_00801:0.02593,GCF_003691675_PROKKA_00532:0.0173043)n3:0.00840556)n2:0.0716819)n1:0.0391943)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000714_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000714_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d84a56b3c40ac8966111ecd9d2f27832b4340ac9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000714_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02017:0.0852771,(GCF_005280335_PROKKA_02124:0.0300342,((GCF_002008305_PROKKA_00806:0,GCF_003691675_PROKKA_00537:0)n3:5e-09,GCF_023573625_PROKKA_00773:5e-09)n2:0.0895638)n1:0.0852771)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000719_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000719_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e095b05a7c50b52cd0762c4e088dfa864e9faad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000719_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02009:0.199228,(GCF_005280335_PROKKA_02118:0.110908,(GCF_002008305_PROKKA_00812:5e-09,(GCF_003691675_PROKKA_00544:0.00386407,GCF_023573625_PROKKA_00781:6e-09)n3:0.00775722)n2:0.0893514)n1:0.199228)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000727_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000727_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1cc5713f2b6158b7d800d4bc72607d67add88f57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000727_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02001:0.129662,(GCF_005280335_PROKKA_02110:0.224277,(GCF_003691675_PROKKA_00552:0.0108719,(GCF_002008305_PROKKA_00820:0.000922964,GCF_023573625_PROKKA_00789:0.00283951)n3:0.00622811)n2:0.349841)n1:0.129662)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000732_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000732_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36f5c928624971213b20130a9eb4144358df0151
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000732_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01994:0.117447,(GCF_005280335_PROKKA_02095:0.110588,(GCF_023573625_PROKKA_00796:0.00530189,(GCF_003691675_PROKKA_00559:5e-09,GCF_002008305_PROKKA_00827:5e-09)n3:5e-09)n2:0.0811064)n1:0.117447)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000742_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000742_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e7206200f97eaae418e465927191cd5b2faf516
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000742_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01985:0.0759583,(GCF_005280335_PROKKA_02085:0.0283632,(GCF_002008305_PROKKA_00850:0.0045159,(GCF_003691675_PROKKA_00572:0,GCF_023573625_PROKKA_00809:0)n3:0.0451704)n2:0.0400941)n1:0.0759583)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000753_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000753_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa9686485b649707b8c395536c2fedcf5947edbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000753_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01963:0.122358,(GCF_005280335_PROKKA_02069:0.0726484,(GCF_003691675_PROKKA_00588:5e-09,(GCF_002008305_PROKKA_00866:0.0197941,GCF_023573625_PROKKA_00825:0.00773485)n3:0.00417379)n2:0.135808)n1:0.122358)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000771_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000771_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8790dc299fca862e9854150eacc7cbd13269c06d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000771_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01940:0.294981,(GCF_023573625_PROKKA_00846:0.811427,(GCF_005280335_PROKKA_02042:0.267656,(GCF_002008305_PROKKA_00895:0.0132619,GCF_003691675_PROKKA_00617:5e-09)n3:0.157648)n2:0.310236)n1:0.294981)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000773_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000773_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b092d3ab4c0b17cd97de4e58d9d21e9896138c37
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000773_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01942:0.158843,(GCF_003691675_PROKKA_00619:0.0146721,(GCF_005280335_PROKKA_02044:0.00566806,(GCF_002008305_PROKKA_00897:0.00352055,GCF_023573625_PROKKA_00848:0.00464878)n3:0.00584395)n2:0.00971723)n1:0.158843)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000775_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000775_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ce4da76e76c5b06c2bddf6c9bdec1883ed3f9da7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000775_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01938:0.0852943,((GCF_003691675_PROKKA_00621:0.00452727,GCF_023573625_PROKKA_00850:0.00296902)n2:0.0554697,(GCF_002008305_PROKKA_00902:0.0123568,GCF_005280335_PROKKA_02040:0.032881)n3:0.036336)n1:0.0852943)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000783_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000783_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39caf44ff0177d401b871103cfb68cbfa79af5df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000783_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01930:0.181312,(GCF_005280335_PROKKA_02032:0.177847,(GCF_002008305_PROKKA_00910:5e-09,(GCF_003691675_PROKKA_00629:0.00840427,GCF_023573625_PROKKA_00858:0.00823546)n3:0.0124189)n2:0.0846871)n1:0.181312)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000784_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000784_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ddfcf22b2c2feb4cd5423bb2fb93dcc1e3c36a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000784_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01929:0.299262,((GCF_002008305_PROKKA_00911:0,GCF_003691675_PROKKA_00630:0,GCF_023573625_PROKKA_00859:0)n2:0.0670965,GCF_005280335_PROKKA_02031:0.132175)n1:0.299262)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000785_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000785_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..571dd8aacec2ce5ed1406bbeae2aa30dd3039f20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000785_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01928:0.17079,((GCF_002008305_PROKKA_00912:0,GCF_003691675_PROKKA_00631:0,GCF_023573625_PROKKA_00860:0)n2:0.0787132,GCF_005280335_PROKKA_02030:0.0938928)n1:0.17079)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000786_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000786_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f63b7e7121537d424f7fcef1a2d106fcf3e37b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000786_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01927:0.0787955,((GCF_002008305_PROKKA_00913:0,GCF_003691675_PROKKA_00632:0,GCF_023573625_PROKKA_00861:0)n2:0.0722424,GCF_005280335_PROKKA_02029:5e-09)n1:0.0787955)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000793_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000793_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89bc9fd5366e9984c3494735e617c29d7073b076
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000793_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01920:0.0117795,(GCF_005280335_PROKKA_02021:5e-09,((GCF_002008305_PROKKA_00920:0,GCF_023573625_PROKKA_00868:0)n3:5e-09,GCF_003691675_PROKKA_00639:0.01169)n2:0.023592)n1:0.0117795)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000809_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000809_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ded0d767c6302dfc6143fafdbb4b37c3424e152a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000809_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01899:0.263204,(GCF_002008305_PROKKA_00937:0.0109527,(GCF_003691675_PROKKA_00656:0.0156981,(GCF_005280335_PROKKA_02002:0.0157551,GCF_023573625_PROKKA_00886:0.00941453)n3:0.00620652)n2:0.00495404)n1:0.263204)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000816_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000816_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1025710307381a859c723b8d05eab9e00d8281c8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000816_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01891:0.0157338,(GCF_005280335_PROKKA_01990:0.111967,(GCF_002008305_PROKKA_00947:0.0101046,(GCF_003691675_PROKKA_00666:5e-09,GCF_023573625_PROKKA_00895:0.0100943)n3:6e-09)n2:0.00951251)n1:0.0157338)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000817_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000817_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5da58b8e5f11b05b6f76f9584e4345a4fc48a565
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000817_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01883:0.0427296,(GCF_003691675_PROKKA_00669:0.00424187,(GCF_002008305_PROKKA_00956:5e-09,(GCF_005280335_PROKKA_01931:0.12227,GCF_023573625_PROKKA_00902:5e-09)n3:0.00945279)n2:0.00530097)n1:0.0427296)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000818_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000818_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..060efcff24affa8806c8f53c220ec60fda562238
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000818_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01882:0.113184,(GCF_005280335_PROKKA_01930:0.0567476,(GCF_003691675_PROKKA_00670:5e-09,(GCF_002008305_PROKKA_00957:0.00558467,GCF_023573625_PROKKA_00903:0.0074646)n3:0.0037284)n2:0.0483898)n1:0.113184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000828_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000828_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b14b1496d3380245e1f6b791a943cced29bae0dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000828_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01861:0.0709844,(GCF_005280335_PROKKA_01914:0.0456317,(GCF_002008305_PROKKA_00976:0.000863419,(GCF_003691675_PROKKA_00690:0.00652788,GCF_023573625_PROKKA_00919:0.00217684)n3:0.00821385)n2:0.0264657)n1:0.0709844)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000833_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000833_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0ccb1916475a90fdf43daf31a1355be1fec2def
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000833_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01856:0.0177384,((GCF_002008305_PROKKA_00981:0,GCF_003691675_PROKKA_00695:0,GCF_023573625_PROKKA_00924:0)n2:0.00451966,GCF_005280335_PROKKA_01908:0.331485)n1:0.0177384)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000836_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000836_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98c1ec550dd12c3bd4503e4ff22e76d5fac4f718
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000836_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01852:0.00310298,(GCF_005280335_PROKKA_01905:0.0210421,((GCF_002008305_PROKKA_00984:0,GCF_023573625_PROKKA_00927:0)n3:0.0215548,GCF_003691675_PROKKA_00698:0.0058396)n2:0.0198602)n1:0.00310298)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000838_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000838_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..320462cbe22bc922bbc5c4dc3da7a5068988c749
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000838_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01850:2.5e-09,(GCF_003691675_PROKKA_00700:0.00421235,(GCF_005280335_PROKKA_01903:0.0126901,(GCF_002008305_PROKKA_00986:5e-09,GCF_023573625_PROKKA_00929:0.00419988)n3:0.00845743)n2:5e-09)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000844_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000844_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed997a74461f07b724b440018d255d2cd6f0e69f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000844_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01842:0.0559705,(GCF_005280335_PROKKA_01895:0.0185443,(GCF_002008305_PROKKA_00994:0.00366295,(GCF_003691675_PROKKA_00708:0.00248994,GCF_023573625_PROKKA_00937:0.00368925)n3:0.00180773)n2:0.0147291)n1:0.0559705)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000853_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000853_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2017db420b410abd793a0ac5f5a80e750689d7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000853_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01814:0.117219,(GCF_005280335_PROKKA_01886:0.0769215,(GCF_023573625_PROKKA_00947:5e-09,(GCF_002008305_PROKKA_01004:5e-09,GCF_003691675_PROKKA_00718:0.00212428)n3:0.0107032)n2:0.0414987)n1:0.117219)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000855_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000855_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..add13526007f6a9e9ce94365447bf75feca4a597
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000855_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01812:0.105109,(GCF_005280335_PROKKA_01884:0.0486267,((GCF_002008305_PROKKA_01006:0,GCF_003691675_PROKKA_00720:0)n3:5e-09,GCF_023573625_PROKKA_00949:0.0184331)n2:0.0201198)n1:0.105109)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000870_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000870_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a89ba6ff052f1e56be6e21a13a6720b764c1afaf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000870_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01741:0.00249153,(GCF_005280335_PROKKA_01851:0.0140419,(GCF_003691675_PROKKA_00746:0.0139769,(GCF_023573625_PROKKA_00975:5e-09,GCF_002008305_PROKKA_01031:0.00347139)n3:5e-09)n2:0.00205179)n1:0.00249153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000873_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000873_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2bcbce7adb528c1e9a2531e9e486a30487898cbc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000873_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01738:2.5e-09,(GCF_023573625_PROKKA_00978:0.00460202,(GCF_005280335_PROKKA_01848:0.0185442,(GCF_002008305_PROKKA_01036:0.00916974,GCF_003691675_PROKKA_00749:5e-09)n3:0.00458686)n2:5e-09)n1:2.5e-09)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000874_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000874_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d3affa8280d41abf3c8896281f364e640e21058
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000874_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01737:0.0153248,(GCF_005280335_PROKKA_01847:0.0222963,(GCF_023573625_PROKKA_00979:5e-09,(GCF_002008305_PROKKA_01037:5e-09,GCF_003691675_PROKKA_00750:0.00275757)n3:0.0110959)n2:0.00320314)n1:0.0153248)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000879_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000879_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2291a492c63db9ca22d873d3c57884933e5fc4b0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000879_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01730:0.0242603,(GCF_005280335_PROKKA_01842:0.0590105,(GCF_003691675_PROKKA_00759:5e-09,(GCF_002008305_PROKKA_01046:0.00150275,GCF_023573625_PROKKA_00987:0.00150448)n3:0.00150795)n2:0.060983)n1:0.0242603)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000889_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000889_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5caf37a2dd3a31676a1a1896acfc46be89d1625
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000889_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01716:0.0912276,(GCF_005280335_PROKKA_01826:0.0918544,(GCF_003691675_PROKKA_00779:0.0016076,(GCF_002008305_PROKKA_01060:0.00915539,GCF_023573625_PROKKA_01007:0.00179191)n3:0.00579284)n2:0.0570679)n1:0.0912276)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000890_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000890_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89c5dc2767763585a1247b69d41f851fd4e4564a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000890_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01715:0.0816542,(GCF_005280335_PROKKA_01825:0.056711,(GCF_023573625_PROKKA_01008:0.00450314,(GCF_002008305_PROKKA_01061:5e-09,GCF_003691675_PROKKA_00780:0.00889846)n3:0.00882157)n2:0.0283294)n1:0.0816542)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000891_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000891_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3df6d464a688f4408bb0c0497ac8917d0cf0c57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000891_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01714:0.0619492,(GCF_005280335_PROKKA_01824:0.0590283,(GCF_023573625_PROKKA_01009:5e-09,(GCF_002008305_PROKKA_01062:5e-09,GCF_003691675_PROKKA_00781:0.00446117)n3:0.0044517)n2:0.0490114)n1:0.0619492)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000892_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000892_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fca24e06542c41fbb5e9c4b4ec8fe37469afe7eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000892_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01713:0.118883,(GCF_005280335_PROKKA_01823:0.0754966,(GCF_003691675_PROKKA_00782:0.00517202,(GCF_002008305_PROKKA_01063:0.0123798,GCF_023573625_PROKKA_01010:0.0179131)n3:0.0178665)n2:0.110498)n1:0.118883)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000900_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000900_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6aca633e2fa07a7fbd5f7368167f918ae37016c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000900_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01701:0.194741,(GCF_005280335_PROKKA_01813:0.115448,(GCF_002008305_PROKKA_01084:5e-09,(GCF_003691675_PROKKA_00803:0,GCF_023573625_PROKKA_01033:0)n3:0.00915809)n2:0.0938553)n1:0.194741)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000915_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000915_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cbb63bbfe1cc893f67acd500838175c31cd083d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000915_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01685:0.158023,(GCF_005280335_PROKKA_01795:0.0673234,(GCF_003691675_PROKKA_00819:0.0113371,(GCF_002008305_PROKKA_01100:0.00557957,GCF_023573625_PROKKA_01049:0.0171892)n3:0.0112109)n2:0.131534)n1:0.158023)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000918_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000918_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31aef63b7c446dad107f64d8458c375edd8ae22d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000918_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01681:0.248652,(GCF_005280335_PROKKA_01790:0.0454688,(GCF_002008305_PROKKA_01104:0.00970662,(GCF_003691675_PROKKA_00823:0.00245505,GCF_023573625_PROKKA_01053:5e-09)n3:0.0206996)n2:0.176925)n1:0.248652)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000934_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000934_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5896c347fd099fd5017e31b54d94eef91fb5921b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000934_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01661:0.0740994,(GCF_005280335_PROKKA_01767:0.0413679,(GCF_023573625_PROKKA_01075:5e-09,(GCF_002008305_PROKKA_01125:5e-09,GCF_003691675_PROKKA_00844:0.00475516)n3:0.00237492)n2:0.0311433)n1:0.0740994)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000945_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000945_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4a923c2e3e90581a68238a6fb0e03c452266c2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000945_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01650:0.152019,(GCF_005280335_PROKKA_01756:0.0359437,((GCF_002008305_PROKKA_01136:0,GCF_003691675_PROKKA_00855:0)n3:5e-09,GCF_023573625_PROKKA_01086:0.00970958)n2:0.0497353)n1:0.152019)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000948_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000948_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09e38aa6c05dbd634d5781553ff5e592e222f810
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000948_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01647:0.101577,(GCF_005280335_PROKKA_01753:0.0309811,(GCF_023573625_PROKKA_01089:0.0047396,(GCF_002008305_PROKKA_01139:5e-09,GCF_003691675_PROKKA_00858:0.00232283)n3:0.00458879)n2:0.0413633)n1:0.101577)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000963_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000963_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4afccdba9455dbfc9de42ec9d6c0df319df29d92
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000963_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01629:0.0752314,(GCF_005280335_PROKKA_01731:0.0305044,((GCF_002008305_PROKKA_01158:0,GCF_023573625_PROKKA_01108:0)n3:0.00248061,GCF_003691675_PROKKA_00877:5e-09)n2:0.0455723)n1:0.0752314)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000967_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000967_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..555a29e87343b341d95834f42f9c6ba3fbf9ec3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000967_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01624:0.209164,(GCF_005280335_PROKKA_01727:0.145151,(GCF_003691675_PROKKA_00882:0.00852711,(GCF_002008305_PROKKA_01163:0.00342818,GCF_023573625_PROKKA_01113:0.0139553)n3:0.0123952)n2:0.11497)n1:0.209164)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000968_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000968_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ac47cc1040629405de79e3ad1ae265054070119
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000968_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01623:0.153732,(GCF_005280335_PROKKA_01726:0.0888931,((GCF_002008305_PROKKA_01164:0,GCF_003691675_PROKKA_00883:0)n3:0.00172012,GCF_023573625_PROKKA_01114:5e-09)n2:0.107446)n1:0.153732)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000973_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000973_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4560afb0a1bc2aeacf8338fc404993745cf9a9cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000973_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01617:0.0929166,(GCF_005280335_PROKKA_01719:0.0721365,((GCF_002008305_PROKKA_01170:0,GCF_023573625_PROKKA_01120:0)n3:5e-09,GCF_003691675_PROKKA_00889:0.00949127)n2:0.056953)n1:0.0929166)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000982_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000982_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..969926ff5f22a37a602187ea496dd8f641ddf077
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000982_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01608:0.113993,((GCF_002008305_PROKKA_01179:0,GCF_003691675_PROKKA_00898:0)n2:0.0156049,(GCF_005280335_PROKKA_01710:5e-09,GCF_023573625_PROKKA_01129:0.0157612)n3:6e-09)n1:0.113993)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000989_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000989_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a01abeb90a97222b931115295386a9588914c529
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000989_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01600:0.168153,(GCF_005280335_PROKKA_01701:0.170887,((GCF_002008305_PROKKA_01187:0,GCF_023573625_PROKKA_01137:0)n3:0.00622513,GCF_003691675_PROKKA_00906:0.00433116)n2:0.117167)n1:0.168153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000991_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000991_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6b71d1a7c5b8723078980368c90de11b8c924cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000991_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01598:0.0909151,((GCF_002008305_PROKKA_01189:0,GCF_023573625_PROKKA_01139:0)n2:5e-09,(GCF_005280335_PROKKA_01699:0.0354355,GCF_003691675_PROKKA_00908:5e-09)n3:0.00856798)n1:0.0909151)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000996_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000996_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0aad602eb04d3a39404d6a4c06c98bf80f60f2b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000996_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01591:0.329598,(GCF_005280335_PROKKA_01693:0.752137,(GCF_003691675_PROKKA_00914:0.0172606,(GCF_023573625_PROKKA_01148:0.116232,GCF_002008305_PROKKA_01194:0.103342)n3:0.0399035)n2:0.389744)n1:0.329598)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000997_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000997_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff4fcf775a45884e94b8fb63c09eebc801b32583
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000997_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01590:0.239093,(GCF_005280335_PROKKA_01692:0.21446,(GCF_003691675_PROKKA_00915:5e-09,(GCF_023573625_PROKKA_01149:0.0380141,GCF_002008305_PROKKA_01195:0.0303531)n3:0.0224701)n2:0.221971)n1:0.239093)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000999_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000999_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0c220a721d9a96d5ca1daf0d64cd4564b9514b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0000999_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01587:0.0530581,(GCF_005280335_PROKKA_01690:0.0514536,(GCF_002008305_PROKKA_01197:0.00554095,(GCF_003691675_PROKKA_00917:0,GCF_023573625_PROKKA_01151:0)n3:5e-09)n2:0.0736651)n1:0.0530581)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001010_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001010_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ad8d8376a42958e7228bfa4cd8dc6b7a4decae9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001010_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01576:0.112898,(GCF_005280335_PROKKA_01678:0.0305208,(GCF_003691675_PROKKA_00928:0.0113677,(GCF_002008305_PROKKA_01209:0.00531273,GCF_023573625_PROKKA_01166:0.00804435)n3:0.00524853)n2:0.0482299)n1:0.112898)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001017_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001017_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3baa96662b6ec575cfb7198ad3664e6c51d1407f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001017_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01568:0.091529,((GCF_002008305_PROKKA_01217:0,GCF_003691675_PROKKA_00936:0,GCF_023573625_PROKKA_01174:0)n2:0.0406792,GCF_005280335_PROKKA_01671:0.0344692)n1:0.091529)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001019_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001019_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..294eab7109a375b44464fa28c68c436c20dc9d12
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001019_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01566:0.104974,(GCF_005280335_PROKKA_01669:0.0498941,((GCF_002008305_PROKKA_01219:0,GCF_003691675_PROKKA_00938:0)n3:5e-09,GCF_023573625_PROKKA_01177:0.00267948)n2:0.0309467)n1:0.104974)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001021_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001021_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a22d18bd2f3fecc483fd26d958ba58370d51808
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001021_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01564:0.0625331,(GCF_005280335_PROKKA_01667:0.0795906,(GCF_002008305_PROKKA_01221:5e-09,(GCF_003691675_PROKKA_00940:0.007157,GCF_023573625_PROKKA_01179:0.00355093)n3:0.00352934)n2:0.0382133)n1:0.0625331)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001025_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001025_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..637f57e2bcfe0a1b135e65bc948b6cd0daf3edd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001025_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01559:0.0266259,(GCF_002008305_PROKKA_01226:5e-09,(GCF_003691675_PROKKA_00945:0,GCF_005280335_PROKKA_01662:0,GCF_023573625_PROKKA_01184:0)n2:0.0104516)n1:0.0266259)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001027_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001027_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f98476a70c64e96f2fb22a31c25abe1b23272317
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001027_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01557:0.208331,(GCF_005280335_PROKKA_01660:0.189019,(GCF_002008305_PROKKA_01228:0.023919,(GCF_003691675_PROKKA_00947:6e-09,GCF_023573625_PROKKA_01186:0.00113386)n3:0.0210053)n2:0.162426)n1:0.208331)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001035_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001035_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..935fac32e3ae511c286d2a963a8374239e9add35
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001035_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01549:0.121143,(GCF_005280335_PROKKA_01652:0.0853002,(GCF_002008305_PROKKA_01236:0.0138221,(GCF_003691675_PROKKA_00955:5e-09,GCF_023573625_PROKKA_01194:0.00225064)n3:0.0164562)n2:0.0360139)n1:0.121143)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001049_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001049_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc48d78ed1903f9602dcd9c9268c15ec745c67a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001049_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01534:0.029537,(GCF_005280335_PROKKA_01637:0.0273814,(GCF_002008305_PROKKA_01251:0.00278903,(GCF_003691675_PROKKA_00970:5e-09,GCF_023573625_PROKKA_01209:0.00240939)n3:0.00695513)n2:0.0337823)n1:0.029537)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001052_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001052_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28474d43471c76f15679da8b920a259f077bf472
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001052_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01530:0.0260765,(GCF_005280335_PROKKA_01633:0.0406365,(GCF_002008305_PROKKA_01255:0.00996264,(GCF_003691675_PROKKA_00974:5e-09,GCF_023573625_PROKKA_01213:0.00109596)n3:0.00676783)n2:0.0225307)n1:0.0260765)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001055_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001055_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a4c99786ac8ac3950b24c396d1d2ff3a3123669
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001055_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01527:0.186754,((GCF_002008305_PROKKA_01258:0,GCF_003691675_PROKKA_00977:0,GCF_023573625_PROKKA_01216:0)n2:0.230005,GCF_005280335_PROKKA_01629:0.119268)n1:0.186754)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001058_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001058_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84a99ceaba9b369ce3357354816ea79c1c9b7116
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001058_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01524:0.0492854,(GCF_005280335_PROKKA_01627:0.178209,(GCF_002008305_PROKKA_01261:5e-09,(GCF_003691675_PROKKA_00980:0,GCF_023573625_PROKKA_01219:0)n3:0.00165645)n2:0.134968)n1:0.0492854)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001070_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001070_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f300276088d09d6348432b9bb12161a3d2565761
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001070_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01508:0.0862737,(GCF_005280335_PROKKA_01613:0.0597133,(GCF_002008305_PROKKA_01274:0.00450655,(GCF_003691675_PROKKA_00993:0,GCF_023573625_PROKKA_01232:0)n3:5e-09)n2:0.0356762)n1:0.0862737)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001073_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001073_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ed19837324f133f2e0353cc1f12ee6c55391aca
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001073_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01505:0.108664,(GCF_005280335_PROKKA_01610:0.119942,(GCF_002008305_PROKKA_01277:0.0148301,(GCF_003691675_PROKKA_00996:0,GCF_023573625_PROKKA_01235:0)n3:5e-09)n2:0.0520094)n1:0.108664)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001074_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001074_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d55b51a96ada2fb14c128e0c70801dcd19f3a189
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001074_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01504:0.0863502,((GCF_002008305_PROKKA_01278:0,GCF_003691675_PROKKA_00997:0,GCF_023573625_PROKKA_01236:0)n2:0.0984807,GCF_005280335_PROKKA_01609:0.151797)n1:0.0863502)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001086_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001086_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bce568fc3e670a2e2169b6176f5f93b73c12698
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001086_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01490:0.189731,(GCF_005280335_PROKKA_01594:0.0684543,(GCF_002008305_PROKKA_01298:0.00421591,(GCF_003691675_PROKKA_01021:0,GCF_023573625_PROKKA_01256:0)n3:5e-09)n2:0.0607981)n1:0.189731)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001094_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001094_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa8a5e04632cd23ac06d212b8c5879966e9a54ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001094_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01481:0.0918026,(GCF_005280335_PROKKA_01585:0.0464285,(GCF_002008305_PROKKA_01307:0.0101237,(GCF_003691675_PROKKA_01030:0,GCF_023573625_PROKKA_01265:0)n3:0.00762183)n2:0.0681646)n1:0.0918026)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001101_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001101_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1690b313f9dc369c19484990624e68aa811861a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001101_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01472:0.0677123,((GCF_003691675_PROKKA_01037:0.00279859,GCF_023573625_PROKKA_01272:5e-09)n2:0.0834725,(GCF_002008305_PROKKA_01316:5e-09,GCF_005280335_PROKKA_01576:0.00278917)n3:0.0815216)n1:0.0677123)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001105_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001105_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7edc3580c0897b22009f125c0aac034628c6553a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001105_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01467:0.110406,(GCF_005280335_PROKKA_01571:0.0143038,((GCF_002008305_PROKKA_01320:0,GCF_003691675_PROKKA_01041:0)n3:5e-09,GCF_023573625_PROKKA_01276:0.0139836)n2:0.0287052)n1:0.110406)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001113_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001113_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11178fe3bc417001f1ef209e74a43f8a22d106a2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001113_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01459:0.344473,(GCF_005280335_PROKKA_01563:0.0296967,(GCF_023573625_PROKKA_01284:0.00542818,(GCF_002008305_PROKKA_01328:5e-09,GCF_003691675_PROKKA_01049:0.00179796)n3:0.0108236)n2:0.0128792)n1:0.344473)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001115_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001115_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12e6b8d72026f16db49a21d5326706e35aa746b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001115_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01457:0.0415082,(GCF_005280335_PROKKA_01561:0.021603,((GCF_002008305_PROKKA_01330:0,GCF_023573625_PROKKA_01286:0)n3:5e-09,GCF_003691675_PROKKA_01051:0.00299689)n2:0.00261763)n1:0.0415082)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001119_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001119_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e236ec80caac0b409677fb7752d59f79733b1d85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001119_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01452:0.148072,(GCF_005280335_PROKKA_01556:0.0566969,(GCF_002008305_PROKKA_01335:0.0142839,(GCF_003691675_PROKKA_01056:0.0174164,GCF_023573625_PROKKA_01291:5e-09)n3:0.0041507)n2:0.0393793)n1:0.148072)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001124_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001124_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6090e88be9bfbfc16fbb99c801e550d39e21e0af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001124_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01446:0.0410767,((GCF_002008305_PROKKA_01342:0,GCF_003691675_PROKKA_01062:0,GCF_023573625_PROKKA_01297:0)n2:0.0295309,GCF_005280335_PROKKA_01550:0.0208298)n1:0.0410767)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001139_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001139_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..731241fe37a032a1b8a41bc155b6d7e481ccbc15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001139_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01430:0.0553245,(GCF_005280335_PROKKA_01535:0.0832429,(GCF_003691675_PROKKA_01078:0.00394935,(GCF_002008305_PROKKA_01358:0.00396096,GCF_023573625_PROKKA_01313:0.00152289)n3:0.00184506)n2:0.0549676)n1:0.0553245)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001142_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001142_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f883a873ae4387ca0416b242f727d29e64501ac1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001142_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01427:0.292828,(GCF_005280335_PROKKA_01532:0.129983,(GCF_003691675_PROKKA_01081:0.0475081,(GCF_002008305_PROKKA_01361:5e-09,GCF_023573625_PROKKA_01316:0.00478042)n3:0.0117944)n2:0.0547211)n1:0.292828)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001152_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001152_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5a9ea30c16793c27e13339d2627bf6d74bbcde9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001152_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01416:0.143823,(GCF_005280335_PROKKA_01520:0.0924355,((GCF_002008305_PROKKA_01372:0,GCF_023573625_PROKKA_01327:0)n3:0.00501651,GCF_003691675_PROKKA_01092:0.00265858)n2:0.143683)n1:0.143823)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001154_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001154_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a2f1567577c6743e6eeefcf4b95c764ba2aefa9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001154_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01413:0.123699,(GCF_005280335_PROKKA_01518:0.0503039,(GCF_002008305_PROKKA_01374:0.0149929,(GCF_003691675_PROKKA_01094:5e-09,GCF_023573625_PROKKA_01329:0.00202037)n3:0.00637381)n2:0.108932)n1:0.123699)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001169_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001169_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9a9ad55525ea4e38427c6e318975fb1974e0ba7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001169_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01391:0.00828786,(GCF_005280335_PROKKA_01484:0.0293645,(GCF_023573625_PROKKA_01365:5e-09,(GCF_002008305_PROKKA_01415:0.00818934,GCF_003691675_PROKKA_01146:0.00173904)n3:0.0126672)n2:0.019489)n1:0.00828786)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001171_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001171_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e7fc323abd86d573df8335d68611538254a8a2d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001171_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01389:0.144118,(GCF_023573625_PROKKA_01368:0.0262648,(GCF_003691675_PROKKA_01149:5e-09,(GCF_002008305_PROKKA_01418:0.0214562,GCF_005280335_PROKKA_01481:0.00589461)n3:0.00592614)n2:0.0194238)n1:0.144118)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001178_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001178_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1082395c7a506e782f0f1d9a54f454baf5fe0e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001178_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01378:0.073294,(GCF_005280335_PROKKA_01471:0.0574691,(GCF_003691675_PROKKA_01159:0.00684174,(GCF_002008305_PROKKA_01428:5e-09,GCF_023573625_PROKKA_01378:0.00220515)n3:0.00425394)n2:0.040638)n1:0.073294)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001182_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001182_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b0c13f70cf4f36baedba7187734088252a166c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001182_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01374:0.185521,(GCF_005280335_PROKKA_01467:0.120485,(GCF_023573625_PROKKA_01382:0.00307426,(GCF_002008305_PROKKA_01432:0.0119077,GCF_003691675_PROKKA_01164:0.00560496)n3:0.00294296)n2:0.0537735)n1:0.185521)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001184_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001184_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b1fee67f6bbf231254e17c2a684e54d1c62bd1ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001184_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01372:0.0587804,(GCF_005280335_PROKKA_01464:0.0393787,(GCF_002008305_PROKKA_01434:5e-09,(GCF_003691675_PROKKA_01166:0,GCF_023573625_PROKKA_01384:0)n3:0.00612598)n2:0.0357293)n1:0.0587804)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001186_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001186_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1ed4f5fe078be3a819e75e1e34e93f84150033e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001186_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01370:0.0659774,(GCF_005280335_PROKKA_01462:0.03973,(GCF_023573625_PROKKA_01386:0.00301258,(GCF_002008305_PROKKA_01436:0.0029426,GCF_003691675_PROKKA_01168:5e-09)n3:0.00287789)n2:0.0408172)n1:0.0659774)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001198_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001198_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7c8785120fd2ea79498c8b4c71d745ac2edfbb7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001198_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01352:0.0525115,(GCF_003691675_PROKKA_01183:0.327972,(GCF_005280335_PROKKA_01448:0.0104906,(GCF_002008305_PROKKA_01451:0.0594445,GCF_023573625_PROKKA_01401:0.00186322)n3:0.30006)n2:0.0765215)n1:0.0525115)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001201_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001201_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96ea6bedcdb32406f2dd365ecde70bb1bc72ef58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001201_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01348:0.101373,(GCF_005280335_PROKKA_01445:0.0607467,(GCF_023573625_PROKKA_01405:0.00316591,(GCF_002008305_PROKKA_01455:5e-09,GCF_003691675_PROKKA_01187:0.00656476)n3:0.00374908)n2:0.107096)n1:0.101373)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001202_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001202_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f6008366a4036c6afd00661359c3a0cda4ed3a40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001202_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01347:0.0549919,(GCF_005280335_PROKKA_01444:0.0343743,((GCF_002008305_PROKKA_01456:0,GCF_023573625_PROKKA_01406:0)n3:5e-09,GCF_003691675_PROKKA_01188:5e-09)n2:0.0275503)n1:0.0549919)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001211_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001211_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9858fbc2b0b1eff11a7b73037accb2f49e4fb36b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001211_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01338:0.202623,(GCF_005280335_PROKKA_01435:0.133022,(GCF_003691675_PROKKA_01197:0.0169723,(GCF_002008305_PROKKA_01465:0.00566505,GCF_023573625_PROKKA_01415:5e-09)n3:6e-09)n2:0.0876133)n1:0.202623)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001222_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001222_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..053c176ef5a7a9789128b8b23422ea3ef0810e08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001222_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01323:0.0943799,((GCF_002008305_PROKKA_01479:0,GCF_003691675_PROKKA_01211:0,GCF_023573625_PROKKA_01429:0)n2:0.340322,GCF_005280335_PROKKA_01423:0.312596)n1:0.0943799)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001225_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001225_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d45e2d6236a455948cadbbc6683382fe85cdd732
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001225_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01320:0.21143,(GCF_005280335_PROKKA_01420:0.107655,(GCF_002008305_PROKKA_01482:0.0162679,(GCF_003691675_PROKKA_01214:0.00815207,GCF_023573625_PROKKA_01432:0.00462201)n3:0.00734508)n2:0.119536)n1:0.21143)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001226_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001226_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6826212befa1a6b3d4aa34d1f2f76bd70f7b9e87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001226_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01319:0.120707,(GCF_005280335_PROKKA_01419:0.0267279,(GCF_002008305_PROKKA_01483:0.017346,(GCF_003691675_PROKKA_01215:5e-09,GCF_023573625_PROKKA_01433:0.0113895)n3:0.00389901)n2:0.0610256)n1:0.120707)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001235_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001235_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfc6fd4b4ec7a77f2ad18b5c42a1de063dfb236d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001235_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01307:0.0743914,(GCF_005280335_PROKKA_01408:0.0436766,((GCF_002008305_PROKKA_01517:0,GCF_003691675_PROKKA_01226:0)n3:0.00135705,GCF_023573625_PROKKA_01444:0.00143984)n2:0.0211732)n1:0.0743914)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001239_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001239_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f30370cf0fc67f7aa0ef493ee1b929c219c0805
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001239_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01303:0.154605,(GCF_005280335_PROKKA_01404:0.0748828,(GCF_023573625_PROKKA_01448:0.00261483,(GCF_003691675_PROKKA_01230:0.0069249,GCF_002008305_PROKKA_01521:0.00345649)n3:0.00260706)n2:0.0653108)n1:0.154605)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001242_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001242_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..966e130d0ed1ea189a472ac9ec2db9b8f403c173
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001242_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01300:0.016527,(GCF_005280335_PROKKA_01401:0.0304606,(GCF_002008305_PROKKA_01524:0.00671291,(GCF_003691675_PROKKA_01233:0,GCF_023573625_PROKKA_01451:0)n3:5e-09)n2:0.0242755)n1:0.016527)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001252_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001252_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aab4696fe1b2b8f11b92652e27ed7e03c22fdcfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001252_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01282:0.0668423,(GCF_005280335_PROKKA_01391:0.0657407,((GCF_002008305_PROKKA_01534:0,GCF_023573625_PROKKA_01461:0)n3:5e-09,GCF_003691675_PROKKA_01244:0.00242318)n2:0.0663916)n1:0.0668423)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001254_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001254_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e1d625c493d3daa3e3a136f9ecc01bdeebb13e7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001254_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01280:0.352682,(GCF_005280335_PROKKA_01389:0.108024,(GCF_003691675_PROKKA_01246:6e-09,(GCF_002008305_PROKKA_01536:0.00893698,GCF_023573625_PROKKA_01463:0.0269781)n3:0.00436621)n2:0.0648652)n1:0.352682)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001264_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001264_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0fdd5db4862e9e6e4717a4b02aa9582a039dbc9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001264_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01269:0.192761,((GCF_005280335_PROKKA_01378:0.134009,GCF_023573625_PROKKA_01474:0.00866948)n2:0.0107505,(GCF_002008305_PROKKA_01547:5e-09,GCF_003691675_PROKKA_01257:5e-09)n3:0.00956964)n1:0.192761)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001270_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001270_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c51cada624f2603c2103428ce39ada5699ad6ea
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001270_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01262:0.0829287,(GCF_005280335_PROKKA_01371:0.0829047,(GCF_003691675_PROKKA_01264:0.00848791,(GCF_002008305_PROKKA_01554:5e-09,GCF_023573625_PROKKA_01481:0.00327152)n3:0.00483193)n2:0.0583908)n1:0.0829287)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001287_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001287_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47398e27c205534af7a6e431817a447e95800d6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001287_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01243:0.13566,(GCF_005280335_PROKKA_01350:0.152543,(GCF_003691675_PROKKA_01284:0.00558097,(GCF_002008305_PROKKA_01574:5e-09,GCF_023573625_PROKKA_01501:0.0056131)n3:5e-09)n2:0.0952798)n1:0.13566)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001302_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001302_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9e4401cf9cb3b790a8f9ab17c7a10aa476c9933
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001302_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01202:0.0064962,(GCF_005280335_PROKKA_01293:0.0187142,(GCF_002008305_PROKKA_01600:5e-09,(GCF_003691675_PROKKA_01312:5e-09,GCF_023573625_PROKKA_01527:0.00603883)n3:0.0122812)n2:0.0508878)n1:0.0064962)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001312_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001312_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c4c3e11a605612ed8a33b432cbeab48482a6e64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001312_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01174:0.13614,(GCF_005280335_PROKKA_01266:0.0415853,(GCF_003691675_PROKKA_01335:0.00468011,(GCF_002008305_PROKKA_01630:0.011796,GCF_023573625_PROKKA_01559:0.00704051)n3:0.00476871)n2:0.0545431)n1:0.13614)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001318_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001318_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74ee3a9746f86ac05504f8ced51b4babd470c7d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001318_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01167:0.21102,(GCF_005280335_PROKKA_01258:0.102795,(GCF_023573625_PROKKA_01566:0.0249449,(GCF_002008305_PROKKA_01637:5e-09,GCF_003691675_PROKKA_01342:0.00991638)n3:0.0199889)n2:0.060719)n1:0.21102)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001320_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001320_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5390db8a317acd6ce76cc0879900dac2726657d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001320_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01165:0.237016,(GCF_005280335_PROKKA_01256:0.211231,(GCF_003691675_PROKKA_01344:0.0180774,(GCF_002008305_PROKKA_01639:0.0328618,GCF_023573625_PROKKA_01568:0.0121318)n3:0.0165394)n2:0.233109)n1:0.237016)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001323_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001323_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cefa56ca983485ca4e7032e27c806bd4d7439922
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001323_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01162:0.404632,(GCF_005280335_PROKKA_01251:0.285132,(GCF_002008305_PROKKA_01642:0.0149853,(GCF_023573625_PROKKA_01572:0.0290484,GCF_003691675_PROKKA_01347:0.0150436)n3:0.00703707)n2:0.0719276)n1:0.404632)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001325_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001325_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c451e016339f12c8a46d8d316a6bfb3768d200f7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001325_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01160:0.109685,(GCF_005280335_PROKKA_01249:0.0685273,(GCF_003691675_PROKKA_01349:5e-09,(GCF_002008305_PROKKA_01644:0.00978678,GCF_023573625_PROKKA_01574:0.00485839)n3:0.00976478)n2:0.0279017)n1:0.109685)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001326_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001326_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11b4bc0808224fd443a9cffa18027f38d20b49e1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001326_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01159:0.261495,(GCF_005280335_PROKKA_01248:0.104391,(GCF_002008305_PROKKA_01645:5e-09,(GCF_003691675_PROKKA_01350:0.00897653,GCF_023573625_PROKKA_01575:5e-09)n3:0.00895337)n2:0.0528974)n1:0.261495)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001343_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001343_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7224b92368b82bc3c9d40fd43bc2cf757f1d1ab6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001343_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01140:0.0762947,(GCF_005280335_PROKKA_01229:0.0463172,(GCF_002008305_PROKKA_01665:0.0157716,(GCF_003691675_PROKKA_01370:0.00263771,GCF_023573625_PROKKA_01595:0.00513342)n3:0.00247935)n2:0.0395669)n1:0.0762947)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001366_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001366_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4331fa5abbb0203047bb785e733741e470eb704
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001366_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01115:0.0225971,(GCF_005280335_PROKKA_01185:0.00516941,(GCF_002008305_PROKKA_01693:0.00286795,(GCF_003691675_PROKKA_01400:0.00293065,GCF_023573625_PROKKA_01622:0.0029331)n3:0.00300076)n2:0.0162911)n1:0.0225971)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001375_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001375_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..440d99b6f39a2fdf5ddd4ebf01cf0a97fbcbe535
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001375_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01106:0.0373823,((GCF_002008305_PROKKA_01702:0,GCF_003691675_PROKKA_01409:0,GCF_023573625_PROKKA_01631:0)n2:0.0179982,GCF_005280335_PROKKA_01176:0.0119979)n1:0.0373823)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001376_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001376_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e276085a1f49a31242b6b1578a007fbf1813ce31
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001376_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01105:0.0321785,((GCF_002008305_PROKKA_01703:0,GCF_003691675_PROKKA_01410:0,GCF_023573625_PROKKA_01632:0)n2:0.0184546,GCF_005280335_PROKKA_01175:0.00518996)n1:0.0321785)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001395_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001395_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b6f978be09308d82d8b812c1467ecc1dcea4cc5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001395_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01086:0.203633,(GCF_005280335_PROKKA_01156:0.0957788,((GCF_002008305_PROKKA_01722:0,GCF_023573625_PROKKA_01651:0)n3:0.0675064,GCF_003691675_PROKKA_01429:5e-09)n2:0.0883895)n1:0.203633)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001397_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001397_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9042dbac58e4593031a84c28158d04ee1c0f29f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001397_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01084:0.0196701,(GCF_005280335_PROKKA_01154:0.0186335,((GCF_002008305_PROKKA_01724:0,GCF_023573625_PROKKA_01653:0)n3:5e-09,GCF_003691675_PROKKA_01431:0.0013946)n2:0.0151939)n1:0.0196701)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001425_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001425_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d21d21b39315a24e84a45f85b02017c301dc6c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001425_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01049:0.0888417,(GCF_005280335_PROKKA_01124:0.0770587,((GCF_002008305_PROKKA_01753:0,GCF_003691675_PROKKA_01460:0)n3:0.00781085,GCF_023573625_PROKKA_01682:0.010066)n2:0.0648468)n1:0.0888417)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001435_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001435_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aebf00777f5fbe40d4df9ed8873174f449f58164
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001435_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01037:0.378488,(GCF_005280335_PROKKA_01112:0.183524,(GCF_023573625_PROKKA_01694:0.00785483,(GCF_002008305_PROKKA_01765:0.00649857,GCF_003691675_PROKKA_01472:0.0196505)n3:0.00514384)n2:0.0881712)n1:0.378488)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001437_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001437_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..287e8316fc8ea31375e2f2c58402c02081c2bb25
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001437_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01034:0.226897,(GCF_005280335_PROKKA_01108:0.10952,(GCF_002008305_PROKKA_01769:0.0135683,(GCF_003691675_PROKKA_01476:0,GCF_023573625_PROKKA_01698:0)n3:0.0160851)n2:0.074433)n1:0.226897)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001455_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001455_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f47dbdb382f4048e2230bff052ff3f524e5cf5b8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001455_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01007:0.126525,(GCF_003691675_PROKKA_01499:0.0156033,(GCF_005280335_PROKKA_01071:0.00716604,(GCF_002008305_PROKKA_01802:0.00712013,GCF_023573625_PROKKA_01723:0.00713816)n3:0.00714238)n2:0.0333108)n1:0.126525)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001461_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001461_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..caf8947ef49d881fe829d12156950cdc59439768
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001461_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01812:0,GCF_003691675_PROKKA_01509:0,GCF_005280335_PROKKA_01062:0,GCF_023573625_PROKKA_01733:0)n1:0.0154508,GCF_020097155_PROKKA_00997:0.0154508)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001462_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001462_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8275bb1e739444dd90fd7ebe5bb58cb8e2656f1f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001462_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00996:0.107832,(GCF_005280335_PROKKA_01061:0.0914967,(GCF_003691675_PROKKA_01510:5e-09,(GCF_002008305_PROKKA_01813:0.00714564,GCF_023573625_PROKKA_01734:0.0119129)n3:0.00471086)n2:0.057808)n1:0.107832)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001471_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001471_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b0a67a8a7f100c3b5b83f602cf9eb1065c6e325
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001471_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00986:0.256678,(GCF_005280335_PROKKA_01047:0.0738842,((GCF_002008305_PROKKA_01822:0,GCF_023573625_PROKKA_01743:0)n3:5e-09,GCF_003691675_PROKKA_01519:0.019803)n2:0.0559659)n1:0.256678)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001477_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001477_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c265689851ef69c4785e2870b8bf0fae26eba17
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001477_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00980:0.184274,(GCF_005280335_PROKKA_01041:0.0970976,(GCF_002008305_PROKKA_01828:0.00832384,(GCF_023573625_PROKKA_01749:0.0274645,GCF_003691675_PROKKA_01525:0.0106122)n3:0.00894516)n2:0.112484)n1:0.184274)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001480_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001480_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d8f920bc07c90126212c27f93e85619d45c82e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001480_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00976:0.0446498,(GCF_005280335_PROKKA_01036:0.026981,(GCF_002008305_PROKKA_01832:5e-09,(GCF_003691675_PROKKA_01529:5e-09,GCF_023573625_PROKKA_01753:0.00308759)n3:0.00308178)n2:0.0347895)n1:0.0446498)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001486_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001486_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a92cf6df8e74354ff4903c52a0cdee4b7b219cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001486_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00970:0.0786173,(GCF_005280335_PROKKA_01029:0.0664948,(GCF_002008305_PROKKA_01839:0.00414933,(GCF_003691675_PROKKA_01536:0,GCF_023573625_PROKKA_01760:0)n3:0.0257301)n2:0.0399492)n1:0.0786173)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001487_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001487_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0e0dd5ee2da5cd8158b33764ae0787eaf952bc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001487_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00969:0.0377421,((GCF_002008305_PROKKA_01840:0,GCF_003691675_PROKKA_01537:0,GCF_023573625_PROKKA_01761:0)n2:0.0109802,GCF_005280335_PROKKA_01028:0.122427)n1:0.0377421)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001488_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001488_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bdf33f7cbcb66831ada3ea8098819bd37aac2917
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001488_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00968:0.181672,(GCF_005280335_PROKKA_01027:0.0438052,(GCF_023573625_PROKKA_01762:0.00675536,(GCF_002008305_PROKKA_01841:0.00052931,GCF_003691675_PROKKA_01538:0.00759442)n3:0.00650215)n2:0.0525877)n1:0.181672)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001501_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001501_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44c0d0a7fc39f330f8930d34091c57106eb1bf6e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001501_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00950:0.0767382,(GCF_005280335_PROKKA_01006:0.249675,(GCF_023573625_PROKKA_01778:0.00263249,(GCF_003691675_PROKKA_01554:0.0123399,GCF_002008305_PROKKA_01858:0.00279421)n3:0.00975818)n2:0.164109)n1:0.0767382)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001511_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001511_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12ffd33c0b80f1aa9c6bb681bb0fb951996a667f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001511_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00930:0.080196,(GCF_005280335_PROKKA_00992:0.0540847,(GCF_003691675_PROKKA_01564:5e-09,(GCF_002008305_PROKKA_01868:5e-09,GCF_023573625_PROKKA_01788:0.00997716)n3:0.0150769)n2:0.0878478)n1:0.080196)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001514_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001514_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..985e1219e0bdcf3e2d7afea9f7a786cfff9b7bcc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001514_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00926:0.100324,(GCF_005280335_PROKKA_00989:0.0242186,(GCF_023573625_PROKKA_01791:0.0110741,(GCF_002008305_PROKKA_01871:0.00303495,GCF_003691675_PROKKA_01567:0.00307384)n3:0.00433737)n2:0.113488)n1:0.100324)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001517_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001517_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7e1544b91990bff872509416a1b93016036a4cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001517_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00923:0.12392,((GCF_002008305_PROKKA_01874:0.0124162,GCF_003691675_PROKKA_01570:0.00904709)n2:0.0316808,(GCF_005280335_PROKKA_00986:0.031653,GCF_023573625_PROKKA_01794:0.0136643)n3:0.00593309)n1:0.12392)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001524_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001524_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc549bb14efc3b6483330b2cc09c9116654b67d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001524_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00912:0.156789,(GCF_005280335_PROKKA_00974:0.0834128,((GCF_002008305_PROKKA_01884:0,GCF_023573625_PROKKA_01804:0)n3:0.0184795,GCF_003691675_PROKKA_01580:0.0229641)n2:0.172417)n1:0.156789)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001527_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001527_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..584fc0e6ade21e5a89a6c8c8c1b361d7d84c15e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001527_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00909:0.0804694,(GCF_005280335_PROKKA_00971:0.0483538,((GCF_002008305_PROKKA_01887:0,GCF_023573625_PROKKA_01807:0)n3:0.00547495,GCF_003691675_PROKKA_01583:0.00365004)n2:0.050692)n1:0.0804694)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001534_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001534_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1e39ae5231d37ef966c261cf33237b5eb2e1f6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001534_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00898:0.0888905,(GCF_005280335_PROKKA_00958:0.025587,(GCF_002008305_PROKKA_01900:0.0069483,(GCF_003691675_PROKKA_01596:0.00233058,GCF_023573625_PROKKA_01820:0.00225971)n3:0.00992883)n2:0.0851098)n1:0.0888905)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001541_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001541_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a1ad5e183c9c7a9287aa02047303ce64b1678c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001541_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00891:0.00514959,(GCF_005280335_PROKKA_00951:0.0102183,((GCF_002008305_PROKKA_01907:0,GCF_003691675_PROKKA_01603:0)n3:5e-09,GCF_023573625_PROKKA_01827:5e-09)n2:0.0102511)n1:0.00514959)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001547_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001547_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfade80d131eaf69c2d9be72cb897d8c81426f44
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001547_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00876:0.148222,(GCF_005280335_PROKKA_00941:0.0276772,(GCF_023573625_PROKKA_01839:5e-09,(GCF_002008305_PROKKA_01919:0.00714953,GCF_003691675_PROKKA_01615:0.00712109)n3:0.00357087)n2:0.0225622)n1:0.148222)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001551_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001551_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d2548fbae03db58cf1a03ef3a5026058004b9d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001551_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00868:0.0354542,(GCF_005280335_PROKKA_00936:1.3516,(GCF_003691675_PROKKA_01620:0.00717489,(GCF_023573625_PROKKA_01844:0.0153333,GCF_002008305_PROKKA_01924:5e-09)n3:0.0160263)n2:0.107324)n1:0.0354542)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001558_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001558_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68cee9ac3ab5e02b8130ab08949f6eeafa72542f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001558_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00860:0.0959074,(GCF_005280335_PROKKA_00926:0.138968,(GCF_003691675_PROKKA_01629:0.00243376,(GCF_002008305_PROKKA_01933:0.00947002,GCF_023573625_PROKKA_01852:0.00703734)n3:0.00221319)n2:0.096014)n1:0.0959074)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001561_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001561_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e379e78f319fc50e963a6229e551746e0211014a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001561_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00857:0.0796545,(GCF_005280335_PROKKA_00923:0.13443,((GCF_002008305_PROKKA_01936:0,GCF_023573625_PROKKA_01855:0)n3:0.0037464,GCF_003691675_PROKKA_01632:0.00454618)n2:0.159843)n1:0.0796545)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001575_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001575_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06e7d1b6f6a0001d4f826ba161374a5c702b654e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001575_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00830:0.170179,(GCF_005280335_PROKKA_00889:0.00918681,(GCF_003691675_PROKKA_01664:0.00913169,(GCF_002008305_PROKKA_01970:0.00134236,GCF_023573625_PROKKA_01896:0.00616198)n3:0.00303255)n2:0.00906262)n1:0.170179)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001588_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001588_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9b6563ac81e9dd0c09d6481dcb5fe839b2f9e64
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001588_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01757:0.112149,(GCF_005280335_PROKKA_00867:0.0361719,(GCF_002008305_PROKKA_01990:0.00741184,(GCF_003691675_PROKKA_01684:0.0147176,GCF_023573625_PROKKA_01916:5e-09)n3:0.00238551)n2:0.0483706)n1:0.112149)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001595_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001595_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e51dd794114558efc37427b5767b49b3eeba53e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001595_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00794:0.180025,(GCF_005280335_PROKKA_00858:0.112836,(GCF_002008305_PROKKA_01999:0.0203078,(GCF_003691675_PROKKA_01693:0,GCF_023573625_PROKKA_01925:0)n3:0.00726006)n2:0.10173)n1:0.180025)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001602_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001602_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ccf7a7a1face01ed1d16ff273af5b76d16ee18e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001602_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00770:0.0352567,((GCF_002008305_PROKKA_02009:0,GCF_003691675_PROKKA_01719:0,GCF_023573625_PROKKA_01947:0)n2:0.0320616,GCF_005280335_PROKKA_00833:0.0184036)n1:0.0352567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001605_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001605_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..546533dd85cc82c31002b0623bf7fc1f00352358
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001605_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00767:0.0536999,(GCF_005280335_PROKKA_00830:0.0334274,(GCF_023573625_PROKKA_01950:0.00444933,(GCF_002008305_PROKKA_02012:0.00753787,GCF_003691675_PROKKA_01722:0.00499352)n3:0.00305676)n2:0.039139)n1:0.0536999)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001625_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001625_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb54537c2f0faa380735f9bac33572a6c41d7181
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001625_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00740:0.0903846,(GCF_005280335_PROKKA_00770:0.121461,(GCF_023573625_PROKKA_01986:5e-09,(GCF_002008305_PROKKA_02052:5e-09,GCF_003691675_PROKKA_01758:0.0109362)n3:0.00545498)n2:0.180299)n1:0.0903846)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001626_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001626_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5483f88fe49e68095d9ca6883713dd453a22d03c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001626_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00126:0.156873,(GCF_005280335_PROKKA_00769:0.0715487,(GCF_002008305_PROKKA_02053:0.0108684,(GCF_003691675_PROKKA_01759:0.0124085,GCF_023573625_PROKKA_01987:0.0108014)n3:0.00542294)n2:0.0748798)n1:0.156873)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001630_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001630_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c322c625399a2e837f24461acb151a7b1c36357f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001630_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00723:0.310184,(GCF_005280335_PROKKA_00760:0.279181,(GCF_023573625_PROKKA_01994:0.064386,(GCF_002008305_PROKKA_02058:0.00920958,GCF_003691675_PROKKA_01764:0.00469288)n3:0.0716632)n2:0.0977894)n1:0.310184)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001632_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001632_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0eaac30fb5ed580865e74ac77076524b14e1d65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001632_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00614:0.00865615,((GCF_003691675_PROKKA_01784:0.0033866,GCF_023573625_PROKKA_02018:0.00678309)n2:5e-09,(GCF_002008305_PROKKA_02080:0.0207589,GCF_005280335_PROKKA_00704:0.0364431)n3:5e-09)n1:0.00865615)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001637_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001637_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9a489ce67f24d0ccce10a97b469a7e15cb35dd2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001637_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00608:0.00284409,((GCF_002008305_PROKKA_02085:0,GCF_003691675_PROKKA_01790:0)n2:0.0085366,(GCF_005280335_PROKKA_00698:0.0114015,GCF_023573625_PROKKA_02024:5e-09)n3:0.00284124)n1:0.00284409)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001652_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001652_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0108b66bc46a00390bf807744f5d3344f7a96f8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001652_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00583:0.112301,(GCF_005280335_PROKKA_00667:0.0833169,(GCF_023573625_PROKKA_02051:0.0223408,(GCF_002008305_PROKKA_02113:0.0114372,GCF_003691675_PROKKA_01820:0.019776)n3:0.0133802)n2:0.0599284)n1:0.112301)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001653_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001653_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9182aa45bd09be9b1ae585ac521bae7c4bf6ed41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001653_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00582:0.176051,(GCF_005280335_PROKKA_00666:0.0948298,(GCF_002008305_PROKKA_02114:0.00603333,(GCF_003691675_PROKKA_01822:0.0577127,GCF_023573625_PROKKA_02052:5e-09)n3:0.0214639)n2:0.134653)n1:0.176051)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001654_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001654_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c5f573842dc8b6be4b58359a540e0ece013a8a5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001654_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00581:0.0342265,(GCF_005280335_PROKKA_00665:0.0190068,(GCF_002008305_PROKKA_02115:0.00215295,(GCF_003691675_PROKKA_01823:0.00215199,GCF_023573625_PROKKA_02053:0.0043264)n3:5e-09)n2:0.0200347)n1:0.0342265)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001662_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001662_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5b94823d60f20ea25df775914f976260435a371
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001662_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00570:0.0132927,(GCF_005280335_PROKKA_00654:0.00659911,(GCF_003691675_PROKKA_01834:5e-09,(GCF_002008305_PROKKA_02126:0.00657533,GCF_023573625_PROKKA_02064:0.0132028)n3:5e-09)n2:6e-09)n1:0.0132927)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001667_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001667_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..911008aaf2fabc109dd199f607a11344e430abb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001667_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00565:0.0177991,(GCF_023573625_PROKKA_02069:0.00712295,(GCF_005280335_PROKKA_00649:0.00708382,(GCF_002008305_PROKKA_02131:5e-09,GCF_003691675_PROKKA_01839:0.0140847)n3:0.00702117)n2:5e-09)n1:0.0177991)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001669_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001669_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2da3c6a93706f6d4cef9dc555d7bcaf044c59bb9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001669_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00563:0.0298859,(GCF_005280335_PROKKA_00647:0.0465344,(GCF_003691675_PROKKA_01841:0.00538141,(GCF_002008305_PROKKA_02133:0.00359892,GCF_023573625_PROKKA_02071:0.00179233)n3:0.00725697)n2:0.0227189)n1:0.0298859)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001672_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001672_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8c99f9a8d3494843254b9e4c9529f692c169de0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001672_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00559:0.0926001,((GCF_002008305_PROKKA_02137:0,GCF_003691675_PROKKA_01845:0,GCF_023573625_PROKKA_02075:0)n2:0.0441244,GCF_005280335_PROKKA_00635:0.0631079)n1:0.0926001)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001673_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001673_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..525c946ca9152f39be310a365bbb7f1a6d680707
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001673_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00558:0.094961,(GCF_005280335_PROKKA_00634:0.0668843,(GCF_002008305_PROKKA_02138:0.00433816,(GCF_003691675_PROKKA_01846:0,GCF_023573625_PROKKA_02076:0)n3:0.00217744)n2:0.0831674)n1:0.094961)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001676_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001676_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e394f077648d788318e2702d6ce2edf4180df5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001676_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00554:0.0312824,(GCF_005280335_PROKKA_00716:0.288232,(GCF_023573625_PROKKA_02079:0.00959592,(GCF_002008305_PROKKA_02141:0.0165277,GCF_003691675_PROKKA_01849:0.00705255)n3:0.00677311)n2:0.061046)n1:0.0312824)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001677_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001677_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a8010088c28360b8f2289dec998bf1c90ab426f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001677_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00553:0.00123081,((GCF_002008305_PROKKA_02143:0.0234286,GCF_005280335_PROKKA_00629:0.0535002)n2:0.144501,(GCF_003691675_PROKKA_01850:0.00265295,GCF_023573625_PROKKA_02080:5e-09)n3:0.00286674)n1:0.00123081)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001695_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001695_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b5f9ff8a59ae115e553b6e13f8ed40d3efaa101
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001695_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00509:0.203799,(GCF_005280335_PROKKA_00583:0.125255,(GCF_002008305_PROKKA_02169:0.0216785,(GCF_003691675_PROKKA_01883:0.0158584,GCF_023573625_PROKKA_02114:0.0135527)n3:0.0125102)n2:0.151479)n1:0.203799)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001709_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001709_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fb8a576bad3f912cf2eb4d8210ea197baa67f3c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001709_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00484:0.181209,(GCF_005280335_PROKKA_00557:0.0369303,((GCF_002008305_PROKKA_02189:0,GCF_003691675_PROKKA_01903:0)n3:0.00541655,GCF_023573625_PROKKA_02134:5e-09)n2:0.103627)n1:0.181209)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001710_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001710_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..460e65f51cd9d141cc630d755e5c0393a90f88b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001710_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00483:0.228641,(GCF_005280335_PROKKA_00554:0.150307,(GCF_002008305_PROKKA_02190:0.00571122,(GCF_003691675_PROKKA_01904:0.00246313,GCF_023573625_PROKKA_02135:0.00981838)n3:0.00411855)n2:0.129918)n1:0.228641)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001725_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001725_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e8c8dc862dc24093ebd21eb771f65394daed15d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001725_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00441:0.0306037,(GCF_005280335_PROKKA_00505:0.0893903,((GCF_002008305_PROKKA_02240:0,GCF_023573625_PROKKA_02172:0)n3:0.00251555,GCF_003691675_PROKKA_01942:5e-09)n2:0.0847725)n1:0.0306037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001734_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001734_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0f2a08dd726c736c5b3bfe191fbdbd0ca06561ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001734_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00493:0.170321,(GCF_003691675_PROKKA_01961:0.00324973,(GCF_023573625_PROKKA_02200:0.00336587,(GCF_005280335_PROKKA_00462:0.0143267,GCF_002008305_PROKKA_02268:5e-09)n3:0.00503831)n2:0.00184903)n1:0.170321)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001736_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001736_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ce31d4ff306ec8065baceeb26703b023a08078b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001736_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00406:0.00749847,(GCF_005280335_PROKKA_00454:0.00857656,(GCF_003691675_PROKKA_01973:5e-09,(GCF_023573625_PROKKA_02221:0.00638225,GCF_002008305_PROKKA_02282:0.00212027)n3:6e-09)n2:0.00421725)n1:0.00749847)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001737_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001737_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a81461affb88a9ecfb8508ea6805e7894f8c81a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001737_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00405:0.0648952,(GCF_005280335_PROKKA_00452:0.00210652,(GCF_002008305_PROKKA_02285:0.00472636,(GCF_003691675_PROKKA_01976:0,GCF_023573625_PROKKA_02224:0)n3:5e-09)n2:0.00261979)n1:0.0648952)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001746_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001746_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92f8871f96d4156c306be5cf07553298e1c8d406
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001746_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00394:0.124766,(GCF_005280335_PROKKA_00441:0.0767483,(GCF_002008305_PROKKA_02295:0.00479375,(GCF_003691675_PROKKA_01988:0.00198921,GCF_023573625_PROKKA_02236:0.00614383)n3:0.0033759)n2:0.097513)n1:0.124766)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001747_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001747_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ea3c744b897565e9d77bd11b74c4c694b975734
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001747_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00393:0.0367796,(GCF_005280335_PROKKA_00440:0.0231874,(GCF_002008305_PROKKA_02296:0.00546354,(GCF_003691675_PROKKA_01989:0.00538894,GCF_023573625_PROKKA_02237:5e-09)n3:0.00259871)n2:0.0130266)n1:0.0367796)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001749_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001749_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa33fcb6c8a3233dfa190ada6273a7b6960bf343
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001749_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00388:0.16458,(GCF_005280335_PROKKA_00436:0.0409479,(GCF_023573625_PROKKA_02242:0.0050456,(GCF_002008305_PROKKA_02301:5e-09,GCF_003691675_PROKKA_01994:0.00166477)n3:0.00512608)n2:0.0484654)n1:0.16458)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001750_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001750_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9eac8496679bbcb74f0523697ac7a5f8068f2a4f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001750_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00387:0.204939,(GCF_005280335_PROKKA_00435:0.314776,(GCF_002008305_PROKKA_02302:0.00971892,(GCF_003691675_PROKKA_01995:0.00458726,GCF_023573625_PROKKA_02243:0.0159027)n3:0.0143438)n2:0.0874093)n1:0.204939)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001757_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001757_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e729e450599273243a6fc9dee92f0199f2d32d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001757_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00378:0.265501,(GCF_005280335_PROKKA_00425:0.0610506,(GCF_002008305_PROKKA_02311:0.0262538,(GCF_003691675_PROKKA_02004:0,GCF_023573625_PROKKA_02252:0)n3:0.0208383)n2:0.0342789)n1:0.265501)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001759_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001759_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83d74e71252c7da5a6cd99774085de0ee9d9225d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001759_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02316:0.196293,(GCF_023573625_PROKKA_00516:0.18016,(GCF_005280335_PROKKA_02432:0.520145,(GCF_003691675_PROKKA_00206:0.939219,GCF_003691675_PROKKA_00237:0.390279)n3:0.0433644)n2:0.258486)n1:0.196293)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001761_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001761_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b0a2811ef4065558f9058b5c288e82aa904bd070
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001761_tree.txt
@@ -0,0 +1 @@
+(GCF_003691675_PROKKA_00329:0,(GCF_003691675_PROKKA_00368:0,GCF_003691675_PROKKA_01967:0,GCF_003691675_PROKKA_02017:0,GCF_003691675_PROKKA_01110:0.23442)n1:0)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001771_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001771_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff104252761d1da484b3a7a470fd4d0c6cd7d3eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001771_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_PROKKA_00041:0.00746674,(GCF_023573625_PROKKA_00036:5e-09,(GCF_003691675_PROKKA_02054:0.00635671,GCF_003691675_PROKKA_02171:1.403)n2:0.155889)n1:0.00848297)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001779_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001779_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a7454778d7463196230300c2f4cfca14faec3c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001779_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00200:0.149229,(GCF_002008305_PROKKA_00118:0.0221156,(GCF_003691675_PROKKA_02131:0,GCF_023573625_PROKKA_00123:0)n2:0.00470181)n1:0.149229)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001785_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001785_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2158345d2c412e40cf1260c41785ba013e6948da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001785_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00225:0.0739775,(GCF_023573625_PROKKA_00169:0.0390352,(GCF_002008305_PROKKA_00177:0.00998402,GCF_003691675_PROKKA_02170:0.00724271)n2:0.0356631)n1:0.0739775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001794_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001794_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e73f7251c0fad02e00bf5be9bd44f76cd7e30a91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001794_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00118:0.0146443,(GCF_023573625_PROKKA_00252:0.00408247,(GCF_002008305_PROKKA_00252:0.00428027,GCF_003691675_PROKKA_02264:0.00143234)n2:0.00276597)n1:0.0146443)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001796_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001796_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4c13c6852f87742afbb92c056506db038ed707a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001796_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_00272:0,GCF_003691675_PROKKA_02287:0,GCF_023573625_PROKKA_00270:0)n1:0.221094,GCF_005280335_PROKKA_00084:0.221094)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001806_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001806_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..992fc07441722764080f002c9a5ca4d709218af1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001806_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02394:0.731301,(GCF_002008305_PROKKA_00369:0.0305306,(GCF_003691675_PROKKA_00085:0,GCF_023573625_PROKKA_00376:0)n2:0.0179193)n1:0.731301)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001813_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001813_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2157bbcfe0f2a9bdac71e33857e35b66e577feed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001813_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_02324:0.322936,(GCF_023573625_PROKKA_00509:0.0268565,(GCF_002008305_PROKKA_00510:0.0192889,GCF_003691675_PROKKA_00230:0.0248159)n2:0.0173435)n1:0.322936)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001817_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001817_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55e8723443844ea4c76710d29272c457525dd335
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001817_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02357:0.00129775,((GCF_002008305_PROKKA_00576:0,GCF_003691675_PROKKA_00308:0)n2:5e-09,GCF_023573625_PROKKA_00577:0.00259695)n1:0.00129775)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001822_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001822_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b5e360494144085d622d61c0b521e354203b36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001822_tree.txt
@@ -0,0 +1 @@
+(GCF_002008305_PROKKA_00625:0.0416767,(GCF_005280335_PROKKA_00749:0.0240307,(GCF_005280335_PROKKA_00734:5e-09,GCF_005280335_PROKKA_00746:6e-09)n2:5e-09)n1:0.0416767)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001830_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001830_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9bdb20244774b0229b1166d80459654c968073e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001830_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02300:0.0239704,(GCF_002008305_PROKKA_00663:0.00185023,(GCF_003691675_PROKKA_00400:0,GCF_023573625_PROKKA_00633:0)n2:0.00185014)n1:0.0239704)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001835_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001835_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67c2ccbb8ad602a2837fcf07109a09d50d15da83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001835_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_02256:0.149163,(GCF_003691675_PROKKA_00435:5e-09,(GCF_002008305_PROKKA_00698:0.0115795,GCF_023573625_PROKKA_00668:0.00924332)n2:0.00694183)n1:0.149163)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001845_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001845_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e36b8e846cdc65af078717c5f2ff1d89504abfa4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001845_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01872:0.00533567,(GCF_003691675_PROKKA_00730:0.00425422,(GCF_023573625_PROKKA_00960:0.00212488,GCF_002008305_PROKKA_01016:0.00425621)n2:5e-09)n1:0.00533567)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001850_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001850_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21bb5ff1880f1c5608965e9cd2d04488c0dd61b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001850_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01674:0.103268,(GCF_002008305_PROKKA_01111:5e-09,(GCF_023573625_PROKKA_01061:0.0153789,GCF_003691675_PROKKA_00830:0.00368084)n2:0.00743056)n1:0.103268)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001854_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001854_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef2d200db268a79012b456c1b7ab1e9569d731cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001854_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01627:0.312697,(GCF_002008305_PROKKA_01160:6.6751e-05,(GCF_003691675_PROKKA_00879:0,GCF_023573625_PROKKA_01110:0)n2:0.00403319)n1:0.312697)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001860_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001860_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc02b3a111e801fcdd370d7473fc160bc337f08b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001860_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01473:0.123193,(GCF_002008305_PROKKA_01315:5e-09,(GCF_005280335_PROKKA_02666:1.3704,GCF_005280335_PROKKA_01577:0.00555071)n2:0.000616746)n1:0.185531)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001868_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001868_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c41700b580c10d699319e9b63bc256120dddad6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001868_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01358:0.341346,(GCF_003691675_PROKKA_01177:0.0166034,(GCF_002008305_PROKKA_01445:0.0154293,GCF_023573625_PROKKA_01395:0.0233433)n2:0.0154582)n1:0.341346)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001870_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001870_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f68ae033352b25ebbbff49ffb46f0dc52885288
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001870_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_01332:0.174783,(GCF_023573625_PROKKA_01420:0.00359242,(GCF_003691675_PROKKA_01202:0.0328296,GCF_002008305_PROKKA_01470:0.0132925)n2:0.0080007)n1:0.174783)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001882_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001882_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..390b6d5cef20ff07db2c804a92fe6eac4ff6c12f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001882_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_01225:0.0709072,(GCF_003691675_PROKKA_01374:0.00573257,(GCF_002008305_PROKKA_01669:0.0170469,GCF_023573625_PROKKA_01599:0.0113343)n2:0.0113385)n1:0.0709072)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001883_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001883_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d3a1efde770e6bd82df5c50e0e7042fdab597ec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001883_tree.txt
@@ -0,0 +1 @@
+((GCF_020097155_PROKKA_01217:1.25017,GCF_020097155_PROKKA_02117:1.77596)n1:0.134178,(GCF_002008305_PROKKA_01679:0.201935,GCF_005280335_PROKKA_01199:0.292849)n2:0.134178)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001899_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001899_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..53366f3f24975e375a0871e4249181b1330b2fa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001899_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00881:0.208066,(GCF_023573625_PROKKA_01834:5e-09,(GCF_002008305_PROKKA_01914:0.025786,GCF_003691675_PROKKA_01610:5e-09)n2:0.00427296)n1:0.208066)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001907_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001907_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cae2aa5e75141e013da5bb1f7c0f3efeda2df065
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001907_tree.txt
@@ -0,0 +1 @@
+((GCF_002008305_PROKKA_01987:0,GCF_003691675_PROKKA_01681:0,GCF_023573625_PROKKA_01913:0)n1:0.00324659,GCF_005280335_PROKKA_00870:0.00324659)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001910_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001910_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d20466f74637e497d512496bb603a133fdc8589
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001910_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00856:0.0968416,(GCF_002008305_PROKKA_02001:0.0257832,(GCF_003691675_PROKKA_01695:0.00282515,GCF_023573625_PROKKA_01927:0.00559341)n2:0.00697984)n1:0.0968416)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001920_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001920_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a9fd84b42b52cbc4cf84bd95a67b18eb29184f5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001920_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00603:0.0130378,(GCF_002008305_PROKKA_02091:0.0389296,(GCF_003691675_PROKKA_01799:0.0192538,GCF_005280335_PROKKA_00687:0.00635016)n2:5e-09)n1:0.0130378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001928_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001928_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8d32afd0beb77b223a6679db97bce496348036c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001928_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00602:0.588293,(GCF_023573625_PROKKA_02098:5e-09,(GCF_002008305_PROKKA_02155:0.0404614,GCF_003691675_PROKKA_01868:0.0155225)n2:0.0110805)n1:0.588293)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001930_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001930_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa7a159c47776ce93643062204ed41d660f11732
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001930_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00507:0.170779,(GCF_003691675_PROKKA_01885:0.015576,(GCF_002008305_PROKKA_02171:5e-09,GCF_023573625_PROKKA_02116:0.00683372)n2:0.0145254)n1:0.170779)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001932_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001932_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc98640c7ca1142c32aadc4ac04da3206e8d7eef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001932_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00562:0.204749,(GCF_002008305_PROKKA_02187:0.00837117,(GCF_003691675_PROKKA_01901:0.00765327,GCF_023573625_PROKKA_02132:0.00383229)n2:0.024301)n1:0.204749)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001937_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001937_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ef95175b6258e48b3046cae1a489e6343d7fc6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001937_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00538:0.0336037,(GCF_003691675_PROKKA_01920:0.00851658,(GCF_002008305_PROKKA_02207:0.0412301,GCF_023573625_PROKKA_02151:5e-09)n2:0.0335129)n1:0.0336037)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001939_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001939_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09cf0f783f35cfdaa6f7606eb9ab4c196cec070a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001939_tree.txt
@@ -0,0 +1 @@
+((GCF_005280335_PROKKA_00531:0.0507557,GCF_005280335_PROKKA_02650:0.869068)n1:0.018535,(GCF_002008305_PROKKA_02213:0.00408644,GCF_003691675_PROKKA_01926:0.00399845)n2:0.018535)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001951_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001951_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83bd1a68ba9caa376cb821771bba3378f8e2598f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001951_tree.txt
@@ -0,0 +1 @@
+(GCF_005280335_PROKKA_00945:0.22153,(GCF_003691675_PROKKA_01991:0.0162411,(GCF_002008305_PROKKA_02298:0.0166339,GCF_023573625_PROKKA_02239:5e-09)n2:0.00722104)n1:0.22153)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001954_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001954_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74f56ee94ce7e9bb07102a5753199422c70e0356
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001954_tree.txt
@@ -0,0 +1 @@
+((GCF_023573625_PROKKA_00844:0.53398,(GCF_005280335_PROKKA_02437:0.189977,GCF_005280335_PROKKA_01224:1.40367)n2:0.155963)n1:0.0811688,GCF_003691675_PROKKA_00238:0.176585)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001963_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001963_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb735e0be4aae0c63d6f2f75a1185b15368cf856
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001963_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00791:0.149695,(GCF_023573625_PROKKA_00736:1.69614,(GCF_003691675_PROKKA_01697:0.0447689,GCF_005280335_PROKKA_00854:0.0162526)n2:0.109979)n1:0.149695)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001978_tree.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001978_tree.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45389cb0ba538e99ca5957025623ad57cd8b12e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/Resolved_Gene_Trees/OG0001978_tree.txt
@@ -0,0 +1 @@
+(GCF_020097155_PROKKA_00415:0.0808378,((GCF_005280335_PROKKA_00733:0,GCF_005280335_PROKKA_00750:0)n2:0.0658012,GCF_005280335_PROKKA_02328:5e-09)n1:0.0808378)n0;
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9ecc65ddc33355d114fa0e5ee3551181b3ac696
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000007.fa
@@ -0,0 +1,51 @@
+>0_150
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_992
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_1245
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>0_1335
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRKQNATLKRLLAEAELEKAALKELAEGNF
+>0_2015
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_977
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1064
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1072
+MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1076
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>1_1970
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>2_1188
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_564
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_566
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1202
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1289
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_1827
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>4_2144
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10a63f83419c6a8076d4bd0922e570bb4c7c4537
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000017.fa
@@ -0,0 +1,102 @@
+>0_519
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>0_1855
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAIARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLGAEVPAGGRTSVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPADAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA
+>1_253
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVTLADEAVALGGETAADSYLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPARRATP
+>1_1562
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA
+>2_2354
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGETAADSYLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAG
+LVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEHGLPVAIKA
+AYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVTEEVTGIDLVREQFRLARGEALGYEDPVVRGHSFEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPSE
+HAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGRRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVE
+PGQTVSAGTVIATIADAD
+>3_861
+MSTPSTTASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYA
+LPGSTSAETYLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAI
+RDLGDKITARAIAQRAGAPLVPGSDGPVPDAAAARAFAQEHGLPIAIKAAFGGGGRGIKV
+VRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGAVAVLGTRDCS
+LQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVN
+TRLQVEHPVTEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPV
+PGPVEAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVVGEDRSQAIARARDALAELR
+IEGVPTVVPFHRAVLEEEAFTSAEALGVYTTWIESEFAAPLAASPHLGASVPGGGRTTVT
+VEVDGRAVRLGLPADLHAALLGGGGARTGASAPAEQSVDEGAVTSPVTGTLASWKVEDGA
+QVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA
+>3_2235
+MTNASAPQASADIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALH
+VKLADEAVALGGETAADSYLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLV
+WIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVNGTDEVVAFADEFGLPVAVKAAY
+GGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHGNV
+VVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQD
+GTLSFLEVNTRLQVEHPVSEEVTGIDLVREQFRIARGEALGYGDPEARGHSFEFRLNGED
+PGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSGAFDSMVGKLIVTGADRRQALQRA
+ARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPTALT
+PAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQLQGAAARAGAGRRRPRGARRAGAAP
+AAPGTDSLTAPMQGTVVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAA
+GDALTAGAVIAVIADAE
+>4_522
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDA
+LHVKLADEAVALGGESAADSYLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAG
+LVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVTGTEEVVAFADEFGLPVAIKA
+AYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVG
+QDGTISFLEVNTRLQVEHPVSEEITGIDLVREQFRLARGEALGYTDPQPRGHSIEFRLNG
+EDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSGAFDSMVAKLIVTGADRRQALQ
+RAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPSA
+LTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPV
+AAAVSTDALTAPMQGTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVE
+PGQTVTAGTVIATIADAE
+>4_1776
+MTTTPAARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLP
+GASSADTYLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRA
+LGDKITARSLAQQAGAPLVPGSDGPVPDAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVR
+ELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHGHVAVLGTRDCSLQ
+RRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTR
+LQVEHPVTEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPG
+PIDAFEAPTGPGVRMDSGVRTGSVVPGEYDSLLAKLIVWGEDRAQAVARARDALAELRID
+GVPTVVPFHRAVLEQDAFTSGDRLGVYTTWIESEFAEPLAESPYLSAEVPAGGRTAVTVE
+LDGRAVRLGLPADLYAALLGGGGAGAAAPAGAAGAGKPDDDGAVASPVTGTLASWKVEDG
+AEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7349f0ac8ec455020199178b0feed920e016b905
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000026.fa
@@ -0,0 +1,70 @@
+>0_126
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>1_2091
+MSTSPSGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
+>2_241
+MSTSPSGSRVAEPGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITAYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQAGLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVA
+SGEEAAASHR
+>3_176
+MNASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFYGSAGGIQTAG
+PGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAV
+VIVADTAAVTKYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIV
+AMIFGGLILMFTGASFTDGTPAGLHNLVDHGGFLPHGFGGVLIALTIVTFSFGGIETLGV
+AAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPFVQIFEGLGVP
+FAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLG
+VMVLGAILITVNPDAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFG
+IVGTVLGLAFVATVVITMATIPESRQALLIGLAWVVALTAAWFVTGVRKTAALHDRTGQL
+PVVHRHH
+>3_177
+MQSTPAPEAPAQAQLQRGLNPRHITFIALGTAVGTGLFYGSAAGIQAAGPGVVLAFMLAG
+AAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVTV
+YMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMF
+SGASFQDGVTPGPHNLVEHGGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASA
+LPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPFVQIFETLGVPFAPHLLNFVVL
+TAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMSV
+KEDTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFV
+AVVAGTMAFDQGGAVLGALGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHD
+RHGTPPPLTWDV
+>3_2128
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGL
+SMRHIQFIALGSAIGTGLFYGSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPV
+PGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFGVYMGFWFPDTPRWIWVTAVI
+LFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMT
+MVVIMSLVPWDRITGEASPFVEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLF
+GMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNAVIPEDVFVVVASIATFATVW
+VWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWFSDTRVAMI
+VGLVWLVLLGAAYRLFLHGHGRSRPDLEEGAASSP
+>4_134
+MSTSPFGSRVAETGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFYGSAGGIQAAGPGV
+ILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIV
+ADTAAITTYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMI
+FGGVILLFTGASTADGTQASLANLVDHGGFLPHGILGVLTALTIVTFSFGGIETLGVAAG
+EAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPFVQIFEGLGVPFAP
+HLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMV
+LGAVLITVDPNAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVG
+TYLGLAFVATVVITMATIPDSRQALIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVV
+RTRQSHED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000028.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000028.fa
new file mode 100644
index 0000000000000000000000000000000000000000..367fa3dd7e75ccf04547c0d8ba7a9427c3fab601
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000028.fa
@@ -0,0 +1,49 @@
+>0_154
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>0_1027
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>1_319
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>1_332
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>1_755
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQVEGAGSDGCHD
+LSW
+>2_707
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
+>4_976
+MGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALLSDAGHMAADVV
+VLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVVEAISRLGDAPE
+VASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSVGVMVAGVLIIL
+TGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGDLDAVEGVEEVH
+DLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQVEGAGSDGCHD
+LSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000046.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000046.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85e94771b65a7387afa52120a64b9e3bd12969d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000046.fa
@@ -0,0 +1,41 @@
+>0_1732
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLKGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPVTRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>0_1986
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALVSPTA
+>1_1703
+MSAAPLAGVRVVTIALNLPGPVAAARLQELGADIVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGAAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+DGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSAALALLWARGADGDGGHA
+TVALADAAHALALPNRHRMTGPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEERGIPLTALASPTA
+>2_1064
+MQPIDQTTSGPATSVGERPLAGIRVVSVAVNLPGPLAAARLAEFGAEVVKIEPPTGDPLA
+AAAPQWYAELIAGQRVLTLDLKTGPGQDHLATLLEGADLLLSSLRPSAADRLGLPASAHA
+AGAVFLEVVGHDGDDADLPGHDLTYQAAAGTLDAPRMPLVPVADLLGGERAVSAALAALR
+SRDHGGPATRVRVTLEDAARAAAAPVRRGLLGPGGPLGGDLPTYSLYASADGHVAVAAVE
+PHFAARLAEHIGSTRDEIARTILTRPGAEWERIANELDLPLAVVRPPR
+>3_715
+MSAGDGASRVPAGDAVVPGPLADVAVVTIALNLPGPLAAFRLAELGAQVTTVLPPAGDPV
+ATLVPALYTELHAGMAELTLDLKQDGDRARMEELLAGADVLLTSHRSGALTRLGLDAAAT
+ARRHPRLVQVDITGFPGERADVPGHDLNYQAEAGLLEPGHPPRGLLADVHGAERAVSAAL
+AGLHARDRDGRGGGVVVALSDAAHAMALPTRHGMTDPGSPLGGANPFYGVYPARSGHVAL
+GALEPHFAHAMVEALQLDPDGDVRAQLTAAFAERDADAWQSWGEEWGHPITALAGPTA
+>3_725
+MDVVGFAGERAGVPGHDLTYQAETGLLLSGESQTPTLPRALVADMHGAEQAVSTAPALLL
+ARDRAGRDAPGGHARVSLAEAAAAVGIPSRHGLLAPDALLGGGTPYYAVYRAAEGHVAVG
+ALEPHFSDALRAELDLPAGAGDDLAAALSAALTARPARDWQEWGEERGIPTGRGAVNGQP
+R
+>4_1921
+MSAAPLAGVRVVTIALNLPGPAAAARLQELGADVVTVLPPSGDPVATLVPALYEELHRGQ
+SVRTVDMKSQAGVAEMEQILAEADVFLTSHRSGALRRLGLDADAVRARHRRICQVDITGY
+AGDRTDVPGHDINYQAAAGLLAPGAPPRILAADLHGAERAVSTALALLWARGADGDGGHA
+TVALAEAAHALALPNRHRMTDPRSPLGGALPHYGVYPAAEGHVAVGALEPHFAAALVEGL
+GLDADGDVRAQLTEALSRHDAAHWQAWGEKRGIPLTALASPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28bf80888955668ede047761781a00d53f5951ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000053.fa
@@ -0,0 +1,35 @@
+>0_2185
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>0_2200
+MDHKQILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+DRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITALGADAHGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPVWGADRWAA
+HVDRLTAIAEGSGGPGRN
+>1_1898
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELECFGEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVLDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>3_401
+MDHKQILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIELEYFGGTF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITALGADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLRSPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGVGWN
+>3_405
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPEDVNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAVADL
+SAPVPVPDAPWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSYELNDLADA
+AAQG
+>4_2118
+MDHKEILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCELEYFDEVF
+GRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEALVFDARGRV
+PWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLRGPGDNLPGWDAERWAA
+HVRRLEGIARGAGPVR
+>4_2132
+MDHKQILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVELEYFGETF
+GRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAALDADAPGRV
+AWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLRAPGNNLPPWDADRWAA
+HVDRLTAIAEGSGGPGRN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000055.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000055.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9af82caed1e042453ea29f6a859c4e17d4e4176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000055.fa
@@ -0,0 +1,42 @@
+>1_1646
+MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTLSGGEKQRVAV
+ARALINEPPLVLADEPTGALDQARTRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWH
+LVDGELAPQD
+>2_836
+MTLLEVHDVDKTFHSGGEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPD
+SGRVLLGGEPLPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRG
+EQRRRAGEALERVGLGTRTGHRARTLSGGEKQRVAVARALINEPPLVLADEPTGALDQER
+TRDVVDLLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQD
+>2_989
+MSDGSAPPLLELAGVLKSFKGADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLL
+DRPDGGSYRVSGTDTMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTP
+PEQRDARAGEALALLGLSHRLDTRAKLLSGGERQRLAIARAIATRPRVILADEPTGNLDS
+VNSRIVIDHLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITELAGHRTAASASADM
+AGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASV
+GLTQTATDQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVA
+QVAPADVVITRHDPSDPEPAVAISLVAASSSYAGLAGLTLPSETSRTLLDSPDARLAWAT
+PAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDASLVVTPAVMTGVA
+QAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVL
+SGVLLVLAVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGA
+AVGSGVILAVSQARGWAAVLPPGAVPLALGLGLVAGVVSALYPGWVASRQRPADALRG
+>3_774
+MSLLEVHDVDKSFTTAASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPD
+AGEVLLEGVPLPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRA
+EQRRRAALALDRVGLADRAHHRARTLSGGEKQRVAVARALINDPPLVLADEPTGALDQAR
+TRDVVKLLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQG
+>3_851
+MTASAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAG
+LSRPLAGRIAYRSPDGSLNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVW
+IHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRLSGGEAQRVALVRALSKRPHLIVA
+DEPTGHLDGVTAREAIALLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED
+>3_923
+MNTAPLTPPVLAARGLTKAYGSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGII
+APDGGRVTLAGADGTVHEVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLML
+NGVDRRAAEQTAARWLGSLGLAGMEDRRPGELSGGQRQRVAIARAQAVEPDVVFADEPTG
+ALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESDQAQAAAGT
+TREQVR
+>4_708
+MSLLTVHDVHRSYRGPAGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPD
+AGSIRVAGRSLPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKR
+ERRTMAAELLTRLGLGDRLHHPVGRLSGGERQRVAIARAVIMGPSLLLADEPTGALDEER
+TDEVMGLFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000062.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000062.fa
new file mode 100644
index 0000000000000000000000000000000000000000..142f9a9314ee90a216cea6b02f5b1d59b3e040f1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000062.fa
@@ -0,0 +1,40 @@
+>0_72
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP
+>1_2036
+MDESIDAAAREANRALLGRLPAGRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRAAAAWVGAHAPGEPVSE
+DVLP
+>2_302
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRSGARAVPPAEEQARILPVIEALLAEDVVVSVDTRHTATARAALALGP
+VIVNDVSGLVHEPEMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RLLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGAPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWVGAHAPGEPVSE
+DVLP
+>2_2287
+MLRSRVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGPAASHPDARPV
+SPADEIRRIAPLLDALSDQMHRVSIDSFQPETQRYALKRGVGYLNDIQGFPDPALYPDIA
+EADCRLVVMHSAQRDGIATRTGHLRPEDALDEIVRFFEARVSALRRSGVAADRLILDPGM
+GFFLSPAPETSLHVLSNLQKLKSALGLPLLVSVSRKSFLGATVGLPVKDLGPASLAAELH
+AIGNGADYVRTHAPGDLRSAITFSETLAKFRSRDARDRGLDHA
+>3_244
+MLPKPFHELPDRTLVMGILNVTPDSFSDGGAHDRVDAAVAHGLDLLAQGADLIDVGGEST
+RTGATPVDPAEEQRRILPVVEALLAEGAVLSIDTMHTATARACLALGPVIVNDVSGLVHE
+PDMPALVAESGAPCILMHNRGHAQVMDSLAHYEDTLGEVVRELSEVTDRFLAAGASPEQI
+ILDPGLGFAKAGEQNWELLRGLERIESLGRPVLVAASRKRFLGTVLAGEDGTPRPALDRD
+HATAAVSAISAAHGAWGVRVHDVRSSVDAVRVGDAWRGAAPRPAGPGEARA
+>4_66
+MDESIDAAAREANRALLGRLPADRTLVMGILNVTPDSFSDGGEHATVRAAVEHARRMVAD
+GADIVDVGGESTRPGARAVPPAEEQERILPVIEALLAEDVVLSVDTRHTATARAALALGP
+VIVNDVSGLAHEPDMPALIAASGAPYILMHNRGNPQTMDGLAVYEDTVPDVVCELRDVAG
+RFLAAGVEPAQLIVDPGLGFAKAGEQNWELLRGLEWLRAMGHPVLVAASRKRFLGTLLAD
+DDGTPAPPAARDAATAAISALAAAQGAWGVRVHDVRASADAVRTAAAWAGAHAPGEPVSE
+DVLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08220df184eff17579b1566492d63004c4a29900
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000066.fa
@@ -0,0 +1,37 @@
+>0_190
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>1_1974
+MAVAVYPLAFYTSIHWAGVAIGSVVSLASAPLASGLLERIVEYRRLSRWWMLAAALGGTG
+AALLCLSQLDQEAASSTATLAGVLLGLVAGATYATYSWAAHRLIHDGISRAASMGAVFGA
+GGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYGLTRVPASTATTITLTE
+PAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTADRHGRTPTSEAIQPALA
+PSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVRGRFRKPYRLRPVSPDH
+GRATCGERTEIMRPARGLDARSVLAATMET
+>1_2137
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQQLTPLDLAGMLLVIAACAAAVWTSRSPGVSGGARG
+>2_187
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAAFDRIPQGVAVTFEVLGPLALSVLANRRWLSVVWAAL
+AFAGIALLGRDGFSAGMDGAGLDPLGVAFALAAAACWAGFILANRHAGTHLPGVQGLALA
+MVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQVLRTMPTGLFSLIT
+CLSPVVAALTAWAVRGQRLAVLDLGGMGLVVLACGAAVWAAERAARPSRRAPRTS
+>3_139
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQVLRRMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTSRSPGVAGGGRG
+>4_190
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEAFARIPQGVAVTFEVLGPLALSVAARPSWRSAAWAAL
+ALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSRRAGTHLPGVQGLA
+LATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQVLRHMPTALFSL
+LTCLSPIAAALTAWAVRGQELTPLDLAGMLLVIAACAAAVWTGRSPGVAGGGRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000072.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000072.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aafbab507c641a99813e890c6e566a81424fa90c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000072.fa
@@ -0,0 +1,66 @@
+>0_241
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEGLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMARYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTLIDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR
+>1_2204
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR
+>2_111
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARQDVPALIIAEDDGRSTERTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGAEDLAKFAGVGEGLRLVHVPG
+VFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMDRYGVTSFCAPPTVWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWG
+ATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVLIDPLTGQEAAEGEICLRLDP
+RPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR
+>3_79
+MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPA
+LIISDAGGGHLSRTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKL
+RVVMVPTTTQMTSADLADRVERAEARWVVASAENLAKFDGVDSGLHLVHIPGVAAQGDAR
+TAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEHTHTSYPVG
+HLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMD
+EFGVTSLCAPPTVWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFG
+MTETTLQIANTPGQKLVIGSMGRPLPGMDVVLIDPLTGEEAAEGEICLRLDPRPVGLLKS
+YYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKISPFELESVLVEH
+PAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFR
+ELPKTISGKIRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR
+>3_2414
+MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVI
+VEEDGTVLRRSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAV
+VIPTTTQLVAADLQDRVDRAGARWAIANAGNLVKFADVVGDCTLIHVPGVYASEAEHALP
+EVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEHTQASYTVGHLS
+TMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGG
+VTSFCAPPTVWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTE
+STLQIANTPGQRVVIGAMGRPLPGFDIELRDPQTGDRVDGEGEGEICVGLDPRPVGLFQR
+YHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLSPFELESVLMTH
+PAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFR
+PLPKTVSGKVRRVELRAEEEQRRAGVAGLGVEHREEDLGIRRQRRA
+>4_241
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQD
+PARADVPALIIAEDDGRSTERTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWE
+FMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGAEDLAKFAGVGEDLHLVHVPG
+VFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDP
+AALMANMERYGVTSFCAPPTVWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWG
+TTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTLLDPLTGQEAEEGEICLRLDP
+RPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVSPFE
+LESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYK
+RIRRIEFLELPKTISGKIRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000079.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000079.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2fef7ebc7a9ee7f27847368c98d0f7d25c7f4b4c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000079.fa
@@ -0,0 +1,36 @@
+>0_304
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVVDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDITGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>1_28
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLEAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQIGDERYADLGKDAPRTEALKQVIDRLLPYWEEQILPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>2_15
+MANTTYTLVLLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELMKAEGIHPDVLHTS
+LLKRAITTANLALETADRQWIPVKRDWRLNERHYGALQGKDKAQVKEEFGEEQFTVWRRS
+FDTPPPALDDSSEFSQIGDERYAELGDDAPRTEALKNVIDRLIPYWEAEIVPDLKASKTV
+LVAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDEDLKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
+>3_11
+MADTFKLILLRHGQSDWNEKNLFTGWVDVPLTEKGRAEASRGGELLAAEGLLPDVLHTSL
+LKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMTWRRSF
+DVPPPPLDDSSEFSQAGDERYRDIGPDAPRTEALKQVIDRLLPYWTEQIVPDLKAGKTVM
+VAAHGNSLRALVKHLDGISDEEISGLNIPTGIPLFYELDQNLKPVTPHGRYLDPEAAAAG
+AAAVAAQGDKK
+>3_670
+MLTLLRHGESTANEAGTFTGLLDVPLTHRGERQASAAGQLLRSNHITPDVVVTSTLRRAV
+RTAELVCDALGTQLPTEAVWQLNERNYGALTGMTKTDARRMLGDDEYVRLRRSRTGTPPP
+MSLHLWEELRSSSALRGLPDGALRRTEALSDVIKRVRPVLHDRLLPMVRSGRSVLVVAHG
+NSLRALCACIDDLTDPELEQLNLPTGQPVQYHLAPTGALVPRGGAFLDPVAAQHAAALVA
+AEGGT
+>4_311
+MANTTYTLVLLRHGQSEWNEKNLFTGWVDVPLTEKGRAEAARGGELLAAEGIRPDVVHTS
+LLKRAITTANLALEAADRQWIPVKRSWRLNERHYGALQGKDKAQVKEEFGEEQFMVWRRS
+FDTPPPALDDDSEFSQVGDERYADLGKDAPRTEALKQVIDRLLPYWEEQVLPDLKAGKTV
+LIAAHGNSLRALVKHLDGISDEDIAGLNIPTGIPLVYELDQNFKPITANGRYLDPEAAAA
+GAAAVAAQGSAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1759c739a0103248663e0cc7d3ecc5e30188ffac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000085.fa
@@ -0,0 +1,61 @@
+>0_402
+MPSPTTTTAPGPASPAGPLRPPHTAAESAERVKRRGALYFAEHQLRNMRRYGAVLIVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWHRTYYAAQATPLSPAQIALGHLAAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPLDVLPVWLRWIGWL
+SPQWHAAQLGRMLSYGMAEPAWLTVAHVAFLLALALGGARLAVRIYTRRLGWVRGTPDRD
+AGTAARRDRAPRLGRRAPRLGRRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPP
+LPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALV
+GDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLD
+VALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWM
+KTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWA
+TAGHVLYFVVMAGVGVWLAARRLGALFLR
+>1_132
+MPSPTTTTTPGPASPAEPLRPPVTAAASAERVKRRGVLLYAEHQLRSMRRYGAVLLVGAL
+GEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALMTASVEFSYPVMGG
+FQWQRTYYAAQVTPLSPAQIALGHLVAVSLRFVFQAAVFLLVMLAFGVVSSPWAWVQVLT
+ATLGGLAVGAPIMAFAASLREDKGQFATLQRLVVMPLFLFSATFYPLEALPVWLRWIGWL
+SPQWHAAQLGRVLSYGMAEPVWLTVVHVAFLLALALGGAWLAVRIYTRRLGWVRGTPDRD
+AVTVARRDRAPRLGCRAARTGAARADVAPAAAQADPAAPSSSVVREHAVAVPPLPEIPVR
+RGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGLGLGALVGDVAGPD
+GTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLSTRLGPLDVALGEIA
+MALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGMAVTSWMKTFQHMD
+WVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAVGVLSWATAGHVLY
+FVVMAGIGVWLAARRLGALFLR
+>2_2478
+MTAAAGAEPAAPSSSVVLEHTAAVPPMPEITLRHGPLAGMYAGNVRAVMERAFLTLKSNN
+WVVFASGFFEPVLYLASMGIGLGALVGDVAGPDGTPIPYGMFIAPALLAVSAMNGAIYDS
+TWNVFFKLRHAKTYQTMLSTKLGPLDVALGEIVMALLRGLIYAVGFLIVMTVGGLVTSWT
+AVLMVPGALLVALGFASLGMAVTSYLKTFQHMDWIQIVLMPMFLFSATFFPLSVYPQAIQ
+WVIQVLPLWHAVELMRALAVGVVTWGTAGHILYFVAMSAVGIWFTSRRLGALFLR
+>2_2479
+MDASTTTTAPGPAAPRASASPAPLSPPISAAESAERVTRRGALYYAEHQLRNMRRYGSVL
+IVGALGEPIVYLLAMGLGLAQLMGGGAAQEGLGGVSYVAFLAPALLASGALMTAAVEFSY
+PVMGGFQWQKTYYAAQATPLTPAQIAVGHLGAVSLRFLFQGLVFFLVMLAFGVVHSPWGW
+LQILTATLGGLAIGAPIMAFAASLTEDKGQFATVQRLVIMPLFLFSATFYPLEALPVWLR
+WIGWISPQWHAAQLGRVLSYGMAEPVWLTVLHVVVLVAMAAVGTWLAVRIYTRRLGWRRG
+TPDRDALARP
+>3_2349
+MAAQIPASAPLQPPITAAESAVRVKARGAWFYAEHVLRSMRRYGAVLIVGALGEPILYLL
+AMGLGMAQVMGGGAPQESLGGVSYVTFLAPALLASGALMTAATEFSYPVMGGFQWHRTYY
+AAQATPLSPAQIAVGHLGAVALRFLFQAAVFFGVMLAFGVVHGPWGWVQVLTAALGGLAI
+GAPIMAFSASLKEDHGQFATLQRLVIMPLFLFSATFYPLEALPVWLRWVGWISPQWHAAQ
+LGRVLSYGMAEPRWLTVLHVAVLLALAFGGAWAAVRMYTRRLGWRPGTPDRDAVARPRAQ
+RASRLGRRATRVDRMAGAHAEAAAASSVVREHTAAVPPMPEITVRRGRLGGLYSGNVAAV
+MERALLTLKSNNWVVFASGFFEPVLYLASMGLGLGALVGAVPGPGGAPIPYGMYIAPALL
+AVSAMNGAIYDSTWNVFFKLRYAKTYQTMLATRLGPLDVALGEIAMALLRGLLYAVGFLV
+VMAVAGMATSWTALLMVPGALLVALGFASLGMAVTSWMKTFQQMDWIQLVLMPMFLFSAT
+FFPLTVYPEPIQWLIRVFPLWHAVEMMRALAVGAVTGATAGHALYFGVMSGLGVWLTSRR
+LRALFLR
+>4_405
+MPSPTTTTTPGPASPGPRSGTSAPSATPAEPLRPPVTAAESAERVRRRGVLLYAEHQLRS
+MRRYGAVLLVGALGEPVLYLLAMGLGLAQLMGGGMPQDALGGVSYVAFIAPALLASGALM
+TASVEFSYPVMGGFQWQRTYYAAQATPLSPAQIALGHLVAVSLRFVFQATVFLLVMLAFG
+VVSSPWAWVQVLTATLGGLAVGAPIMAFAASLKEDKGQFATLQRLVVMPLFLFSATFYPL
+EALPVWLRWIGWLSPQWHAAQLGRVLSYGMAEPAWLTVVHVAFLLALALGGAWFAVRIYT
+RRLGWVRGTPDRDAVTAARRDRAPRLGRRAARTGAARADVAPAAAQAEPAAPSSSVVREH
+AVAVPPLPEIPVRRGPLAGAYSGNVRAVMERAFLSLKSNNWVVFFSGFFEPVLYLASLGL
+GLGALVGDVAGPDGTPVPYGMYLAPALLAVSAMNGAIYDSTWNVFFKLRYAKTYQTMLST
+RLGPLDVALGEIAMALLRGLIYAVGFLIVMTVAGLVTSWTALLMIPGALLVALGFASLGM
+AVTSWMKTFQHMDWVQIVLMPMFLFSATFFPLAVYPEPIQWVIRVFPLWHAVEMMRALAV
+GVLSWATAGHVLYFVVMAGVGVWLAARRLGALFLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000086.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000086.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d8680514493f522bc19299016b30015e5cee7260
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000086.fa
@@ -0,0 +1,54 @@
+>0_427
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>1_157
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAISLAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFRG
+>2_2453
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTKRYL
+GKGVLDAVAAVEEIADELEDEFAVDQRAVDRLMLDLDGTPNKGKLGANAILGVSMAVAAA
+AAQSSDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVEKAGYTLGEDIALAL
+DVASSEFCEKGAYTFEGQKRSAEDMVAYYTELADNYPIVSIEDPLDENDWDGWRLLTEKL
+GDRVQLVGDDLFVTNVERLQRGIDDKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRYRG
+>3_666
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSAFGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAEL
+DGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGAH
+AANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAAP
+EEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRHL
+IDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAAL
+IKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGRG
+ERVAKYNRLTEIAEQHPELPYGLI
+>3_2324
+MAQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDTERYL
+GKGVQDAVNAVFEIAEELEDELATDQRAVDQMMLDMDGTENKGKLGANAILGVSMAVAVA
+AADSADLPLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRM
+GAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLESNRAALDLIAEAVQKAGYTLGEDVALAL
+DVASSEFCENGSYTFEGRQRSAEEMSAYYAELVDAYPIVSIEDPLDENDWEGWEHLTEQL
+GDRVQLVGDDLFVTNVARLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLADAAVYAGRSAF
+PRFQG
+>4_430
+MALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAAVPSGASTGEFEAVERRDGDKKRYG
+GKGVLDAVAAVEGIAEELEGEFAADQRAVDRAMRDLDGTPNKGKLGANAILGVSMAVAVA
+AAQASDLMLYKYLGGPNAHVLPVPMMNILNGGAHADSNVDIQEFMIAPIGAPSFREALRW
+GTEVYHALKTVLQEKGLSTGLGDEGGFAPSLESNRAALDLIAEAVTKAGYRLGEDIALAL
+DVASSEFFDNGSYTFEGQQRSAEEMAAYYTELVDNYPIVSIEDPLDEDDWDGWQHLTAQL
+GDRVQLVGDDLFVTNVERLQRGIDEKAGNALLVKVNQIGSLTETFDAIALAQRHMFHCMI
+SHRSGETEDTFIADLAVATNAGQIKTGAPARSDRVAKYNQLLRIEEDLDDAAVYAGRSAF
+PRFRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000088.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000088.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa33ca11cacdf8f748db67fb233e77120b7db1fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000088.fa
@@ -0,0 +1,56 @@
+>0_473
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALTIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQTLDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGEMSLVG
+PRPHLPHEVEAYGQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>1_203
+MIGSPGDESTALRMGSTARGRVLGRPWERGLPLLVLIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGTEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKARREDYLPIPVSTDLDTVEDVVAHVEERDVEAVVIT
+SGHPFVPSDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY
+>2_1196
+MLTPDSPYEERFAALNQSLRWEVADELRRANLARVDELHPPVTPRDTFYTRHGKRALDVG
+VSGAALLFSSPVIGALCLVTLKDLGQPVLFTQQRPGKHGKPFQMVKLRTMREAYDDQGKP
+LLGELRVTKTGRLIRRASLDELLNFWNIFKGDMSLIGPRPLVPEYVERFSRRHRQRLAVK
+PGLECPPPRPPQGPVTYDDQFENDCWYVENVSLKTDAWLTWRVLQTALDRRQNKARGSST
+RGSFMGYDADGTVITTAALPDWALNTVLERHGLLTSNSADARQEG
+>2_2398
+MFSSPGDESPALRTGSTARGRLLGRPWERGLPLLVFIVDVVAVLLATFVSAQLRFGGPRR
+TTLPGTEVIDYSVISLALSAAWVLALSIQGSRDIRILGVGSEEYKRVLQGTLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHLGRFRRRLLLVGGPKAVRH
+IFQALDSEAGAGYAPVAAALPGYKTRQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMVPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVNAEEIKQRLVSDGGDADVLFKMKDDPRITKVGKFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVVAADGAY
+>3_2281
+MTSSAVTTSQTGRGGSSVHARVLGAPWERGLPRLVLLADVVAVVLAAFLSSELRFGTARN
+AAVPGAESVNYLLVGAVLSASWVVALGVDGSRDIRILGIGAEEYKRVLRGTLYLFGMIAI
+LAYAFAFEVARGYVALALPIGLLLLMLGRFLIRGWVARGRHRGAMRRRLLLVGGPQAVKY
+VHDTLDSEAGAGYKPIAAVLPGYRARDEGWLPIPVTTEVDGVDELVAQVREMDIEAVVIT
+SGHPFVPDDVRRLGWDLQERGISLIMAPALVDVAGPRLHTQPLAGLPLLHLSTPRLSRGK
+AFVKRSFDVVASGLGMLVISPLLLTVAIAVKATDGGPVLFRQERVGLRGEHFTMLKFRSM
+VVDAEEIKQQLMSDRGEEDVLFKMKDDPRITRVGRFIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEQYGQYVHRRFLVQPGITGLWQVSGRSDLSWEDAVRLDLYYVENWSVLGDL
+VILGRTVKAVLAADGAY
+>4_472
+MFASPGDESTTLRMGSTARGRVLGRPWERGLPRLVLVVDVVAVLLATFVSAQLRFGGPRR
+TTLPGAALVDYSVISLALSAAWVLALTIQGSRDIRILGVGTEEYKRVLQATLYLFGTVAI
+LAYAAGLEVARGYVGLALPLGVLLLLLGRFLVRGWVARQRHRGRFRRRLLLVGGPKAVRH
+IFEALDSEAGAGYAPVAAALPGYKARQEDYLPIPVSTDLDTVEDVVALVEVRDVEAVVIT
+SGHSFVPGDVRRLGWELQERGVSLIMAPALVDVAGPRLHTQPLAGLPLIHLSTPRLSEGK
+AFAKRAFDVVASGLGLIAISPLLIAVAIAVKATDGGPVLFRQERIGLGGRPFTMLKFRSM
+VVDAEEIRQRLVSDGGDADVLFKMKDDPRITRVGKLIRRTSIDELPQLVNVLRGDMSLVG
+PRPHLPHEVEAYEQYVHRRFLVQPGITGLWQVSGRSDLPWEEAVRLDLYYVENWSILGDL
+VILGRTVKAVIAADGAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000090.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000090.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38513ade4a6fb0b9ef7ac01683233000c31019f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000090.fa
@@ -0,0 +1,42 @@
+>0_498
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLT
+YAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQ
+TNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSD
+HLVRAWVRSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIH
+TEDHSSAVLRILERGEIGRTYLIGADGEKNNREVVEILLELFDRPADDYDLVADRPGHDL
+RYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>1_229
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVALDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVRATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ
+>2_1194
+MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQTDRELAAQLERAPYPALRRFPQVHPR
+TRLLEAGFLRDGDIVINCAFPWNRGGRAMADGLEYLTRLFQSAHAVALHTFVNVSSQSVY
+SQARTEAADESSPVECDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNR
+FIARFLADEPVSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDI
+AQTVADVVRTHTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALSILQAM
+TSAQSASVGETPTGSVEGGRR
+>2_2375
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAQSDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEAKYRAAGQ
+>3_2257
+MHLLVTGGAGFIGSNFVHHVVRETGHDVVVLDKLTYAGNRENLAGLPEDRVTLEVGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGQGINVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNKEIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPQFTDIRAG
+LADTVRWYRENEAWWRPAKDAVEATYRAQGQ
+>4_498
+MRILVTGGAGFIGSNFVHHLVRETDHDVVVLDKLTYAGNRDNLVGLPESRVRLEIGDICD
+AALVDRLVAESDAVVHYAAESHNDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVST
+DEVYGDLELDDPAKFTETTPYNPSSPYSASKAGSDHLVRAWVRSFGVQATLSNCSNNYGP
+YQHIEKFIPRQITNLIDGVRPRLYGHGVNVRDWIHTEDHSSAVLRILERGEIGRTYLIGS
+DGERNNREIVEILLELFDRPADDYDLVADRPGHDLRYAIDNTALRTELGWEPRFTDIRAG
+LADTVRWYRENEAWWRPAKAAVEATYRAQGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7a0480f7ea3d11a30d7293b82546c1b04dcebfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000092.fa
@@ -0,0 +1,25 @@
+>0_530
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>1_264
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
+>2_622
+MERPAPTAEICPVRPEDTDAVVALWERTLPEYGDPTRPQRAPRPSIRRKLDWGDGLFWLA
+VSDEEVVGTVMAGYDGHRGWIYSLAVHPDHRRGGLGTALVAHAEQELARLGCPKVNLQVL
+ATNADGAEFWAATGYQPDPVLGLGKRLGG
+>2_2339
+MTETAPTVPTPPARPQVRPLRPEDHEAVAALTVASYVDGGHIAPGSRYVKTLRDVAGRAA
+RAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMAVIE
+ERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGPFLV
+YRLPLA
+>3_2222
+MSDVTVRALRPEDHEAVAALTLASYTTGGHFEAESDYLETLADVAGRAAVAEVLVAELDG
+QVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLAEVVRRARATPGVEA
+IALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGPFLVYRLPLT
+>4_533
+MSALVRPLRPEDHEAVAELTLASYVDGGHIAPDDAYVKTLMDVADRAGRAEVLVAEVDGE
+VAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLAEIVARARAEEGVDAV
+VLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGPFLVYRLALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30b848a7ecb07f9bd9f48ebb360f267bca4ee15e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000096.fa
@@ -0,0 +1,41 @@
+>0_589
+MGSHHHAPTGHRGRLAIAFGITTAVLLAEVVGAVLTGSLALLVDAAHMLTDAGGLLMALL
+AATLMARPPTTRRTWGFLRAEVLAALAQAAVLLAVGTYAFIEGLQRLFAPPEVASGPLLA
+FGILGLVGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIAATGWTRADA
+VAGMLIAVLIVPRTLKILGETTRILLESTPRGLDLAEVRTHLQALPHVVSVHDLHASQIA
+TGVPVLSAHIVVEDSCFHDGHAPQILDQLQHCVAEHFDVGVDHSTFQLEPAAHAHHEHPT
+HH
+>1_310
+MVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLLIALTATTLALRPATDKRTWG
+YKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVESTAMLWFGVIGLAGNLIGLAIL
+ASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWNRADAVVSLLIAALIVPRALI
+LLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHASRIDSDTPVLSAHVTVHNGC
+LTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHTETLHP
+>1_1724
+MGAHHHASPAHRWRLAVAFAITTAVLLAEVAGALITGSLALLVDAAHMLTDAGGLLMALL
+ASTLMARPPTARRTWGFLRAEVLAALAQAAILLAVGLYAFIEGLQRLFAPPEVASGPLLL
+FGILGLAGNLASLAVLGSGRGANLNMRAAFLEVLNDALGSVAVIASALVIATTGWAQADA
+VAGMLIAVLIVPRTLKILAEAAHILLESTPRDLDLAEVRDHLEAVPHVVSVHDLHASQIA
+TGVPVLSAHVVVEDHCFHDGHAPQILDQLQHCVAEHFDVAIDHSTFQLEPAAHAHHEHPT
+HH
+>3_527
+MSTPHEHHHDHAHGPSPEEAAADPALRRRLWIALALAGTVVLAQAVGAALTGSLALLTDT
+AHAVTDASGLAVALVAAILMARPATPRRTWGLRRLEVVAALGQAALLLLVGAYSAVEAVR
+RLVEPPAVDGTGMLLFGVLGLAANLAAAAVLASSRGANLSMRAAFLEVVNDALGSLGVIA
+AAAVVAVTGWTRADAVAGLLIVVLIVPRAVSLLRQTLRVLLEFTPEGLDLDEVRTHLLEV
+EHVLEVHDLHASTVATGLPVLTAHVVVEDGCFTDGHAAQILEQLRECTREHFPLAVPHST
+FQLETAAIAADDAHHTAHP
+>3_685
+MGAGHNHGPAASETGHPGDFRKKLWIAFSITATIVVAQAMGSVITGSLALLTDTAHAITD
+ASGLLVALIAATLMLKPANSKRTWGFRRIEVIAALGQSALLLAVGTYAAIEGIRRLFEPP
+EVPASELLIFGIIGLVANIIAITILASSRGSNFNMRAAFLEVLNDALGSLGVIIAAIVIA
+TTGFMQADAIAGLLIAALIVPRAFKLMRETTGVLMEFTPKGLDLDKVRSHILELDHVKDV
+HDLHASTVATGLPILTAHVVVEDECFTDGRAAQTLHEIKDCVAGHFEVSIHHSTFQIETE
+HIAEHEPEISKHD
+>4_1947
+MSGHDHSHALPAAGRRGRLAVVFSITATIMVAEVIGALASGSLALLADAGHMFTDSAGLL
+IALTAATLALRPATDKRTWGYKRAEIIAAAAQAAVLLAVGGFVAVEGVRRLIEPPEVEST
+AMLWFGVIGLAGNLIGLAILASSRGENLNMKAAFLEVLNDALGSVAVIVSAIVIATTGWN
+RADAVVSLLIAALIVPRALILLRDTIDVLMETTPKGLDLEAVRIRLSELPHVLEVHDLHA
+SRIDSDTPVLSAHVTVHNGCLTAAHLGTVLTDLQRCVAQDFQVPIEHSTFQIEPATHPHT
+ETLHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fd2c7763d6a230335bec81e34e06dee5e2739738
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000098.fa
@@ -0,0 +1,33 @@
+>0_601
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR
+GGKAEVQGCRVHSDRGSQGGFNRSSQHPLGITGGMGDGKQGLGEEDQ
+>1_355
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA
+>2_376
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA
+>2_395
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKRPGSDEDS
+>3_2136
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP
+EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR
+ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR
+GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>4_580
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000100.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000100.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88acb0006267631d223102fa5b3843abf4138997
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000100.fa
@@ -0,0 +1,36 @@
+>0_619
+MTSVPTVPFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLE
+TWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAHGFVVIPKSVTPERIV
+SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF
+>1_365
+MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDVSLDKLGTDYVDLYLIHWAKPAQGKYLD
+TWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVVPVIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEVRGATPAQVVIAWHLAQGFVVIPKSVTPERIV
+SNLEAAGVELTDDDVARIDALDREDGRLGPDPAVIDF
+>2_2268
+MTSVPTVPFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGYRHIDTAAIYGNEEGVGRA
+VAASGVPREELFITTKVWNSAHGYDEALAALEESLGKLGTDYVDLWLIHWAKPTQGRYVD
+TWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVVPVIHQVETHPYWQQRELRELEER
+HGILHESWSPLGQGGELLEDPEITAIAEAHGATPAQVVIAWHLAKGFVVIPKSVTSERIV
+SNLAAADVELTEDEVARIDALDREDGRIGPDPATIEF
+>3_567
+MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY
+RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV
+LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA
+PVDQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEPVAAAAARTGRTPAQV
+VLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPDEFGH
+>3_2126
+MTTVPQTPFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGYRHIDTAAVYGNEEGVGRA
+VAAAGVPREELFITTKVWNSDQGYDEALAALEASLAKLGTDYVDLWLIHWAKPAQGKYVD
+TWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVVPVIHQVETHPYWQQRELREVESR
+HGIVHESWSPLGQGGELLSDPVITAIAEAHGATPAQVVIAWHLAEGFVVIPKSVTPERIV
+SNLTAAELELTAEEVDQIRGLDRADGRIGPDPASITF
+>4_589
+MTDVPTVPFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGYRHIDTAAIYGNEEGVGRG
+IAASGVAREELFLTTKVWNSDQGYEEALAALDASLDKLGTDYVDLYLIHWAKPAQGKYLD
+TWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVVPAIHQVETHPYWQQRELREVEGR
+HGIVHESWSPLGQGGDLLADPVVTEIAEARGATPAQVVIAWHLAQGFVVIPKSVTPERIV
+SNLEAAGVELTADDVARIDALDREDGRLGPDPAVIDF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000108.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000108.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dd4ac73b184060872d4e7d5d5e43a9d2ded548bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000108.fa
@@ -0,0 +1,54 @@
+>0_808
+MSLEFRTSEESPDVTRVVATHLPTRHGDFALLGYRDGRGTDHVALTLGDVAADDGELPLV
+RLHSECLTGDALGSYRCDCGEQLDAALQAIGAAGRGVLIYIRGHEGRGIGLLDKLRAYAL
+QDSGIDTVDANTHLGLPADARDYDQSAQILRELGVGKIRLLSSNPAKQEALEALGIHVEA
+RVRLNVADRPENSRYLSTKRARMRHDLPPERNAWDLLAGARVPTGPLTPQEEALVLRYGP
+LVEAGPRLVIGQLGQSLDGFIASRTGDACFVTGEADREHLHRLRALVDAVLVGAQTVAAD
+DCQLTVRAVNGADPARVVVDPHARIPLTAKVLTDPRSRTLWLVGSDASVPASLAPHVSVH
+RLETSTGFEPAAILQYLADQGLGRVLIEGGGLTVSGFLHAGVLDRLYLTSAPLLVGDGVP
+GIRFDGADALSGALSAPVRRFVLGDDVCTEFDFSAAKPASPAALHRADQENQPTGQD
+>0_1020
+MSEHIRLDPVPVAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRLLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPALTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDSERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>1_748
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
+>2_1790
+MSDSIPLDAVPAAIAAFAAGRPVVVVDDADRENEGDLVYAAALATDAVTAFTVRHTSGVI
+CAPMPADLADRLALPPMTARNEDPKGTAYTVSVDAATEVSTGISAADRTRTLRILADPAA
+GPADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLADVAPVAAIAELVHDDGTMMRLP
+ALREFADEHGLVLISIEDLVRHLEEEGPTPVPVPAEATLPTRHGVFRVSVHADAVTGAEH
+VLLVAKKAGEAGEADPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALSRAGSEGGAVL
+YLRGHEGRGIGLANKVRAYRLQEQGLDTVEANIALGLPTEARDWAGAAAVLAAAGHTRVR
+LVTNNPAKVAGLQAAGIDVVERVPAPTPVTEHNLGYLRTKRDRMAHALADRVLEHPVAPG
+HEDPRHETPTHQEDTP
+>3_1678
+MSIDTAVEPAAPVDIRLDPVADAVAAIAQGRPVVVVDDADRENEGDLIYAAALATDAVTA
+FTVRHTSGVICAPLPAELADRLNLPPMTARNEDPKGTAYTVSVDAVAGVTTGISAADRTV
+TLRVLAGEESTAADLTRPGHVFPLRAVPGGVRARRGHTEAGVELCELADLPPVAAIAELV
+HDDGTMMRLPALREFADEHSLVLISIEDLVAHLHEHRPEQRVVPAEAALPTAHGDFRISV
+HPDTATGAEHVLLVADRPGSATGGDADAPVTVRVHSECLTGDVFGSLRCDCGPQLQAALD
+AAARDGGAVLYLRGHEGRGIGLTNKIRAYRLQEEGLDTVEANLALGLPAEGRAYAGAADL
+LREAGLTRIRLVTNNPAKVDALRAAGIDVVERVPAPTPVTEHNAAYLRTKRDRMHHELAD
+RDLGDA
+>4_967
+MSEHIRLDPVPAAIAAIAAGRPVVVVDDADRENEGDLIYAAALATDEVTAFTVRHTSGVI
+CAPLPAGLADRLALPPMTTVNEDPKGTAYTVSVDAAAGVTTGISAADRTRTLRVLADPGA
+APGDLTRPGHVFPLRAVPGGVRARRGHTEAGVELCRLAGVAPVAAIAELVHDDGTMMRLP
+ALREFSDEHGLVLISIEDLVAHLEETTPTLTAVPAEATLPTRHGLFRVSVHVDAETGAEH
+LLLVAGETDPERPLTVRVHSECLTGDVLGSLRCDCGPQLEDALARAAAEGGAVLYLRGHE
+GRGIGLANKIRAYRLQEEGMDTVEANLALGLPAEARDWAGAAAVLTAAGHRRIRLVTNNP
+AKVAGLRAAGIDVVERVPAPTPVTEHNVVYLRTKRDRMAHALADRVLEPPTATGGPATPA
+DDPTTDPTHPTHQEDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000109.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000109.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb5e2e3203a549345ad16a639f0b7090b5f2b2e3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000109.fa
@@ -0,0 +1,68 @@
+>0_853
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>1_584
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLG
+RNGVVPALGHEMRGERAAALAALGVDEAGRPVRASRPGAGNVRGLVHRADAALGMGRPDI
+AETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGAAALAARHPRNRHLARRMAGERDAFRG
+VAPTVPTEPGYRPVPGRVLHVLTNSLPHTGSGYAQRSHAILTSLRDEGFDAAAVTRPGYP
+VQIGVPWAAQRDVVDGIRYARLLPARLAQGQAARIQQHAELLAAHVRRHRPALLHTTTHF
+VNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQEREAEAARRADGV
+VTLGAGMRDRLVAAGVAEDAVVLCPNAVGPAFVAERVDRDEARARLGWDLPTDAFVVGTV
+SSLVDYEGLDILLRAAARLAPHRPGLRVHIAGDGVARPGLQALAAELGIAELCAFPGRVD
+REDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALAELVEDERTG
+LLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLYDRLGVHP
+R
+>2_2007
+MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKRATRIGLKHGVLAPRDALA
+EFLRLRDEAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPARTAYFEQLRRLA
+LRDGQISTALDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPGPVEPVSGCGTNVVL
+HLLKESRPYLSNGFTSRTQWNLLAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEH
+RRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSGRRGYETALVGLALREKTG
+LPLVYEVRSFFEGNWTPDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVARG
+VPAEKVDIVPNGVQLDRFTPAPRDPAIAARHGITLPTFGYVSNMDHPREGHELLIRAALL
+LQERGVEAQCVLVGGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPR
+INERAARYVTPLKPFEAMALRRPVIVSDLPALREIVAAPRRGLTFPVGDVMVLAETIARL
+LEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAGKG
+>2_2009
+MTSILLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAVGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVN
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWDVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAVAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALYRRLGVMAPSA
+>3_1902
+MSPRAPRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRARVGGVLADVPARV
+AVPRGIGLAMLGREEQLQAALVDADDAPGPRERARRAEVLLAAGRDEDAERLLADVPADA
+PGAAEARARLRWHRGDMTGAVLVLSPHGRQGRLRARLAAERDSLLGRPVCLSAEDRALAA
+DYEPRPGHVLFVLTNSLPHTGSGYVQRSHSLLTAVRDAGWSVAAVTRLGWPVQTGVLAAE
+DVDRVDGVAYHRLLPAALAPGFGARLDQHAAALLRLVLRERPAVLHTTTHWVNAAVTAAV
+AEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTREAEAAARADGVVTLAETMRA
+RLAEDGVDPEDVVLSPNAVGGAFLDAPGERAAARRALGLAPDAEYIGTVSSVVPYEGLDD
+LVRVVALLADRRPRLRLLVAGDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQAL
+DVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQELVAEGETGATVPASDPEAW
+AEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELYARLGAVVDVADRGAVRGG
+>4_809
+MTSILLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVGLGRLAESLPARP
+GVVLGAMGLAAAGRHVDLLEHVEAVLPSAGAPDRVRLADVLTAAQEPDRAQAVLDAVPVD
+TPGLAAARARVAWHRGDVEAAISLLGGTGRDGVVRARFASEVRALRGGALPLPRADRDRA
+VGYRPRPGSALFVLTNSLPHTGSGYAQRSHSLACALRDEGWHVEAVTRLGWPVQTGVLTA
+ARRDMVDGIVYHRLLPSSLARGFDGRLAQHARMLLDLVLERRPAVLHTTTHWVNAVVTRA
+VAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAREDDAVRSADGVVTLGEQMA
+RRIAAAGMDRDAVVLSPNGVGGAFLEEPAPREDARRRLGLSMDDEIVGTVSSVVPYEGLD
+DLVRAVAALVDERPRLRLAVVGDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQA
+LDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALSEIVEDGVTGRVLPAEEPEA
+WAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALYRRLGVTAPSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba2bd2a445576946bed8116bb65bcad7f937f81e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000112.fa
@@ -0,0 +1,35 @@
+>0_971
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>1_694
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGYFQAVDHENVTAAFF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVEVDGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAMQLAPGV
+AGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGTDTFTVD
+FHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
+>2_1840
+MTHLGDRPLVWDSAMQLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHS
+ELRAWYIPEEGFVGTDTAAALAAFRGDEAAPAPEDEEE
+>2_1841
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAAWDDAHGPQAGSFQAVDHENVTTAFF
+QTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGAAGEGL
+VRYDVVADGQMLNMGITLQADADLADDQGTAVHSVEARR
+>3_1727
+MFVTRPSCAPRLAAAVLASGLAAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESVDEA
+TFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGEAGT
+GTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADVVMA
+PGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGTDTF
+SLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQMGAL
+PPAPEATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRRPGMAG
+>4_914
+MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAAWDDAHGPQAGYFQAVDHENVTTALF
+QTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGAAGAGL
+VRYDVVADGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAMQLAPGV
+AGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGTDTFTVD
+FHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAFRADEAA
+PAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRRLGLTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad42169b6a556d2065d0b3a5f60342e42d5e7623
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000116.fa
@@ -0,0 +1,29 @@
+>0_1001
+MLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
+>1_723
+MLKPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTK
+TTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAP
+VTADIWRTITRNVADDCSVDSSAWGCTGPIESTPAG
+>2_316
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>2_526
+MPHQLDNADYGSCLNQDESFCPDGEWVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR
+SFTLEEVRTLLLLDPTIESDNAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSF
+HWNYGDGTAPRVTHVGGHAQAEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVL
+IPGTITLDAAPVTADIWRTVTRNVAEDCAADPSAWGCTGPIEAPDAP
+>3_1698
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>4_942
+MSIDEVRTLLVLEPEIRSDNGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFH
+WDYGDGSPTKTTSVAGQSQPEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLI
+PGTISLDSAPVTANIWRTITRNVADDCSVDSSAWGCTGPIESAPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e89644be2b2b9d60bb2a4abd52b7d57ef882d16e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000120.fa
@@ -0,0 +1,31 @@
+>0_1072
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>1_800
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
+>2_153
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALLPRQAVFYANHTSHL
+DFVTLWAVLPPALQRRVRPVAAADYWGSGLRRRVAEGLFHAYLVERGKTRRRGPGAASGS
+GVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRGLHALAAAFPQVPVVPVS
+LVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPASGTAATDAPEPGRGEDE
+AARTAWLERARAVLVQDLSASLRG
+>2_1744
+MATSEPVRRSAAALLRLTCRPEVTGMDQVPAEGPFIMASNHLSFFDSVILQALAPRPVHF
+FAKEEYFTGAGVRGRAQRWFFESVGSVPVRRGEQAASVAALESLVGLLDSGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERLDAYNAAPGARG
+>3_1636
+MATSEQLRRAVAGAIRLSCRPHVRGLEHVPPEGPFIVASNHLSFVDSVILQALCPRPVGF
+FAKAEYFEAPGLRGRAQRRFFEAVGSIPVRRGEQAASVAALEDLVALLDGGHGVGIYPEG
+TRSRDGRLYRGRTGAAWLALTTGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDF
+GHPGRRHSLPQRREATATIMAAIAALSGQERVDEYNAAPAARG
+>4_1022
+MATSEPVRRSAAALLRLTCRPEVVGMEHVPARGPFVMASNHLSFVDSVILQALAPRPVHF
+FAKEEYFTGTGLRGRVRRRFFESVGSVPVRRGEQAASVAALESLVGLLESGQGVGIYPEG
+TRSRDGRLYRGRTGAAWLALATGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDF
+GHPGRRHTLPQRRDATAAIMDAIGALSGQERVDAYNAAPGARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000121.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000121.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ef6dd362ac97aa14805f33bfd6c85c41704a47c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000121.fa
@@ -0,0 +1,36 @@
+>0_1101
+MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>1_829
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>2_753
+MAEFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLEAAERVAEEIKADGGEAAAY
+RLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWDRVIDIDLNGVL
+YGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTKQAGVDYGPRGV
+RVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLLSDKASFLTGAY
+YLVDGGYTAP
+>2_1714
+MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEAHGPVEVLVANAGITNDQLLLRMSEEDFTSVVDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLASDEAAYISGAVIPV
+DGGLGMGH
+>3_1607
+MAEQTEPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGALTVAADVTDA
+ASVDAAFRAVEEAHGPVEVLVANAGVTNDQLLLRMSEDDFTSVVDTNLTGAFRVVQRATK
+GMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLIGMARSITRELGARGITANVVAPGY
+IDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLASPGAGYVSGAVIPVDGGLGM
+GH
+>4_1051
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGEGPEGVLAVR
+ADVTDAASVDAAFREVEEVHGPVEVLVANAGITHDQLLLRMSEDDFTSVIDTNLTGAFRV
+VQRATKGMMRLKRGRIVLVSSVVGLLGSPGQVNYAASKSGLVGMARSITRELGARGVTAN
+VVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLASDEAAYISGAVIPV
+DGGLGMGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3c1ce77a27e39a594318e340f0db61e251df6c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000124.fa
@@ -0,0 +1,42 @@
+>0_1237
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDDVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAGFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>1_965
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
+>2_1570
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTVTLEQDGTDAVVHAALDAGITFFDVADIYGAQ
+PGLSEERLGRALGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAVEASLRRLGTD
+WIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEYVARELGTERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAAPEGSRLSHVRQ
+HMVADADLEQLAAFGEFARARGITEVQAAIGWLAAQGPVSSVIAGATRTGQVAENARAAD
+WEATEADLAELDALFPGPEKVALF
+>3_1466
+MRTVRLGRSGLTVSVVGLGCNNLGRPGTATMEQEGTDAVVHAALDAGITLFDVADVYGAR
+PGLSEERLGRALGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEHAAREIGVERF
+VSAQNHYNLLDRRAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTAPAGSRLSHVRQ
+HMVEEADRGQLAAFGAFARERGITEVQAAIGWLAAQRPVASVIAGATRPGQIAENARAAD
+WEATPADLAELDALFPAPPPVALF
+>3_2030
+MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQLAAAKEGGVNFFDNAEVYAGG
+ESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDVVNMKNTLNRKYLMQGIDGSLERLGLD
+FVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWNIAERHHLHKP
+VMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDGVPEGSRGALKGY
+DFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVILGASSVAQVQEN
+LKALDVIELVTPEVRERLEAVFA
+>4_1194
+MRHTRLGRSGLTVSVVGLGCNNLGRPGTATLEQAGTDAVVHAALDAGITFFDVADVYGAE
+PGLSEERLGRALGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAVEDSLRRLGTD
+WIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEYVARELGVERF
+VSAQNHYNLLDRRAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDAPEGSRLSHVRQ
+HMVADADLEQLAAFGRFARERGITEVQAAIGWLAAQGPVSSVIAGATRAAQVVENAAAAD
+WLATAEDLAELDALFPGPEKVALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5e021899c36b4cd42aac974e912b751fca4b142
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000127.fa
@@ -0,0 +1,81 @@
+>0_1321
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHGAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIEAVAAGLDPDAPDRRPAAQPAE
+GPGADPAPAGPAADGLEDAAPDGNLETRALDAGDHHATRVLPALAESDLDEDMTDVIDTR
+VATHGGDPRPAARPAEPIGPLGLDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAA
+IGAAVTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTAR
+HDELRTEGTVVASSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARF
+TVEVAERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAH
+TTLADEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG
+>0_1893
+MSLPDARWHVVSPSPFEHEQQGLDILREVLPDESPFQVWTNFEFPDEDGQWHEVDALVLA
+RTKFILVELKYYSGVLRGTGLRWERPGHSPQRSPLALAKKKAERFRSLLERTIESKMPGA
+GRQRIVPYVDYAVFLHHDRFRNEMAPQDSGRLFGLPHNETASNLPSIEHLVLAPATDRFP
+LIGEPREQVLVALMEHLNLADARQPEVGSWLLEERLGEPTPDGQDWLASHRFQERHFARI
+RFQQPREGAPSSDLARVREAARREFDLTRALHHEGLLTASDRVDNELGVGLVFPYDESLA
+PLPLWLESRAATLSQQNRLDLLRQLAETLEYVHSNGIVHRALSPEALWVKTPKQGEPRIL
+VADWQLAGVADRDKVDHAASLTQLSTQFGTTVRSTEELAPTSGALFRAPEDARRVSSLGR
+YKLDVFSVGALAAYLLTGAPAANTVAELHEHLATHQGLDVSVALPSVPEPVRQAILHATD
+PRPTARTATLNDFLAGLTEAQATAPQPASPALDPLEAAPGQALDSRFTLVRRLGKGSTAV
+GLLVDDAQTGSRQVLKVALDDEAATRLDDEAQVLRLLPLHKRLVRLLDGPFDVGGRRALL
+LTSAGTRTLSEVLRERQRLSLDHLERFGSELLEAAQALDAAGLRHRDVKPANIGVVRTPK
+HGEHLVLFDFSLARARSTDVRAGTPPYLDPFLEQGGRTGYDSAAELYAVAVVLYEMASGQ
+KPFYGDPEANPAAVRDDLTVPDGIFDPSLQAPLSALFERALARDAQARFHTVAELAAAWE
+ALFRNDADPVTAQDAETLAARATLETPLSEAGLSARGLSALEAIKVTAGPGGVAVEPHDV
+RTVRDLVLVDPIKLNSLAGSTTETRAEVRARAKQWRAAFKKELMRQATQVPQGTLPTPLD
+AAELLLRHAGAAHAEGVRAQLRLVLGLDGEVPALSTHAVLADARGVTPGLVPQLFGRAQQ
+AWTDVAETRSLLDSLDGALRAAVAERGGVSTPDELTSALEQTLSPATPAEVRDAEPRRIV
+QGLLWLLLDRERAAARGEADVPALVQRRREGRVVAVAEMPVLLDVAETLGAAAEAAVDGA
+GDPESALVPADLVQTRVAAVLDAVDGLPEALRSWRRAAALAAHVSATTCLSAAGEWHHRL
+LAPATAAHHALQGASGTVQLSRERAAERVGARFPALSPLPRDAALDRVLAEAELGLVFDE
+DLGPQGAYRSRQTLAPTTGFATRAETRLVEHQRPLSELGVEGQRLLDSQRNRSYLALGVP
+AQRLARLESALVRRFHAEPLDLTDLFIRLLKDQAAAHPKMTWDHVTAADAEPDGSRPAQG
+LNVLVRNLLPELEQHLSRTIGDPGRAASPVLLTGAAVLARYGHLGVLARWADLAEYRARP
+VWLVVPQVAGNVGPRLDGVSVPKNTPGQYVPLTPEWIDGLAALMAAQPLTEESRT
+>1_1050
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRHPAEGPGA
+EPAVAAPAADGPEDAAPDGNLQTRALDAGDHHATRVLPALAESDLDADMTDVIDTRAATR
+GADRRPAAHPAEPIGPLGLDPAPADRHPGRESPRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHNEL
+RTEGTVVASSPAAGEPAGRGTPVELTVSAGPAPVPVPDLTGVVIRRAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDVTGQDPETARTTLA
+DDGWDARVHRLPLPLAGRGESRVLHQSPAAGTALPEGTAVHVWVG
+>2_1494
+MSSTRRDPLVGGIVDGRYEVLARLARGGMSTVYLALDTRLDREVALKVMHPHLAEDPVLV
+GRFEQEAKTAARLSHPHVVAVLDQGHTEDASGEVLAYLVMEHVPGHTLRTVIREQAPLTP
+REALRHLRPLVDGLAAAHRAGLVHRDAKPENVLVRTDGRITVADFGLSRAATAHTSAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAAGIILFELLTGRQPFTAGTALQVAYRHVHERVPV
+PSSLQPGLPEALDDLVLWCTEPDPADRPADAGEVLDRLDAVAAELGPAELDRPPVLVPDA
+VEGRPGPEHDETTTLDALDRLDPKDPLDDADGDETTSLDAGDHHATRVLPSLPADALPTE
+ALAADDVVRRSPARRRRRP
+>3_1389
+MSSTRRDPLIGDLVDGRYEVLDRVARGGMSTVYRALDHRLDREVALKVMHPHLAEDPALV
+GRFEREAKTAARISHPHVVAVLDQGHTADEAGDVLAYLVMEHVPGRTLRAVIREEAPVAP
+RRAVALLEPVVEGLAAAHRAGLVHRDVKPENVLVRTDGRITVADFGLSRAATGHTSAGQT
+VFGTPAYLAPELISGTGGDARADVYGVGIMLFELLTGTQPFTAATPLQVAYRHVHERVPV
+PSSVRPGLPEALDDIVLWCTEPRPADRPEDAAALLPELRRVAALLPQTAPADEAPAADDA
+PTVALAVSPTVPTVPVPDAADATARLEPRRPDPRRAEPVPTPATATAASPSSDLSSAVPE
+APRPAPVAPRPASARQRRRTARTPEVVLGAGMGRTVAVGAAVTLLLAGMALLLGWILGSG
+GISGPAGVVVPPLWGLEQQEAAARLAEAGLTSAVVSRHDERFSDGVVLDVSPAAGSTVDA
+GGPVRLTVSDGPAPVPAPDLAGLTVTDAHAVAEDGRVGVVVADRVADRAVPAGAVVSQSP
+EAGAEMTPGDEVAVVLSTGPATHPLPDLGGLTVGEARTRLADLGFVPDVRTLPLPGPSGD
+AARVLRQGTPAGTVLPEGASVQLWTL
+>4_1275
+MSSARRDPLVGGIVDGRYRVVERLARGGMSTVYLAVDERLDRQVALKVMHPHLAEDPVLV
+GRFEQEAKTTARLSHPHVVAVLDQGHTEAEDGDVLAYLVMEHVPGRTLRTVIRDRAPLSP
+REALRFLRPLVDGLAAAHRAGLVHRDVKPENVLVRDDGRVTVADFGLSRAATAHTMAGQA
+VVGTPAYLAPEHIAGAPADARSDVYAVGIILFELLTGRQPYTAATALQVAYRHVHERVPV
+PSTLHPGLPEDLDDLVLWCTEPDPADRPAGAGELLHRIDAVAAGLDPDEPDRRPAEGPGT
+DPAAAAPAADGLEGAAPDGDLPTRALDAGDHHATRVLPALAESALDDDVTDVIDTRAATH
+GGDPRPAARPAEPVGPLAVDPAPADRHPGRGSRRRLRRAARRPALDLGQGTGRAAAIGAA
+VTLLLTGVALLLGWTLGSGGLGVGGVAVVPDLDGLAREAAEERLTAAGFTAAVTARHDEL
+RTEGTVVDSSPAAGEPAGRGAPVELTVSAGPAPVPVPDLTGVVIRQAHGVARDARFTVEV
+AERRTDPAVPAGAVIEQHPAPGEQATPGTAVRVVLSEGRAVRPVPDMTGQDPETAHTTLA
+DEGWDARVHRLPLPLSARGESRVLHQSPAAGTALPEGTAVHVWVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000129.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000129.fa
new file mode 100644
index 0000000000000000000000000000000000000000..421bbbd157f7c611f9fbfe1ced99290999f7a8cb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000129.fa
@@ -0,0 +1,51 @@
+>0_1398
+MPPGPGALLGGRRVRLLPAILALALGSFAIGTTEFAMMGLLPQAVADLGVGLEAGGVLIS
+MYALGVVIGAPLLAASFARVDRRVTSIVLMLLFVVGHVAAFLAPDMGSMMAARFVSGLPH
+GAYFSAAALAAADLAGPARRGQAVAWVMAGLSVANVLGVPGATALGQAVGWRWMFVIVAV
+CAALCVGATAWLVPSVPAPAGASVGRELRGLASGRLWATVAVGVIGFAGMFALYTYIAPL
+LTEVAGLEERWVPAVLALYGVGMVIGTLVSGALTDRDPVGTLRLSFGLSAVSLAAVALTA
+PWAPVMIVFLFCVAVSGSGIAPSLQVLLVDSAPTAPQLAGSLNHSALNMANAMGAWVGAA
+AIGAGASLRTPPLVGAGIALAGLVLAFLLVRRDVAASPGVRADDGGSPR
+>1_1139
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDAATMMAARFICGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPAATALGQSAGWRWMFVIVATCAALCVAATAWLVPPVPAPEGASVRRELR
+GLASGRLWATVAVGVLGFAGMFALYTYIAPLLTTVSGLDERWVPAVLALYGVGMVVGTLV
+GGALTDRDPVRTLRLSFALSAVFLLGVGLTAQWAPVMVVFLFLVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLIGAAIALGGLVLALLL
+VRRTPAVGAVPHDGPSAATV
+>2_1423
+MTTPASGDPAASPSVSARPDPADAAGSPAAGAVGPQSLLGGRRVRLLPAILALALGSFAI
+GTTEFAIMGLLPQAVADLGIGLEAGGVLISMYALGVVVGAPLLAAAFARVDRRTTGIVLM
+LLFTVGHTGAFLAPDTATMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAIAWVMAG
+LSVANVVGVPAATAIGQAAGWRWMFVIVAACALACVAATAWLVPPVPAPEGASVRRELRG
+LASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLDERWVPAVLALYGIGMVVGTLVS
+GALTDRDPVGTLRLSFGLSAVSLLAVGLTAQWAPVMVLLLFCVAVSGSGIAPSLQVLLVD
+SAPGAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAAIALAGLVLAFVLV
+RRASPTSAATAADAR
+>3_1327
+MRLLPAILALALGSFAIGTTEFTMMGLLPEAVTDLGVGLETGGVLISMYALGVVVGAPVL
+AAALARMDRKLSSILLMGLFVVGHLASLLAPSLGALMAARFVSGLPHGAFFSAAALAAAD
+LAGPARRGQAIGWVMAGLSVANVVGVPAATALGQAAGWRWMFAVVAACALGCIAATALLV
+PRVPAPAGASVAAEIRGLASGRLWATVAIGVVGFAGMFCLYTYIAPLLTEVSGLHPRWVP
+AVLALYGVGMVIGTLVSGALTDRDPIRTLRWSFGVSALGLLAVSLTAPWWPALLVSLLVV
+ALSGSGIAPALQVLLVDAAPTAPQLSGSLNHSALNMANAMGAWVGAAAVGAGASLRMPSL
+IGAGIALVGLLMSVALLRRPASAPPGA
+>3_1738
+MSAVSNAPRPRLPWGALLALSASGFLAIFTETIPAGLLPELSRGLGVTESAAGQLVTLYA
+MGSVVAAIPLVAATQTVNRKKVLLAAVATLGAFNLVTAAAPWLPVILAARFVAGAAAALV
+WGVLAGFARSLVAPQLQGRALAVTGLGQPIALAGGVPLGSFAASVMDWRWVFVAISVAAG
+GLAVWIAAAVQNVEGSPRRQREPLRRVVMLPGVRLIFAVTGCWILAHNMLYTYAAPLLNR
+TDLRLDVGLGLFGVASMIGISLVGMVIDRALRLVSAICVTAMCLATTVWLLPQVGIALAV
+ASVVAWGLSFGGAPVLLQTALADRAGEHTDAAQSVFVTVFNLAVAGGGFMGGMLLASSGT
+AGIATTSAVLCLVAVGMIVLARAAFPAGHRHKDETDESVVAPSECSA
+>4_1347
+MPTPTPAADGAHDRSPRAPRPTRPDPSIPPTAPTGPGALLGGRRVRLLPAILALALGSFA
+IGTTEFAMMGLLPQAVADLGIGLEAGGVLISMYALGVVIGAPLLAASFARVDRRVTSIVL
+MLLFVVGHVAAFLAPDMGSMMAARFVSGLPHGAYFSAAALAAADLAGPARRGQAVAWVMA
+GLSVANVLGVPGATALGQAVGWRWMFVIVAVCAALCVGATAWLVPSVPAPAGASVGRELR
+GLASGRLWATVAVGVIGFAGMFALYTYIAPLLTEVAGLEERWVPAVLALYGVGMVIGTLV
+SGALTDRDPVGTLRLSFGLSAVSLAAVALTASWAPVMIVFLFCVAVSGSGIAPSLQVLLV
+DSAPTAPQLAGSLNHSALNMANAMGAWVGAAAIGAGASLRTPPLVGAGIALAGLVLAFLL
+VRRDVAARPGVRADDDGSPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..577368a17be30507281494b2d3595a9d814437ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000143.fa
@@ -0,0 +1,37 @@
+>0_1633
+MPDVTPPPPSRSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMGSANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG
+>1_1347
+MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG
+>2_1166
+MPEQSPTPSSRPWARRTVLGGTGLAIAAGVAGCSRPEAGEEAEETEAAPKRLPAPDILTT
+AQWGALQPNYHLQTLDERPSYLVIHHTTTPNVTDGSREAAESIAKSIQNAHMSTLNDWGD
+TGQHFTVSRGGFALEGRHGSRYTLEQGQTFMLGVHALGFNAYALGIECEGLYTLNPPPQS
+LYAGLVPLAAYICQQYELPPSRIIGHRDVTATSCCGDAFYGKLPVLREDVRLSLATGEYH
+VSEGFGADNLFDDAHVTPDYLQEQGY
+>3_30
+MKHALPRHVQHAPVPPAAASPGRRAVLVGGLAAAGAAGAAAAGAVPAAAFAGPVVHSTAQ
+WGARSPRSAAEVVRARPTRLVIHHMASPNTAETSLAHAYGLARACQQDHMGRGFDDSGQH
+FTVSRGGHCLEGRAGSLAALRAGDRHVKGAHVSGQNTGKIGIECEGSYVTGLPTPAQYRA
+LVQLAAHICRQYGIRPADIVGHGDLMATQCPGGAFHARLGVLRADVARTLATGRLSVSDP
+SGRAASIPADPRRAATTTPSAAAPASRRVLGPGSRGADVKRVQALLTTAGHRVPRTGLYA
+ARTTAAVRAFQRRSGLAQDGFTGPLTWAALEAAGRR
+>3_1097
+MPDHQILSSSWPRRAVLGGAGLAIAGTVAGCGTGGDAAQSTSADGSAASTGPRLPEPEIL
+STIDWGARIPENWQQTLYEKPSYLVIHHTTTPNVTDGSRDAAIALAQRVQNQHINQQWGD
+SGQQFTMSRGGFAMEGRHGSLYALQGGETFILGVHALGFNAYAVGIECEGFYMVSPPPQS
+LYAGLVKLSAFICQQYELPPSRIIGHRDVVKTSCCGDAFYAKLPILREDVKRSLETGEYQ
+ITEGFGADNLLDDAKINVENYEDFQKRS
+>4_1562
+MPDVTPPPLPHSWTRRSVLGGTGLAIAAGVAGCGRDEQAEQSSEGDEQATRLPAPDIITT
+AQWGAMQPNYYLQTLNERPSYLVIHHTTTPNVTDGSREAAESIAQVVQNAHMSPANDWGD
+TGQHFTVSRGGFAMEGRHGSRHALEGGQTFMLGVHALGFNAYALGIECEGLYMLNPPPQS
+LYAGLVPLVAYICQQYELPPSRIIGHRDVTATSCCGDAFYAKLPILREDVRLSLASGEYH
+VSEGFGADNLFDDAHVTPEYVEEERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000144.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000144.fa
new file mode 100644
index 0000000000000000000000000000000000000000..47682249a01d74045cae31889259fa9e1edeae65
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000144.fa
@@ -0,0 +1,44 @@
+>0_1721
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVAVPMRVRFRGTDLRHALLLRGPAGWGEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRETIPVNATVPAVDADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTELA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRVRAAHAVLAAQG
+>1_1438
+MSTAPALPPLPGAPGGPALPSVEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHECAAWLAAAIEAGWQGWPGPVRQTVPVNATVPAVAADDVEAVLARYGDGIT
+AVKVKVAEHGPEGGLVPGGREADLARVRRVRALLPHAQVRVDANAGWTPAEAVDVLTALA
+DVGLEYAEQPVPGITALAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERAPAPDPELLDRIRADGTRQAWWADRLRAAHAVLAAQG
+>2_1077
+MRVRFRGTDARQALLLRGPAGWAEFSPFPEYGPAESSAWLAAAIEAGWQGWPAPVRDVVP
+VNATVPAVEAEAVESVLARYGEGITAVKVKVAEHRPGGGLVPGSHSADLARVRRVRELLP
+DAHVRIDANAGWTPAEAIAMLTDLADVGLEYAEQPVPGIKKLARVRRELRARGVSTPIAA
+DEAVRKAEDPLAVAAAGAADLIVVKVQPLGGVRRAAAVVAAAGLPAVVSSALDTSVGIAG
+GAALATHLPALPHACGLGTAALFDDDVVTPAWTPRQGVLEAPGERAPEPDPALLARVRAD
+ERTHAWWRDRVAAAHAVLAAGGR
+>3_1002
+MTVPAAHDDADPRPGSALPPLPGAPGGPALPDVDELLEHAVAVTLPMTVRFRGTTERRAL
+LLRGPAGWAEFSPFPEYGPAEASRWLAAAVEAGWQGWPAPVRSEVPVNATVPAVDAADVE
+SVLARYGDGITAVKVKVAEHRPGGGLVDPTHAADVARVRRVRELLPEAAVRIDANAGWDE
+DRAFAVLGALQDVGLEYAEQPVPGIAGLAALRSRLRAAGIATPIAADEAVRKETDPLAVA
+QAGAADLIVVKVQPLGGVRRAAAIVAAAGLDAVVSSALDTSVGIAGGAALAAHLPSLPFA
+CGLGTASLFAHDVVSPAWRPADGSLPAPGERAPEPDPALLAAARADAAEHAWWAERLRAA
+HAVLAARGR
+>3_1768
+MSPAPGQAPVSVAAVRRHRHRAPLLHPFVTAARRTEAVEYVVVEVELSDGTVGQGSAAET
+VAVTGEDAASIETAVDGVFGPALTGATGGLDGLLARLPAPARGATSARSAVDVAVHDAVA
+RAAGVPLTALLAPAGTAVKQTLENDMTVSLEDPATMAARAAEAVAAGTRILKIKLGRDVA
+EDRRRLHAVLEAAPQARLRLDANQGWSVEDAIAIISGMEDEGLPVDLVEQPVAAADVAGL
+ARVRAAVTTPIMADEALWSSEDARRLIEAGAADLFNVKLAKTGGLADAVAIADLAAEHGI
+GCMVGSMMEPRISIAAAVQLSLAHPAVTMVDLDAPLWFASDAPAGGYTQEGADLRLLPGE
+GLALERLDPGTDPV
+>4_1650
+MSTAPALPPLPGAPGGPALPSIEELLADAVAVALPMRVRFRGTDLRHALLLRGPAGWAEF
+SPFPEYGPHESAAWLAAAIEAGWQGWPAPVRQAVPVNATVPAVDAADVEAVLARYGDGIT
+AVKVKVAEHGPEGELVPGSREADLARVRRVRALLPHAQVRVDANAGWTPTEAVDVLTALA
+DVGLEYAEQPVPGITDLAEVRAELRARGVPTPIAADEAVRKAEDPLAVAAAGAADLIVVK
+VQPLGGVRRAAAIVAAAGLPAVVSSALDTSVGIAGGAALAACLPSLPHACGLGTAALFEH
+DVVAPAWRPRAGALPAPGERASAPDPELLDRVRADGARQAWWADRVRAAHAVLAAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5d785f41c2a0d84a6315ca9121b84562e1408733
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000145.fa
@@ -0,0 +1,30 @@
+>0_1731
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>0_1990
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEGAAEQASPRVRLVVDPPR
+>1_1707
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQEVSAARDAAFADLLADHPVVGAYVRRSLLEAGGG
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLMVDPSADRIWRRIAE
+TQEAAAEQRSPRVRLVVDPPR
+>2_1065
+MDAPASDLTGKARIRHAALRLFAHHGVEGTSMRAIAEEASVTVGLITHHYGSKAGLHREV
+DAAVADDFAAAIASVPAEGTARDVTLRRDAAVAEMLRARPDVLEYVRRHVLLGEPAADSQ
+LVEKLTALAREQVRQLRAAGLISGRRDEVPQVVSMIMRMLGELFFEPLVDRIVDAVDRDA
+ARPAVVVRVQAAEDETARGGRA
+>3_711
+MNTARPLTREDLSSAARLRLSALELYAERGEHAASIRDVGRHAGVAPGLVRHHFGSKDGL
+TRAVDDDIIDLVRATLEAVPLEGTPLEISAARDAAFQELLQERPLIGGYLAQALTASRAS
+GESVLDRLVDLSAEQTRQLIDRGLDPRRGLRTSVFTTVVRQVAVFLVAPVAERAWNRLGH
+TLEGASDVAPMPPVRVVVGPAPEEDRR
+>4_1925
+MNTPLPFDQDDLSSPARLRLAALELYAERGVEMASVREIAQRAGVAPGLVRHHFGSKAGL
+TRAVDDDVLRLIAATLDEVPLVGTPQVVSAARDAAFADLLADHPVVGAYVRRSLLEAGGE
+TESLLERLVDLTTEQTERLRRSGFAPRRSMPTSVFGTVIRQMGHLLVDPSADRIWRRIAE
+TQEDAAEQASPRVRLVVDPPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000151.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000151.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b873f936a85360113e49fa1ad85e1a2b47fa1783
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000151.fa
@@ -0,0 +1,57 @@
+>0_1861
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRVVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>1_1568
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQQGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLMLIAVAAAGAWAAWRLVGVIEKGILGRYQETSVEHRRERRIRTQTILIRRILNAVI
+VVVAVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVVKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMDALRARLAQLLESTDLWDGREHALQVTDATGGVVRIRAVVSARNSGDLWDLRCLV
+REDLVAFLRHEHPEGIVVQRMVVRHPAHDDAAPASEGSDAGARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPHTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHADGPLDDAVTRRRQDDED
+>2_768
+MDLPQITPLAVAVGLAVAVVGWLLGRLLGAGVAWLFARRGRSPSSARVFGKLVAAGITVL
+SLGAAVTVVFPSVKPVDLLGGIGVISIAAGIAFQTVLGNMFAGMVILARDRFRVGDQIQV
+GEHAGNVVEMGLSSTAVKTFDGRLVLIPNQMLHSQAVTVQTGFSAVRSSLRVDVETGNDL
+ARTREIAVRAMSELPQVLRDPAPQALLASVGVTTVGMDLRFWSGARQMETKEAMDAVIHA
+VLTAFEKNGVATGDDVRVVDAGPELRRILEGPGAPRGQGGPDYPGGLAGPGEPDRAARPG
+SD
+>2_919
+MLLAALSGPASPPVLGSLARLFAGENVPAGVEGNVQDGAAATTAALGVEWGTLLTVLVAF
+AVGATLVYAALQVTRVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQTWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVAIAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTQPFENWTRVGTEVSGVVELDVD
+WRVPMPALRERLTQLLDSTDLWDGRESSMQVTDAIGGTVRIRAVVSARNSGDLWDLRCLV
+REDLVTFLRSEHPEAIVVQRVVERHPAHDDAVPASEGSDAGARGGDPTGEPGPDGSGVAA
+REPRPRTAALPRVEGGEPRPDTVTTPLTRVDDHAGLYTGSITAVQRNRELHGPGEDAFAE
+RRAQQAKQAAEAATADEAGRRSGAGSHADGLLDDAVTRRRQDDED
+>3_855
+MPVPALLPVLAQTASSDAALSDAVLSAADQVVPGSVEQDVQQGASAASAALGVEWATVAA
+VLGAFLAGGLVVLGVFLVARLALFRRDRLKADAARLTVPVSLFAGFLTARVGLEVMAHGQ
+PWFEAAAFVLLLAVAASAAWAAWRVVDVVESGILARYHQPGVNDRRERKIRTQTMLLRRV
+LNAVIVVVALAVVLLAIPQVRSLGAGLLASAGLISVIAGLAVQSTLTNVIAGFQLAFTDS
+IRVGDVVDMQGVFGTVEEITLSNVVVKLWDGRRMVYPSKHFTSEPFENWTRTGAAVAGVV
+EMDVDWRVPMDPLRARLTELLESTDLWDGRENAMQVIDAVGGMVRIRAVVSAKNSGELWD
+LRCLVREDLVGFLRAEYPEGIYTQRLVERRPSDPAPEAHDDPAPDAHDDAAPAAAPAAPA
+PSDRGSSTRAEPTPQTRPMPTVTGSVPLARAGENASLYTGSIRAVERNQEMDGPGEEAYA
+ERRARAAEREDRAARDAGRGGAHAARS
+>4_1782
+MVLPVLPALATPPLLTALDRLLAGETVPSGVEGDIQDGAAATTRAFGVEWGTLLTVLMAF
+AIGAAVVYLALQVARVVLVRRPAFQHGAARLSLPAAVAAGLLASRIWLGVMAEEQAWYRP
+ASFLLLIAVAAAGAWAAWRLVGVIEAGILGRYQETGVEHRRERRIRTQTILIRRILNAVI
+VVVVVAVVLLGVPEVRSLGAGLLASAGVISVIAGLAVQSTLTNVFAGFQLAFTDAIRVGD
+VVDMEGVFGTVEEITLSNVVLKLWDGRRMVYPSSHFTTRPFENWTRVGAEVSGVVELDVD
+WRVPMDALRARLTQLLESTDLWDGREHALQVTDATGGIVRIRAVVSARNSGDLWDLRCLV
+REDLVSFLRHEHPEGIVVQRMVVRHPAHGDASPASEGSDAEARGGDRTGEPGPDGSGVAA
+REPRPRTAPLPRVDGADPRPDTLTTPLTRVGDHSGLYTGSMTAVQRNRELAGPGEEAFAE
+RRAQQAKQAAEAAAADEAGRRSGAGSHTDGLLDDAVTRRRQDDED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000157.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000157.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3474a7d4d892ee6d5223ee43b02f4a0929f3e883
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000157.fa
@@ -0,0 +1,36 @@
+>0_1957
+MTDQQHTPDTVPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAKERI
+EADLAASLERGKIDGDLDEWAQRLTVSVDRADFARCDLVVEAVFEDMQVKIDALTDVEAH
+LREDAWLASNTSSLSIGEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>1_83
+MGQTQKVAVIGAGAMGSQIAMLAAMAGCQTTMVDVDQERLDAARDQVLQTAQRQAERGRL
+EADAVEQAAARLTTEPDLAAAVAEADVVVEAIIEDLEAKRDLFAQLGEHTRPDTILATNS
+SSIVSSRLAQIPHPERVCNMHFFNPALVMRLVEVVGGDHTSQKTIETVKALAERMGKTPV
+VVRQEIFGFIANRIVAAIFDEAISLYEQGIASAEDIDTAVTHGLGHPIGPFALLDLTGID
+VNVGIKRLEAQETGDPSRGPSQTLLDLMAQGRLGRKTGHGFYEYGDR
+>1_1677
+MTDQQHTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPRSAEAAQERV
+ESDLAASLDRGKIDGDLDEWAQRLTVTVDRADFARCDLVVEAVFEDMQVKIEALTDVEAH
+LREDAWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKNAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>2_785
+MTETPDTSRASVPAVVGVLGGGRMGGGIAHAFLTSGSSEVVVVERDPQSAEAAKERIESD
+LAASLERGKLDGDLDVWAERLTVSVDRADFARCDLVVEAVFEDMQVKIDALTDVESHLRE
+DAWLATNTSSLSVDEIATHLRRPERFCGLHYFNPVPASKLVEVVIGAQTGDELKALTTEW
+VRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVGPLA
+LTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYSKG
+>3_744
+MTENQQTTGSVPSIVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAEAAQERIVADL
+AASLERGKIDGDLNVWAQRLTVSVDRTDFARCDLVVEAVFEDMQVKIEALTDVEAHLRED
+AWLASNTSSLSIDEIATHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALSTEWV
+RGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVGPLAL
+TDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
+>4_1895
+MTDQQRTPDTAPSSVPAVVGVLGGGRMGGGIAHAFLVSGSSEVVVVERDPQSAQAAKERI
+EADLAASLERGKIDGDLDEWAQRLTVSVDRADFARCDLVVEAVFEDMQVKIEALTDVEAH
+LREDAWLASNTSSLSIDEIASHLQRPERFCGLHYFNPVPASKLVEVVIGEQTGAELQALS
+TEWVRGLGKTPVVVKDAPGFASSRLGVAIALEAIRMVEEGVASPEDIDAAMVLGYKFPVG
+PLALTDIVGLDVRLGIAEYLESQLGERFAPPQLMRDMVARGELGRKSGKGFFDYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000159.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000159.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0f657c3f4a4b305f018ba68efe680644049ff4c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000159.fa
@@ -0,0 +1,22 @@
+>0_2009
+MSTTTSITAAGLETMNGPEGCCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG
+CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI
+A
+>1_1068
+MDVKVYVPEFAVEFDTCQYVPMSMSGLSARDAALGYCTPLAREPITPAQAEGVSRMLKAL
+ADPVRLRLMSMILSHEGAEACAMCDLTEGFDLSQSTLSHHLKVLHDAGLVDRDKRGVWVY
+YKARTEAMDALRTLFSGDLAAPQLA
+>2_542
+MTACSVPVSTAAAPVLADDCCSLADGPLGAEDAAELAVLLKALADPMRLRLLSHVAARGC
+ADVCACDLTEELGIAQPTVSHHMKRLVDAGLLTREQRGRWAHYTVVPEAFARLRRVLVLG
+>2_725
+MVATTTIPAPEDTDRPEGDDALGSVACCSLSAGPIDAAQAQRAAGMFKALADPMRLRLLS
+HVAAQGCAAVCSCDLTEELGISQPTVSHHMKKLVEAGLLTREQRGRWAHYTVVPAAFAEL
+GRMLELG
+>3_469
+MTTTAPSPSDTCCAPAGPALLPAEHAARLAAVFKALADPTRVRVLAHVAASPEGTVCACH
+LPEPLGISQPTLSHHLKTLTAAGLVTREQRGRWAHYTAVPAALDAARAFLADPAGA
+>4_1938
+MSTTTAITAAGLETMNGPEECCTLSAGPVDSVEAERIASLLKALSDPTRLRLLSHVAAQG
+CNSVCACDLTEPLGISQPTVSHHMKKLVDAGLLTREQKGRWAHYSVVPSAFAELRSFLDI
+A
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bd1afde9b8569912ede76061b571b75d57b1794
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000164.fa
@@ -0,0 +1,90 @@
+>0_2061
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHAADHDGVDHHDH
+MAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHSA
+AFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFETAAV
+ITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVLI
+RPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATRVGSD
+TTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSALRAG
+VAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGTVTEG
+RMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARAIVAG
+AEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGSVLET
+ALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIARLKELGLR
+PLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVRRLQSEGHVVAMVGDGVNDAP
+ALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAFAYNV
+LGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>1_1780
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHGEEHAADH
+DGVDHHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALW
+AAWPFHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHS
+LYFETAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAQSL
+APGDVVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVA
+RATRVGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMLVTGD
+LPSALRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLD
+KTGTVTEGRMALADVLVLDPAFVAETGASRSAFVAETAPDQAADVLLTLAAAVERGSEHP
+IARAIVAGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALGSGAHDAAGPAPVRVAV
+GRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKETSADAIA
+RLKELGLRPLLVTGDNAAVATQVAAAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMV
+GDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNL
+FWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>2_640
+MAASPSPSDRAAEALGRTALQDAEGTRRVDLDVTGMTCASCVGRVERKLGKIEGVEASVN
+LPLERATVTVPASVSDQDLLDAVAKAGYTAAVRPDAQARPARRGRHDDGGTRPGADHAGH
+PDHRDHETPGEDHAGHEGHDDHMAHGPRADVLRPRLIVAAILTVPIVLISMVPALQFPHW
+GWVALALSAPVALWCGWPFHSAAFRAARHGSSTMDSLVSVGVLVAWTYSAVELVLEPGMT
+AHVGGTMAEMMRHSLYFETAAVITTFLLLGRWLEARAKREAGRALRSLLDLGAAQATVLP
+NWDAQTPHPSTSAAATPVAAVSGDFSEVEAASTSDKSPQTHHDGGADALTERVIPAEELE
+PGDVVVIRPGEKVPTDAVVLEGTSAVDASLLTGESVPVEVGPGDEITGATVNTSGRLIAR
+ATRTGADTTLAQMGRLVSDAQTGKARVARLADRISAVFVPIVLVLAVLTFVVWMLVTGGD
+VAPALRAGVAVLVIACPCALGLATPVGLLAGTGRASQLGILIGGPEVLEDTRTVDTIVLD
+KTGTVTEGRMALSDVHAFADDAALTEDRILALAAAVEAGSEHPIARAIVAGARERGLTVP
+RVADFASTAGGGVTGTVALPEAGSVRVAVGRGDLVGEPSPAQQAEFDAAEQAGATAVWVA
+VDGRVAGVLSVKDTVKPSSAAAIARLKELGLRPLLVTGDNAAVAAQVAAAVGIPAEDVVA
+GVRPEDKVDVVTRLQSEGRVVAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMG
+DDLDQVVQALDLSRRTLGIIRMNLFWAFAYNVLGIPVAALGLLNPMIAGGAMAASSVLVV
+LNSLRLTRYAR
+>3_558
+MTHPASSAPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APADVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAHTSEHGEGHGEEHAADHDGVDHHD
+HMAHGPGEDVLKPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWPFHS
+AAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFEAAA
+VITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGDVVL
+IRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDAVTGATLNTSGRLVARATRVGA
+DTTLAQMGRLVADAQTGKARVARLADRISAVFVPVVLGLAVLTFAVWMLVTGDLPSALRA
+GVAVLVIACPCALGLATPVGLLAGTGRASQLGILIRGPEVLEDSRTVDTIVLDKTGTVTE
+GRMALADVLVLDPAFVTDTGASRSASVAETDAPRSAFVAETAPDRATDLLLTLAAAVERG
+SEHPIARAIVTGAEERGLTVPDVADFASTAGGGVSGLVALPHDDGALASGAHGAAGPAPV
+RVAVGRGSVLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSA
+DAIARLKELGLRPLLVTGDNAAVATQVADAVGIPAEDVVAGVRPEDKVDVVRRLQSEGRV
+VAMVGDGVNDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGII
+RMNLFWAFLYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
+>3_700
+MSTSAPPTGGPDIELEIGGMTCASCANRIEKKLNKLDGVAATVNYATEKAKVTVPAGYDP
+SLLVAEVEKTGYTAALPKPKDTTANTSETEAGEEEDSELTSLRHRLIGAIVLTVPVIAMA
+MIPALQFTYWQWASLALAAPVIIWGAWPFHKAAWTNLKHGAATMDTLISMGTSVALLWSL
+YALFLGTAGTPGMTHPFEFTIAPSDGAANIYLEVGAGVTMFILAGRYFEKRSKRQAGAAL
+RALLELGAKEVAVLRDGVEVKIPTSELAVGDEFIVRPGEKIATDGLVTSGSSAVDASMLT
+GESVPVEVREGDSVTGATVNAGGRLVVRATRVGSDTQLAQMAKLVEDAQTGKAEVQRLAD
+RISGIFVPIVIVVAFITLGAWLGGGFPVAAAFTAAVAVLVIACPCALGLATPTALLVGTG
+RGAQMGVLIKGPEVLESTRKVDTVVLDKTGTVTSGKMTLTDVITEPGVDRAELLRFAGAL
+EDSSEHPIAQAIAKGATQEVGQLPTPEDFANVEGKGVQGIVEGTPVVVGRESLLADWSQK
+LSPEVAQAKAQAEGEGKTVVAIGWDGAARGILVVADTVKPTSAEAIRGLKEIGLTPVLLT
+GDNEAVARQIASEVGIDEVIAEVLPKDKVDVVTRLQEEGKIVAMVGDGVNDAPALAQADL
+GLAMGTGTDVAIEASDITLVRGDLRAAVDAIRLSRKTLSTIKTNLFWAFAYNTAAIPVAA
+LGMLNPMLAGAAMAFSSVFVVGNSLRLRGFTSVASK
+>4_2000
+MTHPASSTPAGPQSETTRRVDLDVTGMTCASCVGRVERKLGKLEGVTASVNLPLEQATVT
+APAGVSDEELVAAVEKAGYGATVRRPAPPAGHAGHAGHAHTSEHGEEHGEEHAADHDGVD
+HHDHMAHGPSEDVLTPRLIGAAVLTVPLVLISMVPALQFPHWGWVAFALAAPVALWAAWP
+FHSAAFRAARHGSSTMDTLVSLGVLVSFSFSAVELILAPDMTAHVGGTMAEMAHHSLYFE
+TAAVITTFLLLGRWLEARAKREAGAALRALLDLGAAQATLYDPETHDERTVPAESLAPGD
+VVLIRPGEKVPTDAEVLEGTSAVDASLLTGESVPVEVGPGDALTGATLNTSGRLVARATR
+VGSDTTLAQMGRLVSEAQTGKARVARLADRISAVFVPIVLGIAVLTFAVWMIVTGDLPSA
+LRAGVAVLVIACPCALGLATPVGLLAGTGRAAQLGILIRGPEVLEDSRTVDTIVLDKTGT
+VTEGRMALADVLVLDPAFVAETGASRSAFVDETAPDQAADVLLTLAAAVERGSEHPIARA
+IVAGAEERGLTVPGVADFASTAGGGVSGLVALPHDDGAPGSGAHGAAGPDPVRVAVGRGS
+VLETALDGGIPAEHRAAFEAAEQAGATAVWVAVGGRVAGVLSVRDTVKDTSADAIARLRQ
+MGLRPLLVTGDNAAVAAQVAEAVGIPAEDVVAGVRPEDKVDVVTRLQSEGAVVAMVGDGV
+NDAPALAAADMGIAMGSGTDVAREAAQITVMGDDLHQVVQALDLSRRTLGIIRMNLFWAF
+LYNVLGIPVAALGLLNPMIAGGAMAASSVLVVLNSLRLTRYAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da34dcaed377e7283b4b98893bd9bbebb2c986af
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000172.fa
@@ -0,0 +1,65 @@
+>1_1967
+MKRSPKGRLELTWMGKDSALIPVEDGKYDYSFVDPNDPRALEVKSIEVLEQVGEVEGPTG
+ANENLLIIGDSGDALRSLGTIPEYAEKYGGKVKLVYIDPPFNTEQAFDHYADQLEHSIWL
+TMMRDRIRDFKPLLHPDASIWVHLDDSEVHRMRALMDEEFGAENFIATVVWQKKYSRDNR
+PAIGTVHDYILVYAPAGAQRWKTLRNRIPRISAAQYRNPNNDPNGPWRPVPMDVQGGHAT
+ASQFYDVITPSGKIVRPANGRAWSVTAPVMQAMRDRGEVYFGLDGSGKPNTIRYLKDDEG
+LVPWTWWPHEEVGNNDDAKKEIIALFGEDQVFDTPKPERLLERVIRIATNADDLVLDCFA
+GSGTSAAVAHKLGRRWLTVELSQEVADTFTVPRLRKVQRGTDSIGISVREAEGFADADMD
+GRVKPDDAKALLRAIKEVQKVGLKSLSPEAGAALVQELRERLKPVSARQSVCQDGGFTVA
+KMGPSMYEVDDEHGMVFLSPEATNGAWSKAIAGQLKFTLTPDDPVFCGVRKRQRLAVIDG
+VADETVVRTVVEHLGEKERAVIVAKGVLPEAGDLLQRLSPGSRIKKAPEDMFPKGTVN
+>2_1471
+MTDEIYETPSTTPNFQTELAAQLADLIPEAIADGKVDVEKLKELLDGDAADSNERFGLFW
+PGKKRALRAAQEPTTATLKPDFEDSKDWDTTQNVFIEGDNLEVLKILQKHYHAKIKLIYI
+DPPYNTGKDFVYPDNYKEGLDTYLEWTRQVNEEGKKVTTNAETEGRYHSNWLNMMYPRLK
+LARNLLTDDGVIFISIDDNEIDNLLRLAKEVFGEPNVSTTFIRQKKKKPSFLHANVGSMT
+EYLVCITRNKAFTFPFSVDTTTAGKKYPINNAGNSLGKLTFPAGAVRFSQKFAEYEPQDM
+SEGNIVTRLLDHVVVSEGVNRNAFTLEGEWRYSQVTLDEFITAGDLITISKAPFRPNHVK
+AGGEIKKMHNLLTPSTYGVGTNEDGTAELEDLMEGSYFDNPKPTSLVRVLAQAVTYDDPS
+AIVLDFFAGSGTTADAVFRLNAQDGGNRRVISVQLPEPLDERSEAWAAGYRTISQLAKER
+IRRAGVRVLDREALLLEGRGVPLDTGFRAYKLSDTNFSKWRLSSDVEEDALQQHLLSLRD
+SATDDANADELLTEILLKQGYSLTEAVSPAEVAGLDVRFVRDRDGDVAVLAYLNEHVKPT
+LEQLRALVDEEPTRIIVLEDAFQGDDELKTNLAQLAKSKGIELWTA
+>3_274
+MEMSMDKLRGTSPDLTQDNVARLAELFPTVVTEARDEDGQVTRAVDFDLLRQELSDHVVE
+GPQERYHLDWPGKRAAAFAANAPTTATLRPDREESVDFDTTKNVFIEGDNLEVLKVLQES
+YLGKVKMIYIDPPYNTGNDFVYADDFAESTADYLQRSGEIDDDGARLRANPETNGRFHSD
+WLSMMYPRLKLARNLLTEDGAILASIGEREVSNLRAILNELFGETNFVGELVWEKKKKGA
+FLSSHVTNVKEYILVFCRDRSSFGGLIGEVTHAAETYPVIKSTNSRGIRTIPAGIASNYS
+ERDHEVGAGTRLTSGNMEMILLSDLIIRDGRLAHDVEVESNWIYSQTLIDQFSLSGDLYI
+TRDLYIRRHVREPRTKMLKDLLMMRGESTSGSTFTLEPSLHSDGWGTNEDAFGELHSILG
+EQNLMDFPKPSKLIAKLIRSVTWADSDAIILDFFAGSGTTGQAVTQLNAADGGRRQYLLV
+QLNEAAEESSALRRAGFSSISALSRERLRRSAAAVRETSGTERLDLGFRAFRLDASPFVE
+RNHSADSITPDMLAELENPVLADRSPEDLLTHVLLAWGLDLSATIETVSLAGEEVYDVED
+GALLAALGSTVSDELAHAMAERHPDRALFLDSGFVSDAARINVEQIFREVSPGTDVKVL
+>3_333
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEEHRPEAVELPSREVRKGDK
+VRILPPRGETKKGDQTLWRVQRINRADDIAHLVEVDGEQGAEAALADLVVVAEFRDHMYP
+GLVETGRVERGGDKPFHTVINAENFHALEMLTYTHRHQVHCIYIDPPYNTGAKDWKYNND
+YVASDDDYRHSKWLSFMERRLQVARELLNPEDSVLIVTIDEKEYLRLGMLLEQTFPQARM
+QMVSTVINPKGSHRAGGFARSDEYVFFLFVGASQPAPMPLSSEWKVVQDSRALGLRWADL
+LRTADGSTRAARPNMFYPVFIRLAGDGPVFVSVGEPFYDADLTAVEAPEDAVAIWPIKAD
+GSQGRWQIGADTLRDLITKGYVRIGRWRGSKTTLTYLKAGEQAKVEDGRFPVRGRRADGS
+VLVDASEYSASFVPTSQWRISSHNAEQGGTNLLKSIMGDKRFPFPKSLYAVEDALRFLIK
+KNPDAVVLDFFSGSGTTAHAVMRLNKQDGGRRQCISVTNNEVSAEEQKGLRKQGLRPGDP
+EWEQWGICDYVTKPRVTAAITGRTPTGDPIKGDYKFTDEFPMSDGFEENAAFFTLTYESP
+LMVRQDLAFKRIAPLLWMRAGSRGRVITEVHARGWDVAEAYGVLTKVDRATPFAEAVAEA
+GVGTVYVVTDDERRYQAVCALLPEDVTPVRLYESYLTNFEINTGGRAGA
+>3_677
+MSRLTDLLAQARKTDPQLAADLEAEFRQLTQRSQFGLVFERHQPEAVELPGRPVRRGDTV
+RVLPPRGTLTIGDTRHWVVTDLERTPDGKQAHLTEADVDPEVREPATSTAALEDLVVVAR
+FEDPIYPGLVETGRVENGGPDKPFHTVINAENFHALEMLTYTHRHKVDCIYIDPPYNTGA
+KDWKYNNDYVEADDDYRHSKWLSFMERRLQVARELLNPDDSVLIATIDEKEYLRLGMLLE
+QTFPEARIQMISAIINPKGSSRRDQFSRFDEYIFFVMNGSARPAAVAGDMTMRQARSKEK
+VRWAGLMRQGANGRRSARPNLFYPIFVANETGRVHSVGDSLPLDVPRSEVSPPPGTTAIW
+PLSKAGGESTWGRDPESLRKALSAGYVKIGRFTPGSERCGFTHLQSGQIKAIEEGALVVT
+GRDSDGSLQVEFAEGGQTAMPGTAWHRPAHSASEHGSTLLNAILPDRKFPFPKSLYAVED
+AVRFFVHGKPDAVVLDFFSGSGTTAHAVMRLNRQDGGRRQCISVTNNEVSAEEQKGLRKK
+GLRPGDPEWERWGICDYITKPRITAAITGKTPAGDPIKGNYKFTDEFPMADGFEENAAFF
+TLTYEAPRQVRRNRAFARVAPMLWFKAGSRGRIISSLPERGWDVAQAYGVLEDMDHAPEF
+LAALEADPQVGMAFIVTDSEVAFQSVARQLPEHATAVRLYESYLHNFQINRRA
+>4_106
+MSSLSDLLGQVRATNPDLAANLEREIKNRTRRQRQFGLVFEGHRPEAVELPSRPVRKGDK
+VRILPPRGETKKGDQTLWHVDHIDRTTGTARLTAVDGEQEAQAAISDLVVVAEFRDHMYP
+GLVETGRVENGGGKPFHTVINAENFHALEMLTYTHHRKVDSCRASDLGHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..130e90deeec2d699f3d1f4737f2ac527a33537d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000173.fa
@@ -0,0 +1,47 @@
+>2_83
+MDLTYKLWEGSWDEGAVLQDKGGSRHADPEKVHKIHHVSERYRVEGPHLPAPSPQRTPVL
+FQAGSSGPGRAFAARNAEAVFLIAPSVEAARQQIEDPRRQAVEFGRRPEDIKFFQGLSFV
+IGDTEEEAQAKLEEYERYVSVDGYLAHAALVDPDGRVYPPDTPLRELETNTQKGFAESLQ
+KAITDREPVVADVAWRSHRDSRVVGTPEQIADELQRWQDAGVDGVNVINWVIPGSFEEFI
+EKVLPVLRERSLAQSDYGEGTLRHRLFGEGDRLPDRHPAAKYRGAFTGTPRSQRAPRTEP
+QGADPAPAA
+>2_84
+MTKTARRRPLHLNAFAMNTTSHIHHGQWRRPDARQHEFADLRTWTELARTLEDAAFDAMF
+FADVVGHYGDADADYAVYVEEGLQIPSNDPTVLLGALAAVTERIGLATTSNVFQAHPFQF
+ARQLSTLDHLSRGRIAWNIVTGT
+>2_185
+MMTPVHQSPGLWRHPESRIAEFDRLAYWTGLARTVEDGGFSALFLADVLGLYDVYGGGIE
+ATVRGGVQWPVLDPAVAVPAMAAATERIGFGVTASVTYERPYLLARTLATLDHFTGGRVA
+WNIVTSYQDSAARNLGLDRQIPHDARYDLADEALDALYRLWEGSVEPGAVAFDRAAGVVA
+DPDRVHPAAVAGAHVRVPDAALTHPGPQGTPYLFQAGASARGRRFALDHAEAVFAIGPTP
+AHVRRFVDQTRAGLTEAGRSADAIRVLAMVTVVVAETDEAAAQRLAGYAEHVDVAGALAL
+WGGWTGVDVAGLDPDAPLEHVVTDANRSALAAFTEDPSGRTWTLRDVAEFVAIGGRGPVI
+VGSPETVADELQRWQAETGVDGFNVSAAVRPADLERFAALVSPELRRRGVLREPEPGRTL
+RENLSGAGPALPADHRGHAFRTAG
+>3_123
+MTGTHPSTPRPRTADRQLILGAHFPGVNNTTVWSDPESGSQIAPESFIRFAEIAERGRLD
+FIFLAEGLRLREQRGLLHDLDVVGRPATLPILAALAAATEHIGLIGTLSTTYNEPYELAR
+QLAGLDALSGGRAGWNVVTSPDAFTGENFRRGGYLPRERRYQHAGEFLATAQQIWDAASG
+RPPHVDVDVEDFSVHGTVDAPAPVHGRPVILQAGDSDEGRDLAAREADAVFTRHGDWEAG
+QEFTADMRRRAAAAGRPDGAVRVLPGVTVVVGDTDEEAAAEAEQIRRAQVSGATAVLTLE
+RIWNRDLSGWDPDGPLPDVEPVLEDTGLSQGRVRHVADPHAEVARLREISQRQGLTLRET
+VIATGQRQDFVGSPETVAQELIRHVEHDVCDGFILIPHLTPGGLEPFVDRVVPLLQERGA
+LRTDYPEDGGGLRGLLGAAVHPTAGRAS
+>3_136
+MTATPAPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVF
+LADILGLYDVHGGGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLL
+ARTLTSLDHFTGGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGS
+VERDAVVADRESGVFADPAKVHPIDVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRR
+FALEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQAR
+LASYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTV
+REVAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPE
+LRRRGVLREPEAGRTLRENVAGAGPLLPEDHRGAGFRR
+>4_193
+MTATPAPFILSAFDMVTPVHQSPGLWRHPESRAHEFDRLSFWTDLARTVEEGGFTAVFLA
+DILGLYDVHGSGVDATVRGGVQWPLLDPFTVVSAMAAVTERVGFGVTASVTYEQPYLLAR
+TLTSLDHFTEGRIAWNVVTGYQDSAARNLGLDRQPGHDERYDRADAYLDAMYRQFEGSVE
+RDAVVADRESGVFADPAKVHPIGVEGPHVRLPGVALAHPGPQGTPFLFQAGASSRGRRFA
+LEHAEAVFYIGPTTAHVRRFVEQTREGLREAGRPEDAIRVLAMVTVVVADTDEEAQARLA
+EYHEHVDVESALALFGGWTGVDLSGLDPDAELEHVESEASRTALAAFTTQSPDRRWTVRE
+VAEFVSVGGRGPVIVGSPATVADELERWHRETGVDGFNISAAVRPTDLERFARLVSPELR
+RRGLLREPEAGRTLRENVAGGGPLLPEDHRGARFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9eddd45f8f5a01a60a3dd374e0adeef2f55d887b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000177.fa
@@ -0,0 +1,23 @@
+>0_3
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>1_1959
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTPSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
+>2_402
+MSSVFGRLIRDRGWSTPVAVGSVLTRWDELVGPEIALHCRPESFEDSVVRVRTSSTAWAT
+QLRLMTPVLLQRFDDALGPGVVTRLEVAGPQAPSWRKGPRTVRGGRGPRDTYG
+>3_356
+MRERSPEPDALAELPPDRPDLALVQLRRVRDAARQRGEAPLNRRGTAAGLAQSMAGSEAA
+AAAGGAVARSGHRRPGAPADRDPAVVSSVFGRLIRDRGWSTPVAVGSVLTRWADLVGPEI
+ALHCRPESFEDSVVRVRTSSTAWATQLRLMSPMLLSRFDEALGPGVVTRIDVAGPAAPSW
+RHGPRTVRGGRGPRDTYG
+>4_3
+MAETPAPFEPDRPDLALVQLRRVREAARERGEAPLRARGTGAGLAGAMAGTTSAGRERQD
+RRRPFGGADRDPATVSTVFGRLIRDRGWSTPVAVGSVLTRWAELVGPEIALHCRPESFED
+SVVRVRTSSTAWATQLRLMSPVLLQRFDEALGPGVVTRIEVAGPQAPSWRKGPRTVRGGR
+GPRDTYG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000188.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000188.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53df82f77cd44dc3376d519b8d5f3b1393a4b4dc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000188.fa
@@ -0,0 +1,66 @@
+>0_16
+MDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGPDRAV
+AWTRGVLEALEHAHEEDIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKDPQDRFPTGAAFLAALEEAAADPHAGPGRHTPPLDAVHP
+ALVGAGGAVLGATPAEHGADVADVPTAAVPLTRPAPSVPAEPDTAQPQAVNHAVAGAGLP
+GAASAAQLAAAAAMDGPRPVTGGQPVTPGAAATPRPEPPPRDTPAPATATPRRVRRRVRR
+RTLLAAGVVLVALALVLAPWLAAALRTTAEVPAVVGLQQDEAVAALEDAGLVAVVSSAYM
+ADAPDGTVTQSDPPTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLR
+VSSVQYQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQL
+ALSAPELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTTSSWIAPTAEPSEPAP
+PSSEAPEPTPSASTSPSPPSSESPEPSESPEPSESAEPSPSPSASATPSPEPTTTATPSP
+TQSPSPPSAAPSTSSEPTEQSPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>1_1985
+MSVDEQRTLNGRYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRK
+EARSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDR
+AVAWTRGVLEALEHAHEEGIVHRDVKPANVMVTETGAVKVMDFGIAHALADTSATTSQTQ
+AVVGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPP
+APSDVDPDLPPAFDPVVLRALRKDPEDRFPTGTAFLAALEEAAADPHAGPGRHTPPLDAF
+PPALVGAVLGAAAAEHGADVPTAAVPLTRPTPSVPAEPDAAQPQAANHAVAGAGLPGAAS
+AAQLAAAAAMDGPRPVTVGQPVMPGAAATPWPEPQGDTPAPATATPRRVRRRLRRRTLPA
+AGVVLVALALVLTPWLAAALRTTVEVPAVVGLQQDEAVVALEDAGLLAVVSSAYMADAPD
+GTVTQSDPPTGTEVPRGAEVRIRVSRGKEGIALSDSLHGLSEDAARRELERLGLRVSSVQ
+YQDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAP
+ELRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPYSEA
+PEPTPSASASPSPPPSESSEPSESAEPSPSPSASATPSPEPTTTATPSPTQSPSPTSAAP
+SEPTEQPPSTSPTATPVDPLPTLTPDPEPSIDPPPST
+>2_361
+MEEQWTLNGRYRIDALIGRGGMADVFRGTDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSVASLNHPSIVSVYDTGEVSLEDGHHPVDCPYLVMELVTGRSLREVLHAEGAVGTERAV
+AWTREVLEALEHAHQEGIVHRDVKPANVMVTDAGSVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYATGCVLFELLTGRPPFTGDTPLAVAYQHVREAPPAP
+SEVDPDLPRAFDPVLLRALEKDPEDRFPTGAAFREALEAAAADPHAAVDADTAALDLVRA
+GAAGAGGAAVAAGREVRRDGARDSADVPTAAVPLTPAPAPAAPAEPAEPPGGEPRRGRGR
+AARRRLRRPAGGRRLRGRPAPGHRLPTPPSRGPRRPAPRPPPGSALPPPLPPPDGAAAGG
+AACRSPGCCWPASSC
+>3_344
+MQGQRILHERYRVDELIGRGGMADVFRGHDLRLNRTVAVKMMRPDLARDPAFQARFRTEA
+RHAAALNHPNIVSVYDTGDALLDDGPQSVECPYLVMEHVDGRTLRELLDAGEVAWRDAVE
+WTRGLLHALDHSHRQRIVHRDVKPANVMVTRDGGVKVMDFGIARALSDTSAHTGQTQAVV
+GTALYLPPEQAQGARVDARSDLYAAGCVLFELLTGRPPFTGETPLAIAYQHVREEPPAPS
+AVDPSLSTEFDSVVLRALQKDPGLRHQHAREFLSALDFAAARAARAADDDAPTRVVPASG
+AAPLATGSGALAAAVAGSTAAGPTASGSTALGAGGAPEARPATGPPATTPLGAAAGPTEP
+LIAGHAVAGAAVPGAPSASQLAAAEAVETAPAAASTTGGSAGAGATSGAERAGRRHRLSW
+AVLAAVAAVAAVAAILALGAALLIGSRDPGPVTVPALAGRTEAEAVSALTGLGLRSAISP
+DYHSTEPDGRVLKVHPGAGAAVEPGSTVNLSVARGGEGVVLPTSLRGASEARVRQELARL
+GLNVASVEDTPSGELDRGALVQTDPVLGSRVPPGSAVVLHLADGTARVPSLVGMTGADAR
+TTLAALDPEMTVRFQGAAGADPDTGVVVLQDPAAGTVVDNTAMITLITSAEATPTASAVT
+VAPPDPALPSATTTTAPAEPSPGVPAPTTPAAPAVDTPAPAPATTPAPAPESSSTPGAGT
+DPAPTESAPTPDDGPGSTGTPSTEAPTEAPTDPVGTPAPSPSGEPVPQPSPSVEPLPEPT
+APTEAPTADPAG
+>4_16
+MDEQRTLNERYRIGELIGRGGMADVFRGEDLRLHRPVAVKLMRRDLARDPHFQARFRKEA
+RSAASLNHPSIVSVYDTGEVSLEDGLHPVDCPFLVMELVSGRTLREILHAEGAVGTDRAV
+AWTRGVLEALEHAHEEGIVHRDVKPANVMVTDTGTVKVMDFGIAHALADTSATTSQTQAV
+VGTALYLAPEQATGRTVDGRADLYAAGCLLFELLTGRPPFTGDTPLAVAYQHVREEPPAP
+SDVDPDLPPAFDPVVLRALRKNPQDRFPTGAAFLAALEEAAADPHAGPGRHPPPLDAVHP
+ALVGAVLGATPAGHGADVPTAAVPLTRPTPSVPAEPDTTQPQAANHAVAGAGLPGAASAA
+QLAAAAAMDGPRPVTAGQPVTAGQPVTPRPEPPPGDTPAPATATPRRVRRRVRRRTLLAA
+GMVLVALALVLAPWLAAALRNTVEVPAVVGLQQDEAVAALEDAGLVAVVSSAYMADAPDG
+AVTQSDPQTGTEVPRGAEVRIRVSRGEEGIALSDSLHGLSEDAARRELERLGLRVSSVQY
+QDDGRLERGLLARTDPAMGTHVPPGSSVVLHLSSGMVAVPDVVGMSAPDARRQLALSAPE
+LRVRIQDEDGATTDTGTVVAQDPPAGVRVDNRSSLTLTASSWIAPTAEPSEPAPPSSEAP
+EPTPSASAPPSPPPSESPEPSESAEPSPSPSASATPSPDPTSATPSPTQSPSPPSAAPST
+SPEPTAQSPSTSPTGTPVDPLPTLTPDPEPSIDPPPST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15f72558e289be273f3e624a2db2990f54cc60e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000190.fa
@@ -0,0 +1,50 @@
+>0_18
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTIVSGMKAIMEAVVT
+E
+>1_1987
+MNEAIRRTWTVMAAMILVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHEPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPSFDSN
+ALSSHSPAEAQAAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREVA
+ERFGFNDSFDYPLPVTGSVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
+>2_359
+MNEAIRRTWTVMAAMMLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSDDAYHYQRVYHDPELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRVAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSATEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWPLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVKLGQDRIREVA
+ERFGFNDSFDYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIKAVRRPDLTTVEEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGIGHQTIVSGIKAITEAVVT
+E
+>3_342
+MNEAIRRTWTVMVAMFLVLAVAASVIQVVAADSLKENKLNNRQLFLEFGAPRGPILVDGT
+PVAQSVPSGDAYNYQRVYRDSLLYAPLTGHYSLAYGTAGMEKAMNGELAGTSSSQFLDRA
+LEIVTGSTPEGDQVELTLDSELQKLAYESIPDGVKGSVVATDPKTGRVLAMASKPSYDAN
+TISSHTRSEATAAMSAYEGVPGLTVGQNRPTQQRVAPGSTFKLIDLVAMLESGDYAPDQV
+LDVPAAWTLPGTRTQMSNFDGGRCNGVGRATLTWIVANSCNTPFAQAAVALGQDEIRSVA
+ERFGFNQDGSMPLPVTASVFPEDLDDAALAQSAIGQRDVQATALQMNMVAAGIANDGMVM
+EPNLVQAVRRPDLTTVSEFSPREHGRAMDPDVAHQVRDMMVATVEDGTASAAKSSTLQIA
+AKTGTAEKDGTANVNTWVTGFAPAQDPKVAVTIVYEDQNSSSAHTQAVESMQRIMEAVVA
+E
+>4_18
+MNEAIRRTWTVMAAMLLVLALAASVIQVLAADQLKTHALNSRQMFLEFGAPRGPILVDGE
+PIAESVPSGDAYHYQRVYHETELYAPLTGFYSLTYGTDGLEAAMNEQLSGTPTSQFVDRA
+MEIITGATPEGDQVELTIDPELQRLAYDALPDGVRASAVVTDPTTGEILAMVSKPGFDSN
+ALSSHSPAEAQSAMAAIDQIPGASAYRNRAAEQLVSPGSTFKLIDAVAMLESGDYTPDGT
+VDIPAAWTLPGTTTELPNYDGSPCNTVGRQTLTWALAQSCNTPFAMAAVELGQDRIREAA
+ERFGFNDSFEYPLPVTASVFPSDLDDAALAQSSIGQRDVQATALQMAMVAAGIANDGVVM
+EPQLIEAVRRSDLTTVQEFSPRERGRATTPEVAGQVSDMMVSAVEDGILGSVQSDTVRIA
+AKSGTAEVGDTGNVHSWITGFDASENPRAAVTIVVEDEPPGVGHQTVVSGMKAIMEAVVT
+E
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000199.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000199.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6c810f116faa591f5ef7823d4f95f14763749a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000199.fa
@@ -0,0 +1,33 @@
+>0_36
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAEAEAGAAVVDGADPAGHGDDDARHPVWDVALAWLKAADSELVQAFVGVARGRRGASS
+R
+>1_2000
+MAKGVKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQL
+VNHDDAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGGVDPRHVHLVGVYSE
+LPVVCVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSAEPMDAAELPGAGERM
+ALEIAASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQ
+ARAQAEAGAAVVDGADPAGQGDDDARHPGWDVALAWLKAADSELVQAFVGVARGRRGASS
+R
+>2_345
+MGPRRGLPEGEGPLSGARGGRGAGRQRASRGGPARSTRTGGRAGAKGGGPQRAGSGSRAG
+GEGRRRAPSAPADLAAPPETLFLATIPGATPSTWVDRFTTRQRVVQLVNHDEASQLAHLA
+HDDAGMPRHPLPQLGYVRRRRDVEAEEMLRAAGVDPRRVHLVGVYAELPVVCVGRDHLLA
+AWDAEADGPVPLAELDSHEELDPARFAAAPVEDPLDSAELPGAGERMALEIAASGAGHVV
+LPMSVARMFGRKDVVVLPLASALDDTVGMSRADREAAATRAEVEADAGDAGTAAAGPGEA
+DDDAARHPGWDVALAWLKEADSELVQSFVGVARGRRGNSSR
+>3_287
+MPAAPADLPTPPETLFLATIPGATPSTWVQRFSSRARTVQLVNHEEAQQAAHLAHDAAGA
+PLHPLPQLGYVRWLRDAGVESVLRESGVDPRFVHVVGVYSELPVVCVGKEHLLAAWDLEA
+DGPVPLAELDPAEHMDPARFAPEPGAASNPLDSAELPGAGERMALEIVASGVGHVVLPQS
+VARVFGRKDVVVLPVACELDDVVGLSRADREAAATRAEVAEEGDGVVPDGADAPATTAPR
+HPGWDVGLAWLKEQDSELVQSFVGVARGRRGGTSR
+>4_31
+MKPAGRAGGEGRRRPAPAPPADLPVPPETLFLATIPGATPSTWVERFTTRQRTVQLVNHD
+DAAQLAHLAHDDAGQPRHFLPQLGYVRRRRDVSAEEFLRAGDIDPRHVHLVGVYSELPVV
+CVGRDHLLAAWDVDADGPVPPAELDPDEELDPARFAPAPSPEPMDAAELPGAGERMALEI
+AASGAGHVVLPMSVARMFGRKDVIVLPLASTLDDTVGLSRADREAAATRSALADEQARAE
+AEAGAAVVDGADPAGQGDDEARHPGWDVALAWLKAADSELVQAFVGVARGRRGASSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000204.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000204.fa
new file mode 100644
index 0000000000000000000000000000000000000000..903d66052c17e78f61f7ea2a98be829a0c26c5e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000204.fa
@@ -0,0 +1,25 @@
+>0_42
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>1_2006
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVVLVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPYE
+FL
+>2_334
+MGRRADAPAGPGRAVVVPTTTSSPAPASAPVHTPAPAPATSSAPAGSLGQVSESTTYLLV
+DGENIDATLGTSILQRRPQPDERPRWNRLLSFMGEHWDQPVKGLFFLAIDGDIPVPFVQA
+LTAIGYKPIMLRGAGKVVDIGIQKTMEALQEREDDVVLVSHDADFAPQLTDLAATPDRRT
+AIIGFEEFLSHELRRIPDVEFFDLEYGVGAFDTPLRRLRVIDIDEFDPLEFL
+>3_280
+MSRRADLPTGPATAVPAAPAAPVSPTAEDRSAATPADTLDTMSARTTYLLVDGENLDATL
+GMSVLNRRPNPEERPRWNRVLRHVERAWGQEVRPLFFLAVDEDGDIPFGFVQALTTMGYQ
+PILLRGAGKVVDIGIQRMAEALIGRDADVVLASHDADFAPQMLDLAAHGHKIAVMGFDEF
+MSAELRAVNGMEVWDLEHDVAAFDVPLPRLRVIDIDDFDPRDFL
+>4_37
+MSERTTYLLIDGENIDATLGTSILQRRPQPDERPRWKRLLGYLEDRWDQPVKGLFFLAID
+GEIPIPFVQALTALGFQPIMLRGEGKVVDIGIQRTAEALLGREDDVILVSHDADFAPQLT
+DLAATPGRRTGIMGFEEFLSHELRRIPGVEFFDLEHAVGAFDSSLPRLRVIDVEAFDPNE
+FL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..754a5bb46ee5df77290be33065e0bbc5b1b576b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000205.fa
@@ -0,0 +1,40 @@
+>0_43
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGHFGAAVVNVLAHLAVLTVIMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLVPLAQALGLSRATLTPYVSAFLTDG
+PYRLPLFLTWALLGAVLVRTVHGTTTAAPARSARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLTVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGTDDTWFNLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
+>1_2007
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEAEWLGRGRAVPRALVRAAALCGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATSTADVVDRLVPLAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLAVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFNLAVLVVGALLLPLLWRAVVRVGPFRAGPLEGVVRLLTAPFD
+RAR
+>2_333
+MPRVSSRPHTGRDRLVWVDVARGVALVSMFVAHVAPSGGPAGVLNLSEHLTAALFAALVG
+VSARLEVQGLGVGRALVRAMVRAAALLGAAWLTSLFDAAVVDVLTHLAVITVLMALLAAL
+PLAVHLVLALLAGGGGILLTASGTLAVADALAPAARALGLDPAELVPAVAGFLTAGPYRL
+TAFLGWALLGAVLVRTVHGTTTALPRSGRLVGLGWGVGGVVLAGLVILLSRVQTGAAPVP
+YTGTAAEILVDTGLVLGVLGLCAAVVPSRPSPATDLLAVPGSMTLSVYVAHQAYLGWVLT
+AGPGPWVDGRGADDTWFNLAVLLAGGILLPLLWRGLVRVRPFRAGPLEGVVRLVTDPIGR
+RSRGEH
+>3_281
+MTLAAGHRLTWVDVARGLALVSMFVAHTAPTGGPGGVLNLSEHLTAALFAALVGVSAHLE
+QRRHGFWRAFLRAVVRAAALCGAAWLTSHFGAAVVDVLTHLAVLTVLMSVLALLPGLVQL
+LLVPAAAWAGVRVGALTADDVAARLEPARALVPAQVRPGPAVVAEQAAAFFTVGPYFLLF
+FTAWALLGAVVVRSVQGGGLRAALRLGGHPGPGLGGRAAGGVWAGVGLLVGGAGVALARQ
+RTEDSPVPYEATWDYALLAAGLVLIVLGACAAVVPSHVPWLTAVLAVPGSMTLSVYVAHQ
+AYLGWVLRAGPGPWLSELGTDDTWFNVGALCAAGLLLPLLWRALVRAEPWRRGPLEGPVA
+LVTHGLARR
+>4_38
+MPAPSSHAPAATHTARGRLVWVDVARGLALVAMMVAHTAPAGGPGGVLHLSEHLTAPLFA
+ALVGVGARLEVEWLGRGRAVPRALVRAAALFGAAWLTGLFGAAVVNVLAHLAVLTVLMAL
+LAALPLAAHLVLAVLAGGGGLLLAATPTADVVDRLLPAAQALGLSRATLTPWVSAFLTDG
+PYRLPLFLAWALLGAVLVATVHGTTTAAPARRARLTGLAWAAGGIALAGVVLALSRTQTG
+AAPVPYTATPAEALLDTGLVLIVLGACAALAPRRAGLLAVPGAMTLSVYVAHLWYLGWVR
+RLGPGPWRSATGADDTWFTLAVLVAGALLLPLLWRAVVRIGPFRAGPLEGVVRLLTAPFD
+RAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000206.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000206.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f4bc2982f0862445f15262a308dcac0bddd87b58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000206.fa
@@ -0,0 +1,25 @@
+>0_46
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAGLGAETATLDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEADYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKATRDAETPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGT
+>1_2010
+MAALTDRAVLIAGATSASGRAATRTLLDAGAHVVPTGRDAAKLAPLAALGAETAALDLTD
+EAAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLTGQTEDDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVKSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
+>2_338
+MGTLTGRTVLISGATSASGLAAARALLAAGADVVATGRSPERLAPLAALGADTAALDLSD
+EAAVRGLVEDLHARGVRVDGLLHLVGGWRGGGGLAGQSEEDYRALESSLTALRHVSRALD
+DDLRASSAGRLAIVSSTAVARPLAGGAAYAAVKAASEAWTRAVAQGWDKAARDAGTELRG
+AAVVLRVKSLAGLEDRLAEQFVRLWSADAAQLNDSILAVQEKETA
+>3_1194
+MSAPAAPDLTGALVLVTGASSGIGSALARGLAAAGADLVLVARRAGRLAALADELRAAHR
+TEVTVLPRDLAAPDAGPALRAELSSRGPRVTGLVNNAGFGSGLPFGREDPARLEAMPAEE
+ERGRERVLCVSPSSTGTEFFDVAGTPGAGGGFARRAAPDDVAAAVLRVLARRGGPAEVVP
+HDRAVTVAARLLPRTVLRGMGAMHRRGAARR
+>4_41
+MAALTDRAVLIAGATSASGRAAARTLLDAGAHVVATGRDAAKLAPLAELGAETAALDLTD
+ETAVRGLVEDLHARGTRIDGLLHLVGGWRGGGGLAGQTEEDYRALEASFTALRHVSRALD
+DDLRASSAGRLAIVSSTAVTRPLAGGANYAAVKAASEAWTRAVAQGWAKAARDAEAPLRS
+AAVVFRVRSLAGLEERLAEEYARLWKAEAGALNDAVLTLQEKGTD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000208.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000208.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e6f5226a62dc90fc8598fd76739f95a4087ae72
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000208.fa
@@ -0,0 +1,55 @@
+>0_51
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGRDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGHAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRQQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQAEAQKLVDAVIG
+>1_2015
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYRTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQRLVDAVIG
+>2_327
+MTEHTAAPPASERPGTPALPQDLIDVDALLTAYRTGRPDVSDPAQKVVFGTSGHRGSALK
+TSFNDDHIAAITQAVVEYRAEHGITGAVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRDLTPAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANALLAAGLEGVRRVAAADVDGHAKLGGFDFLDRYVTDLPDVID
+VEAIREAGVRIGADPMGGASVAYWGEIARRHGLDLTVVNPDADPRFGFMTLDWDGKIRMD
+CSSPHAMASLIERMTPDADGQAPYDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHRERWPADAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVKLDGGPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGSPAYARIDAPA
+TAEQKARLKTLSPDDVTVTELAGETILATLTNAPGNDAPIGGLKVVTQNAWFAARPSGTE
+DVYKIYAESFRGPEHLKQVQEEAQRLVDAVIG
+>3_267
+MSTPAAGRAGTPALPEDLIDVEALLAAYRDLHPDPADPAQKVVFGTSGHRGSALKSSFND
+DHIAAITQAVVEYRAEHGITGAILVGKDTHALSGPAQDTAVQVLLANDVEVLVDSRGGFT
+PTPAVSHAILHLNAGRDLTAAGFSADGDNAGLVDGLVITPSHNPPADGGFKYNPPHGGPA
+DTDATSWIAARANDLLAARLDGVTRLAPEDVEGHAKLGSFDFLDRYVTDLPQVIDLDAIR
+EAGVRIGADPMGGASVAYWGEIGRRHGLDLTVVNPDVDPQFGFMTLDWDGKIRMDCSSPN
+AMASLIERMTPDADGHAPFDVATGNDADSDRHGIVTPDGGLMNPNHFLAVSIDYLYRNRS
+QWPQNAGVGKTLVSSSMIDRVATDLGRELVEVPVGFKWFVPGLLSGTGVFGGEESAGASF
+VKFDGGAWSTDKDGLLLCLLAAEIQAVTGQSPSERYRDLVALHGDPAYARIDAPATAEQK
+AALKALSPDDVTATELAGETILAALTNAPGNDAPIGGLKVVTKNAWFAARPSGTEDVYKI
+YAESFLGEEHLKQVQQEAQAIVDAVIS
+>4_46
+MTENTAALPAAERPGTPALPQDLIDVDALLEAYHTGHPDVTDPAQKVVFGTSGHRGSAFT
+TSFNDDHIAAITQAVVEYRAHHGITGPVLVGKDTHALSGPAQDTAVEVLLGNDVEVLVDS
+RGGYTPTPAVSHAILHLNAGRELSPSGFAVDGDNAGLVDGLVITPSHNPPADGGFKYNPP
+HGGPADTEATTWIADRANELLAAGLAGVHRVASADVAGHAKLGGFDFLDRYVSDLPQVID
+VEAIREAGVRIGADPMGGASVAYWGEIADRHGLDLTVVNPEVDPRFGFMTLDWDGKIRMD
+CSSPNAMASLIERMTPDADGQAPFDVATGNDADADRHGIVTPDGGLMNPNHYLAVAIDYL
+YRHREQWPQSAGVGKTLVSSSMIDRVAGDLGRELVEVPVGFKWFVPGLLTGTGVFGGEES
+AGASFVQFDGSPWSTDKDGLLLCLLAAEIIAVTGQSPSERYRDLVALHGDPAYARIDAPA
+TAEQKAKLKTLSPDDVPVTELAGETILATLTNAPGNDAPIGGLKVVTQHAWFAARPSGTE
+DVYKIYAESFRGPEHLTQVQAEAQKLVDAVIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000214.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000214.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa0b0f2f90d8401e73a65d50812be3cbc4d35ddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000214.fa
@@ -0,0 +1,35 @@
+>0_58
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVPAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVAISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>1_2022
+MTGTGSADATPSRLRYAFLGPAGTFTEAALRKVADPAEAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAMEDVRRVTTHPH
+AWAQVRGWAETALPGVDFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
+>2_318
+MTRDDAAPLGRCTFLGPAGTFTEAALRAVPGAEQAELIPATSVPAALAAVRAGEADHAMV
+PIENSVEGGVSATLDDIASGDDLQILREELVQISFVLVGRPGVELADVRRVSTHTHAWAQ
+VRGWVEANLPGVEYTPSGSTAAAARALADAEPGSEPFDAAVCAPLVAEQTGLPVLARAIE
+DVTGAVTRFVLVGRPGPLPAHTGSDKTTLTVPLPDDHPGALREILDQFATRGINLSRIES
+RPTGEGMGKYFFSIDLEGHLAEERVAAAMGALHRIFPGVRFLGSYPRAEHRPVAVRRHTS
+DDAYRAGRAWVDGLLAR
+>3_260
+MSPAPRYAFLGPAGTFTEAALRQVASPEDVDLLPASSVLAALAAVRVGEAERAVVPIENS
+VEGGVTATLDDIGADEPLQILAEVLVPISFVLVGRPGVALEDVRRVTTHTHAWAQVRGWM
+EAHLPGVEFTPAGSTAAGARALLPSAGGDGAVASFDAAVCAPLVAEQTGLPVLAEAIEDV
+TGAVTRFVLVSRPGPVPEPTGADKTTLTVPLPDDHPGALREILDQFATRGINLSRIESRP
+TGEGMGRYFFSIDLEGHVAEERVGAALAALHRTFPGVRFLGSYPRAEGRPPTVPEHVTDA
+AYRRGTAWVRGLRSR
+>4_53
+MTGTDSADATPSRLRYAFLGPAGTFTEAALRKVADPAKAEFVSAGSVLSAVAALRRGEVD
+RAVVPIENSVEGGVSATVDEIALGETLQILAEVHVPISFVLVGRPGVAIEDVRRVTTHPH
+AWAQVRGWAETALPGVEFTPAPSTAAGAGLVAQGDFDAAVCAPLVAEQTGLPVLAERIED
+VPGAVTRFVLLSRPTALPAPTGADKTTLVVPLPEDRPGALGQILAEFTTRGVNLSRIESR
+PTGEGIGRYFFSLDLEGHLAEARVGDALAALYREYPDLRFLGSYAQAEPVPTRVPAEFTD
+AAYRSGRAWVESLRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08fbc2cf18ca9372e4a651736d59f9bebe7e52a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000221.fa
@@ -0,0 +1,25 @@
+>0_68
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>1_2032
+MDAQDVQNDLTHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>2_305
+MDAQDVQNDLTHVLMRREEVQETVKDLAAQIDRDYEGKDLLIVAVLKGAIMVVADLTRAL
+HSHVQIDFMAVSSYGSGTKSSGVVRILKDLDADLTGRDVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPDAMKVEIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>3_248
+MDAQDVQNDLTHVLMSKEEVQDTIRDLAAQIDRDYEGKDLLIVAVLKGAVMVVADLTRAL
+HSHVEMDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+TRGPASVEICTFLRKPDAMKVDIDVKYVGKDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
+>4_62
+MDAQDVQNDLSHVLMSREDVQDTITDLARQIDRDYADKDLLIVAVLKGAVMVVADLTRAL
+HSHVELDFMAVSSYGSGTKSSGVVRILKDLDADLTGRHVLIVEDIIDSGLTLSWLKANLE
+SRGPASVEICTLLRKPEAMKVDIDVKYVGRDIPNEFVVGYGLDYAEKYRNLDFVGTLAPH
+VYS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000223.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000223.fa
new file mode 100644
index 0000000000000000000000000000000000000000..74fc66f3390a11f95f9dc9bf6b80070f867500dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000223.fa
@@ -0,0 +1,25 @@
+>0_71
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>1_2035
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGTAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
+>2_303
+MTEQTHHDDAARGPVPAADGSAAAPTASTPAAAGVPGTFDPDSTAIDRPRIEAAVREILL
+AIGEDPDREGLQDTPKRVAKAYAEFFAGLHQGPEQVLGTTFDIAHEELVLVKDIPFYSTC
+EHHLVPVHGTAHIGYIPSAAGRVTGLSKLARLVELYARRPQVQERLTTQVVEALMEHLAP
+RGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRSEAMSLIMHG
+>3_245
+MTEQHRDAALADAHLHRPHEAAADVAPTTGAGAALAGAVPGVPGTFDPDQDTVDRPRIEA
+AVREILLAIGEDPDREGLQDTPKRVAKAYAEFFAGLHQRPEQVLGTTFDLSHEELVLVKD
+IPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTGLSKLARLVELYARRPQVQERLTTQVVEA
+LMEHLQPKGAIVVVEAEHMCMSMRGVRKPGAKTVTSAVRGQLRDPSTRAEAMSLIMHG
+>4_65
+MTAHTPDDAVPGTFDPDSTAVDRPRIEAAVREILLAIGEDPDREGLADTPARVAKAYAEF
+FAGLHQSPDQVLGTTFDIAHEELVLVKDIPFYSTCEHHLVPFHGAAHIGYIPSAEGRVTG
+LSKLARLVELYARRPQVQERLTTQVVEALMEHLAPRGAIVVVEAEHMCMSMRGVRKPGAK
+TVTSAVRGQLRDPSTRSEAMSLIMHG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000225.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000225.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6261a1179ff26d299a2f633521039f86650e2633
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000225.fa
@@ -0,0 +1,25 @@
+>0_74
+MSTVDWSHLAEGPAPVPALGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTAPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVVPLRPACPDALGREDT
+>1_2038
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
+>2_300
+MSGVDWRHPAEDPAPTPALGARPAEPVAAVLALGANLREPAQTLDAAVAALSALPHVTDV
+QASPRAVTAPVGGPPGQPDYLNQVLTLRTTLSAWELLAVAHRLEQEHHRRREVRWGARTL
+DVDVIAYGDLVSDHPDLTLPHPRAAERGFVLLPWLWLDPDAVLAGRPVAELAALAADAPG
+VRRAEPERHRLLAGRDDVVPVRPRAVRAPGRDAIDGSGP
+>3_242
+MSRPEAAHPAEGPAPTPELAARPSSPVTAVLALGANLGDPSETLDASVAVLTVTPGIEAV
+AASPRALTAPVGGPPGQPDYLNQVVRIRTALSPWELLGVAHRLEQDHHRRRTVRWGARTL
+DVDLIVYGDLTSDHPDLVLPHPRAAERGFVLLPWAWLDPEAELAGESVAELGARAADAPH
+VRREPARTAHLDGPRPDVLRPDSTPGLPSAPLPDGAAIARPWSDPT
+>4_68
+MSTVDWSHPAEGPAPIPELGARPDAPVAAVLALGANLREPAQTLDAAVAALSALPHITDV
+RASPRAVTTPVGGPPGQPDYLNQVVTLRTDLAPWELLAVAHRLEQDHHRRREVRWGARTL
+DVDVIAYGDVRSDHPDLTLPHPRAAERAFVLLPWLWLDADATLAGTPVADLAAVAADAPG
+VRRQEPERHRLLAGTDDVAPLRPARPDALGREAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000227.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000227.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7df135b6e59983f5eeb188d5d7e13250bf5bccb4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000227.fa
@@ -0,0 +1,20 @@
+>0_76
+MPGIDLSGVAFTPASPRLTTVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>1_2040
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
+>2_298
+MPGIDLTGVTFAPASPKLTPVKLISSSIGHLIWLVVFSVPLVLKLLGPWEGLWAWTAWGL
+PAIVVVSWLVDLVLIPRRVRAMGWAEREDDVLWREGLLFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAASGSDVTLEGLPRETADELREVLMARGQARLAGL
+>3_240
+MPGIDLQGVEFTPVSPALVRVEAVRELIALVIWLAVVSVPLVLKLTGVWPDMWSWTAWGL
+PALVLAWSLVELVLIPRRVVAKGWAEREDDVLWREGILFRRVVAVPYGRLQYVDVTDGPL
+LRWAGLQKLTLKTAGGADVELVGLPRETCDRLREVLMARGQARLAGL
+>4_70
+MPGIDLSGVAFTPASPRLATVKLIATTIGHLIWLAAFSVPLILKLTGPWAGMAAWVAWGL
+PAVVVVSWIVDLILIPRRVRAMGWAEREDDVLWREGILFRSVHAVPYGRLQYVDVSDGPL
+LRRVGLQTLTLKTAAAGGDVTLEGVPRERAEELREVLMARGQARLAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000229.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000229.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a7801a4ca056e39ab027a2a7b5dab82b1c7aab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000229.fa
@@ -0,0 +1,35 @@
+>0_78
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLPPDVRAVWETLARATTDRAETRGTLRADTA
+ARLREVLDDSDDPHDD
+>1_2042
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
+>2_296
+MTGGLDLTLDPTDPTQRPGRLGVGVVGAGRVGAVLGAALRNAGHTITGVHAVSEASRTRA
+EALLPEAPVLEIPEILRRSEMVLFAVPDDVLPELVAGLAAAGHVQTGHLVVHTSGRHGVG
+ALNPVRAHGAIPIALHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALAVEMGGEPV
+VIKEADRGVYHAALSHGSNHLVTLTAQAAQLLRSIGVQDTERLLRPLMHASLENALADGD
+GALTGPVARGDVETVRGHRETLRELVAEGMPADVLAVWETLARATADRAEARGALRPDVA
+ARLREALAPDA
+>3_238
+MSRMDMSPELTGADPADRPGRLGVGVIGAGRVGAVLGAALRGAGHTITGVHAVSEASRTR
+AEALLPGVPVLELPEILRRSEMVLFAVPDDALPELIAGLAAAGHIQTGHLLVHTSGRHGV
+RVMDPVRAHGAIPLAVHPAMTFTGLSLDLARLQDCVFGVTADPVVLPVAQALVVEMGGDP
+VVVKEADRAAYHLALSHGSNHLVTVTAQARQILEEIGVAEPERMLRPLMQASLENALTDG
+DGALTGPVARGDVETVRGHRDTLRELVDGGMPADVLAVWESLARATAQRAARRGALRADA
+AERILAVLDGADDGPDATG
+>4_72
+MTGGLDLSLDPHDPAQRPGRLGVGVVSAGRVGAVLGSALRAAGHTITGVHAVSEASRDRA
+EMLLPGVPVLEIPEILRRSEMVVFAVPDDALGELVAGLAAAGHVQTGHLLVHTSGRYGVG
+VMEPVRAHGAIPLAIHPAMTFTGLSLDVARLQDCVFGVTADPVVLPVAQALVVEMGGEPV
+VVKEADRAAYHLALSHGSNHLVTLTAQARQILETIGVADPERVLRSLMTAALENALTDGD
+GALTGPVARGDVDTLRTHRETLGELEAGGLSADVRAVWETLARATTDRAETRGALRADTA
+ARLREVLDDSDDPHDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000238.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000238.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec89996201d80501e339d9f94b7d464e4abfec7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000238.fa
@@ -0,0 +1,65 @@
+>0_89
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+LDAFHEAFGTREGDPMWLAPEERVTIW
+>1_2053
+MTATAEPRVPSPREDLYRHVNTGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEGAVR
+EVGAGFDPAQARVQATAAAGAHRDAPLAPLDAEDTEGMEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVTTPAELLTLSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLTLAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHMTPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPVEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
+>2_283
+MTATAEPRVPAPREDLYRHVNAAWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGAGFDPAQARVDATAAAGAEHHTPLEPLDAEETEGMELPEVKRRIAALYASFMDDETV
+EARGLEPVATDMAAVASVQTPAELLELSGRLQRQGVSGLVNTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHAGRLLGLAGIGADSAEAAEAGVRVVELEKRIAAL
+HWDVVRSRDAVARYNLMTHEQLVELFPLAEAWLEGVDAAGERSREVVVWQPDFLSGVQAL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRHRWKRAVAF
+VNGAAGEDVARLYVDRHFPEGHVAAMDELVNLLQEAYRRSIDELEWMSEETRQRALEKLS
+MFRPMVGRPVRWVDYSSLEVHAGDLLGNARAASEFEWERDLRKIEDGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEKSMAANLGAIGAVIGHEIGHGFDDQGSRYDGSGR
+LEDWWTQEDRAAFTELTSRLVAQYNVLSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFSAWAAVWRQLTRPETMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTQEGDPMWLAPEERVTIW
+>3_229
+MTATAEPRVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRRIAEDAAR
+DAAMAAPAPEVEAPAQDEASQDPAAAERAARERIAVLWSAFMDEEAVEAAGILPLAADLE
+AVDAVASPAELLALSGRLQREGVSGLIGTGALNDAGDPERMLLHLIQSGLGLPDESYYRE
+EAYAEILAQYTEHVGRLFALAGVGGDEAGAAALGERVVALEKRIAAHHWDVVRSRDAVAR
+YNLLTRDQLLELLPLAPGWLEGIGAADARADEVVVWQPDFLTGVQALLEGPDAADLADWK
+AWLTLQVLRSRAGFLPDAFVQENFSFYGRRLAGTQEVRPRWKRAVAFVNGGVGEDVGRLY
+VARHFPEGHVAAMDQLVGLLLEAYRRSIDALDWMGEQTRQSALEKLAMFRPMVGFPETWR
+DYSALELTPGDLVGCARAVDRFEWDRDLAKIETGPDPREWHMTPQTVNAYYTPLENAIVF
+PAALLQPPFFDPERSMAANLGGIGAVIGHEIGHGFDDQGSRYDGSGRLHDWWTEQDREAF
+AERTGRLVAQYSALSPAEAPDRQVNGEFTLGENIGDLGGLGIAHQALEIWREEQDGSTED
+ESSGDREFFQAWAAVWRQLTRPETMVTRIASDPHSPNQFRCNQVVKNLDAFHTAYGTREG
+DPMWLAPEERVTIW
+>4_84
+MTATAEPEVPSPREDLYRHVNAGWLDTHEIPADQGAYGAFLELRDAAELAVRHLCEDAVR
+EVGTGFDPAQARVQATAAAGAHRDVPLAPLDEEDAEGTEHPELKRRIAALYASFMDDETV
+EARGLEPIASDLAAVATVSTPAELLALSGRLQRQGVSGLINTGALNDAGNPDRMLLHLLQ
+GGLGLPDESYYRDEAYAEILEQYTEHTGRLLALAGIGADRDEAAALGVRVVELEKRIAAL
+HWDLVRSRDAVARYNPMTHDRLTELFPLADAWLEGVDAAGERAAEVVVWQPDFLSGVQGL
+LEGPEAADLEDWRHWLILQVLRSFAGFLPDAFVQENFSFYGRRLAGTEEVRPRWKRAVAF
+VNGAAGEDVAQLYVARHFPQGHVAAMDELVGLLQEAYRRSIEELEWMGEETRQRALEKLA
+MFRPMVGYPSKWLDYSALEVHAGDLLGNARSSSELEWERDLRKIADGPDPEEWHITPQTV
+NAYYSPLENAIVFPAAILQPPFFDPEASMAANLGAIGAVIGHEIGHGFDDQGSRYDGAGR
+LEDWWTEEDRAAFTERTSRLVAQYNALSPAEAPDHRVNGEFTLGENIGDLGGLGIAHRAL
+EIWRDEGDGASLDAAAGDREFFTAWATVWRQLTRPEAMVTRIASDPHSPNEFRCNQVVKN
+IDAFHEAFGTREGDPMWLAPEERVTIW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000245.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000245.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aec1ea092a865cdfd60fa0bddf0f2d0302c8963
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000245.fa
@@ -0,0 +1,12 @@
+>0_97
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVNKGVDGAQEKFLSGDEGEQQA
+>1_2061
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHADTVNKGVDGAQEKFLSGDEGEQQA
+>2_274
+MGIGDLNNLANQHSDKINEAVDGAQEQHGDKLGEHADTVNKGVDGAQEKFLSGEKNEGEQ
+QA
+>3_221
+MVGFDDVKNLANENSDKINEQVDAAQAQHSDKLGQHADLADKGIDGAQDKFLNGQSAENE
+GEQQA
+>4_92
+MGIGDLNNLANQHSDKIDEAVDNAQEQHGDKLGEHGDTVDKGVDGAQEKFLSGDEGEQQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..702e12a3731f7cbb8b8dfd9adaecd097183fd860
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000252.fa
@@ -0,0 +1,40 @@
+>0_105
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>1_2069
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
+>2_266
+MSTAIDDVSTRQDTPPSKHRQNSLTAGQKPGWVWMAIAAAAVLLGLGIEALLSGAAPFSE
+DFSLARFVVLAGVLYIAGMYLVTRVMENRRRASDGLWKNLVWTAFLIALVPLVSVIWTVL
+EGGGPTLLSNPQVLWNDMDGVTGATDAAYDQAGSPAGGLPGGFAHALIGTLVITIIATLI
+AVPIGLLASIYLVEYGRDGWLSRAITFFVDVMTGIPSIVAGLFAYAAMTVLLELIMGPGP
+AALQAVKMGFTAAVALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLP
+TAISGIASGVTLAIARVTGETAPILVTAGYAMTTNWNAFDNWMTALPVYIYRQIVSPTSP
+TAADPSMARAWSAALVLIFIVMALNLLARVIAKAFAPKTGR
+>3_208
+MSTALNDTPTRENTPASKHTQNSLTAGQKPRWTWMAVAAGAVVLGLGLEALLAGGFADFS
+IARFIILAAILFVAGMYVATRVLENRRQATDGLWRNLVWAAFLIALVPLISVLWSVVADG
+GATLFGNPQLLVNDMQGVTGVTDAQYVQAGEPMGDLPGGFAHALVGTFLITVIATVIAVP
+IGLLTSIYLVEFGRDGWLSRAIIFFVDVMTGIPSIVAGLFAFAAMSVVLEMVMGSGPKAL
+QSVKMGLTAAIALTVLMIPVVVRSTEEMLRVVPNELREGSYALGVRKWRTIFKVVLPTAI
+SGIASGITLAIARVTGETAPILVTAGFASAVNWNPFDNWMTALPVYIYRQLVAPTSPTAM
+DASTSRAWAAALVLIIIVMVLNLLARIVAKAFAPKTGR
+>4_100
+MSTVSTSPRATEDSVTPRRHSLTEGQKPGWTWMAVAAAAAVVAAGLTVLLSGAFNVVGFV
+IIAAILYIAGLYVATRVMENRRRAADGLCRNLVWLAFLVALVPLVSVLWSVLSAGLPTLI
+ANPQIMAYDMKGITGIDDSAWVEDGKPAGGLAGGFGHALIGTVVITIIATLISVPIGMLT
+SIYLVEYSRGGWFSRAIVFFVDVMTGIPSIVAGLFAYAAITWVLTLVTGSKSTALQSVQM
+GLTAAIALSVLMIPVVVRSTEEMLRVVPNELREGAYALGVRKWQTIAKVVLPTAISGIAS
+GVTLAIARVAGETAPILVTAGFATSINWNPFDNWMTALPVYIYRQLVAPTSPTAADPSTA
+RAWAAALLLVTIVMLLNLAARFIAKAFAPKKGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e71760b5495abed52cd1ed161d43661a702b6970
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000259.fa
@@ -0,0 +1,45 @@
+>0_112
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDREHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSVVGALAGLAIHGV
+ATLFL
+>1_2076
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
+>2_256
+MSLSPDPARQLLSAGTLERERGLRRMKAVALGLLVALAVVFAVAFPLQDVHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGIPVPHTALIPRKKDQLGAALTEFVQENFLDSDVARE
+KVEGLEVAAAAGGWLRRPENAERAAREVATAARGAMAAADDDAVQELLRQLMQRHMVEPE
+WSPTLAGVLQDVVTGRHHERVVDLVVEHTGDWVAAHPEMFVETVRRRSPEWSPDLVDRLL
+AERLHAEALKYLAGIRDDRDHEARRAVDDWLTRLSAEMRDDPHTRASVERFKHSLFADER
+LRAWAGRAWTSLRDSLLDALEDPASDLHRALVAALRDLGARLQEDPVLRDRVDGHARAAA
+AYALSTYGPAVTGVIEETVARWDGDQTARTLELFVGRDLQYIRINGSIVGALAGLTIHAV
+ATLFL
+>3_188
+MAPSPVPADSPFPLTPAALERAAGLRRMKAVALGLLIVLAVVFAVAFPLQRVHPAWGFVR
+AAAEGGMVGALADWFAVTALFRRPLGLPIPHTALIPEKKDQLGAALTEFVQENFLDSDVA
+REKVAGLQVARAAGGWLRERPHAVHAAGEIAMAARGAVAATDDDAVQDLLQQLMQRHMVE
+PDWSPTLAGVLEDVLAGRHHEKVVDLVVEHTGDWVATHPEMFLETVRRRSPEWSPDLVDR
+LLAERLHAETLKYLAGVRADRDHEARRSVDDWLARLAGNMRDDPATRASAERFKADLFAD
+EQLRAWAGRAWITLRDSLLAALEDQDSDLHRALVDALVDLGVRLQEDPALQASVDGRARA
+AASYALSSYGPALTGVIEETVARWDGRQTADTLENLVGRDLQFIRINGSVVGALAGLAIH
+TLASLVF
+>4_117
+MSLSPDPAQQLLSAGALERAAGLRRMKAVALGLLILLAVVFVVAFPLQDTHPVWGYVRAA
+AEGGMVGALADWFAVTALFRHPMGVPVPHTALIPRKKDQLGAALTEFVQENFLDSEVAHE
+KVDGLKVAEAAGGWLRREENAARTAREIATAARGAMAAADDDAVQELLRQLMERHMVAPD
+WSPTLAGVLEDVVAGRHHERVVDLVVAHTGDWVAAHPELFVETVRRRSPEWSPDLVDRLL
+AERLHAETLKYLAGIRRDRQHEARRAVDDWLDRLADEMRNEPATRASVERFKRNLFADER
+LRAWAGRAWVSLRDSLLDALEDPSSDLHRALVAALRDLGARLQEDPELRDRVDGHARRAA
+AYALSSYGPALTGVIEETVARWDGEQTARTLELFVGKDLQFIRINGSIVGALAGLAIHGV
+ATLFL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000261.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000261.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c2654c4eb2fdc5d88636e6e67f4f0a7855aacaa1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000261.fa
@@ -0,0 +1,18 @@
+>0_118
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHSGELDGKLERLEAALAEDGNGDAADAR
+>1_2083
+MIVAFSVAPSGQPADSAHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGDWD
+EVMEVVRGAVDAVSSYGSRVSLVLKADIRPGHTGELDGKLERLESALAEDEGRRAAPAPH
+DGDAG
+>2_249
+MIVAFSVAPSGTPADAAHQPGDEDSASVHRAVAAAVAVVRESGLPHRTSSMFTEIEGDWD
+EVMDVVRGAVDAVAPYGSRVSLVLKADIRPGHTGELDGKLARLEAALASDDVS
+>3_183
+MIVAFSVSPSGAPADAAYAPSSDGDSASVHRAVAAAVAVVRASGLPHRTSSMFTEVEGEW
+DEVMGVVKRAVEAVEPYGSRVSLVLKADIRRGRTGELDGKLERLEAALTDGTPATPDRFR
+A
+>4_126
+MIVAFSVAPSGQPADAEHLPGDADTASVHRAVAAAVAVVRASGLPHRTSSMFTEIEGEWD
+EVMEVVRAAVDAVSPYGTRVSLVLKADIRPGRTGELDGKLERLESALAEDEGRRAAPAPR
+DGDAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000263.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000263.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b887da5ab9a9951db1a9b169c3c15fcbe4ee740c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000263.fa
@@ -0,0 +1,34 @@
+>0_120
+MSRRSGRSSGRSSAASSSSRGSAARRGRAAEPEGIVPGVHEISHGTAEIREDPYEPGAFV
+LYVNGVESSPLDPDHPERMGFEYMRWAVAAVRAHWPEPTPLRALHLGGAGCALARWVDHA
+HPGSHQTAVEIDAGLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAP
+DPTDLTGARHITPPGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFE
+HVEVIADPPMLKGRRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAE
+DPRGFPAGVAPGITGLVPGPEA
+>1_2085
+MSRRSSARRGRAAGGSAGPAGIEPGVHAITHGTAEIREDAFEPDAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
+>2_247
+MITPGVFAISSGTAEILPDPWTDGVYLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLAH
+RFAPDAERLRVLHLGGAGCTFARWVTHTWPQAHQLAVELDAGLAELARTHFDLPRAPQLK
+IRVGEAGQVLAGLREATREVVFRDVFAPADPLSLAPDSPHVTPAHLTGADAAAHAARVLV
+PGGVYVLNIGGGPDLASVRREVAALRTAFAHVEVMADPAMLKGRRRGNVIAAASSVPLAA
+EELGGRAALARALRSDALPAQLVDDVARFAGGLAPDPTPLVQASDGTSEGASTQASPGPA
+Q
+>3_181
+MITPGTFPISSGTAEIVPDPWTDGVFLLKVNGVESSQLNPDRPETLGFEYMRWAAAVLTH
+RFAPDARLRVLHLGGAGCTFARWVTHTYPASHQLAVELDAGLAAVAREHFDLPRAPQLKI
+RVGEAGEVLAGLRDATREVVFRDVFAPDPADPTGALHVTPAHLTGLDAAAHAARVLTPGG
+VYLLNIGGGPDLTSVRREVAALTETFAHVEVMADPAMLKGRRRGNVIAAASSAPLSADGL
+GGRSALARALRSDALPAQLLDDVVAFTAGLTPDATPLVTPAEG
+>4_128
+MSRRSSARRGRAAGGAAGPAGIEPGVHAITHGTAEIRENAFEPGAFILYVNGVESSPLDP
+ERPERMAFEYMRWAAAAVRAHWPEPTPLRALHLGGAGCALARWVDHAYPGSHQTAVEIDA
+GLAALARERFGLPRAPALRIRVADAAEVLATAHPASRDLIIRDVFAPDPTDLTGARHITP
+PGLTGLDAARAAARVLAPGGLYVLNVGGGPDLTSVRADVAAVVAAFEHVEVIADPPMLKG
+RRRGNVIVAASDAPVARPAADAPPGSDPRDRLARALRMDAFPARLAEDPRGFPAGVAPGI
+TGLVPGPEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000267.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000267.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7ac0fe53c68758a69d340affff7ac8de3ee7493f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000267.fa
@@ -0,0 +1,60 @@
+>0_125
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAAGRDRVLLPWVFWPSAVIVLSF
+VGATLLAPAQMTVGIGLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYVMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>1_2090
+MSDPTPPSTEPMIPEQPGNHPSSATAPDAGVAPATSAAADRDRVLLPWVFWPSAVIVLSF
+VVATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLFKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRPRLRRHEH
+>2_242
+MSESIPPSHPSAPPGPASAHPAAPAAGAADAREASGAVAPASSDAATGARVLLPWVFWPS
+TIVVLLFVGATLLFPEPMTAAIGTVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGAIT
+LGKPDEKPEFSTLSWFALLFAAGMGIGLVFFGMTEPLMHFVSPRPDLAATDPNPAQAAQA
+ALATTFLHWGLQPWAIYAVVGVAVGLAIHRRGRPLALRWAFEPLLGERRVRGGWGHLIDN
+IALIGTVFGVATSLGLGVTQMSAGLRSLGVVPEESAWVEYAMIGLVTLVVLYTVVSGVER
+GMKWLSNVNLVLAAGLLLFIAIVGPTAFLFKEMVQSFGAYLQTFFGASLNVSAFQGAEGD
+AWQAGWSAYYWGWWMSWTPFVGIFIARISRGRTVRQFLAGVLLVPTLIGVVWFGVLGGTA
+IYLETVRPDGYTSVVGADGSIDSNTALFQVVEQLPAGALLVIGAIMLSAIFFVTSADSGA
+LVMGMLATGGDVNPKVPVKIFFAIATALMSAALLAAGGLSAIQTLAITIGLPFSVLMLVM
+CLATFRSLGYSVARVEAVRRQAMLASIKDRFGLDTDDDEVVDGGPVAASQWWASLSRDRQ
+RTIAQAASAGPDDEIRLAGSSAEEPAGSPDARR
+>3_178
+MTPAPAGRDADAPAANRPHRTGPDPDVKHPAPATADQADRGHAGLLPWVFWPSTLIVLLF
+VVATLAFPAQMTDVIGDVQAAIIRNFSWWYAIVAFAFVVFCAYLVFSRKGSITLGKPDEK
+PEFSTMSWFALLFAAGMGIGLVFFGMTEPLMHFTSPRPDLAAANPTEAQAAQSALATTFL
+HWGLQPWAIYAVVGVAVGLAIHRRGRPLSLRWAFEPLLGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMAAGLRSLGIVPADSPWLEYAMIAAVTCVVMYTVVSGVERGMKWLSN
+INLVLAAGLLLFIALVGPTPFLLKETVQSFGAYLQNFFADSLNVSAFYGAEGDAWQAGWT
+AYYWGWWMSWTPFVGIFIARISRGRTVREFLMGVLLVPTLVCVVWFGILGGTAIWLETVR
+PAGYTSVVGADGAIDSNSALFQVLEQLPAGLLLVIGAIILSGIFFVTSADSGALVMGMLA
+TGGDVNPKTAVKIFFAIATAFMAAALLAAGGLSAIQTLAITIGLPFSVLMLVMCVATFRS
+LGYSAARVEAVRRQAMLASIQDRLGKDTDDDEVVEGGPVAASQWWASLSRDHQRTIARLA
+SPGPDDEIRLHEDATATSARPDTTRGGSTAR
+>4_133
+MSDPTPPLKNPLDPERADTRPSSAPTADGAVAPATSAAAARDRVLLPWVFWPSAVIVLSF
+VGATLLAPEQMTVGISLVQQAIITNFSWWYALVALFFVLFCGYLAFSRKGDITLGKPDEK
+PEFSTLSWFSLLFAAGMGIGLVFFGMTEPLMHFTSPRPDVAAANPTQAEAAQSALATTFL
+HWGLQPWAIYAVVGVAVALAIHRRGRPLALRWAFEPLIGERRVRGGWGHLIDNIALIGTV
+FGVATSLGLGVTQMSAGLRALGIVPEDSPWLEYAMIGAVTCVVLYTVVSGVERGMKWLSN
+TNLILAAGLLLFIAIVGPTAFLLKEMVQSLGSYMQYFFANSLNVSAFYGAEGDAWQAGWS
+AYYWGWWMSWTPFVGIFIARISRGRTVREFIAGVLLVPTLVCVVWFGILGGTAIFLETTR
+PAGYTSVVGADGAIDSNTALFQVLEQLPAGMMLVVGAIILSGIFFITSADSGSLVMGMLA
+TGGDVNPKATVKIFFAIATSLMAAALLAAGGLSAIQVLAITIGLPFSVLMLLICLATFRS
+LGYSVARVEAVRRQAMLASIKDRLGLESDDDEVVDAGPVAASQWWASLSRDHQQRIADAA
+AGVPASEGPRRTRLRRHGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000274.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000274.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9518e4b93c630b958eef0c38cd5c5b389d797bde
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000274.fa
@@ -0,0 +1,37 @@
+>0_133
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYIDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SEQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNSALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>1_2098
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
+>2_233
+MIDNAVYVDGRRVHAPSTLEDTWEAAEASGGMAWLGLYRPDADELRAVADELHLHPLAVE
+DALEGGERAKLDRYGEDLFMVLHFQHAIRALPVIVEQLQGGARARLREEEHRREVGAPRT
+GDVHEWDQDELSEEGVFEVENLRRLRDVHDHAVQINERVAAMRQMLANALELDSTLASKR
+LAEQSIEQNEQVKQISSWAAIIFAPQLVGSIYGMNFDGMPELHWAFGYPFALGLMLAVAL
+TLFVLFKRADWL
+>3_167
+MTLIDNAVYVDGRRVFAPTSLSDTWDAIERTGGMAWLGLYRPHPDELQEVADELPLHPLA
+VEDALTPGQRAKLERYGDDWFMVLHPARYIDATETVEFGELDVFTGKDYVVTVRHAEEPD
+LADIRAGMEQRHTDRLAQGPSQVAFEILDHVVDAYFPVAEGLEQDIREIEDQIFSGDAAV
+SRRIYELSREIIGFERATRPLPRMIEQLQEDMRARLGDAANGSHASHLEAPEPEPGEEER
+AELVETLRALRDIHDHAVQVTDRVAAMRQMLENALELDSTLASKRLAEQSIAQNEQVKRI
+SSWAAIIFAPQLIGSVYGMNFQHMPELEWPLGYPWALGLMLGVAVALYALFKKADWL
+>4_141
+MIDNAVYVDGRRVHAPSTLEDTWEECERTGGMAWLGLYRPDVAELQAVAEELRLHPLAVE
+DALAGGERAKLDRYGEDSFMVLHPARYVDRTETVEFGELSVFTGEHYVVTVRHAEEPDLA
+AVRRSLETEGRERLAMGPWQVTLEILDRVVDDYFPVADGLEQDIAEIEDQVFAGDGHVSR
+RIYELSREVLNFQHAIRALPSIVEQLQEEVRTRLHEDTRRLDADGLPRRDDAHAWEDEEL
+SDQARLEVENLRRLRDVHDHAVQINERVMTMRQMLNNALELDSTLASKRLAEQSIAQNEQ
+VKQISSWAAIIFAPQLVGSVYGMNFDGMPELHWAFGYPFALGLMLAVALTLFVLFKRADW
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b60ba6f91b7dc0adc8459e203cc5bf94ec408c82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000275.fa
@@ -0,0 +1,20 @@
+>0_134
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>1_2099
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLATRGPAVTGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
+>2_232
+MNSPRHAAPVVRDGRTLLPAHAVTTAPIAAFGLIGGYLTARETGIRPLGGVVLAAAGAYA
+GRTWLAKRGPAVAGGLTALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDREGA
+R
+>3_166
+MSKDTSTPVARDGKTLLPADAVTTAPIAALGLVGGYLVARETGIRWLGGVVLGAAGLYAG
+RTWAAKGGPAVAGTLGALYLGGFGASHPLAKKIGAWPSVLSVAAASAGAAYAAVDRKDGR
+R
+>4_142
+MKTPRHAPPVVRDGKTLLPAHAVSTAPVTAFGLIGGYLTARETGIRPLGGVVLAAAGLYA
+GRTWLAKRGPAVAGGLAALYLGGFGASHPLAKKIGAWPAVLSVAAVSAGAAWAAVDRSEA
+GR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cee56e28e8c2ca734ffe17b66ec2c6d444e2b46
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000276.fa
@@ -0,0 +1,23 @@
+>0_135
+MAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTE
+WAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGS
+TRSINAGVAAGIAMHAWIRQHAAVP
+>1_2100
+MLDHYRYWSLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRW
+NRRGAMVTDRYLHVRHHETVAAFTEWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFG
+QEGPGLSAEVRAASSAVLSIAQYGSTRSINAGVAAGIAMHAWIRQHAAVP
+>2_231
+MGPGTSENSPETREKREEREGREEREVGVGPWEGPWPEDPRYDPELLRDGDRRNVVDGYR
+YWTLEAIVADLDARRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHVIGRRRWNRRGAM
+VTDRYLHVRHHATVEEFTAWAAAEGLPVLGVDLFPESVPLESFELPRECVLVFGQEGPGL
+SEEVRAASAAVLSIAQYGSTRSINAGVAAGIAMHAWVRQHGGVPTSSS
+>3_165
+MGSGEGVDAREVGREVGAPPWEGPWPEDPRYDPALLRDGDRRNVADRYRYWTVEAIVADL
+DRTRHPFHVAIENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVHHH
+ETVEAFTAWAAGEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSEEVRAASEAV
+LSIAQYGSTRSINAGVAAGIAMHAWIRQHGGPAPV
+>4_143
+MPREVGVGPWLGPWPEDPRYDPELLAHGDRRNVLDRYRYWRLEAIVADLDARRHPFHVAI
+ENWQHDLNIGTVVRTANAFNAAGVHIIGRRRWNRRGAMVTDRYLHVRHHETVAAFTEWAA
+GEGLPVLGVDLFPESVPVETFDFPRACVLVFGQEGPGLSAEVRAASSAVLSIAQYGSTRS
+INAGVAAGIAMHAWIRQHAAVP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000278.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000278.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fdd6217c16c0d6ebeb9e27152138355ad1af32fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000278.fa
@@ -0,0 +1,35 @@
+>0_138
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKHSVNIALHTDHCPQDKLEDFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGENGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGR
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>1_2103
+MPIASPEKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVADGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
+>2_228
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAIRGFAEAGSDGIIQVSTGGAAYF
+SGASVKDMVTGSLAMAAFAREVAKNYSVNIALHTDHCPKDKLDAFVMPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGKELLARTHANKQILEVEIGVVGGEEDGVAHEINDKL
+YTTVEDGIATIEALGLGEQGRYLTALTFGNVHGVYKPGNVKLRPQILEDIQKAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYAGVLKVDG
+EVGDKKMYDPRVWGAKAEEAMAARVVQACQELNSAGTSIG
+>3_163
+MPIASPDKYAEMIDAAKNGAFAYPAINVTSSQTLNAAVRGFAEAGSDGIIQVSTGGAAYF
+SGSSVKDMVAGSLAMAAFAREVAKKYSVNIALHTDHCPKDKLDGFVKPLLDASEAEVKAG
+RDPLFNSHMWDGSAETLEENLRIAQELLARTHANKQILEVEIGVVGGEEDGVANEINDKL
+YTTVEDGIATIEALGLGENGRYLTALTFGNVHGVYKPGGVKLRPQILQDIQQAVGEKFGR
+QRPFDLVFHGGSGSAAQEIADSVSYGVVKMNVDTDTQYAFSRPVAGHMFENYDGVLKVDG
+EVGNKKMYDPRVWGAKAEDGMAARVVQACQELNAAGKSIG
+>4_146
+MPIASPEKYAEMIDAAKNGAFAFPAINVTSSQTLNAAIRGFAEAGSDGIVQVSTGGAAYF
+SGSSVKDMVAGSLAFAAFAREVAKKYSVNIALHTDHCPQDKLEGFVLPLLDASEAEVKAG
+RDPIFNSHMWDGSAETLEENLRIGRELLARTHANKQILEVEIGVVGGEEDGVAHEINEKL
+YTTVQDGIATVEALGLGEHGRYLTALTFGNVHGVYKPGNVKLRPEILQEIQQAVGEKFGK
+ERPFDLVFHGGSGSAAQEIADSVEYGVVKMNVDTDTQYAFTRPVAGHMFENYDGVLKVDG
+EVGDKKQYDPRVWGAKAEEAMAARVVQACTELNSAGKSIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..24b172131b004376847f3b377f35afbe5a04e69a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000285.fa
@@ -0,0 +1,25 @@
+>0_146
+MATPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVQDAWSQDGPQEEARDAQAELGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>1_2111
+MATPLLELAASRGVCFPLRTRRLTLTPFRGLDAPAVWSFCRLEQVWSWTSGRPESENALR
+ESYLGAGDRLTVRAGDVIVGVGKVAVRDAWSQGGPREEGRDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFDDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
+>2_452
+MATPLLDLAARRGVVFPLRTERLTLTSFAADDAPAVFDFCRLEEVWTWTSGRAGSAGELR
+ESYLAAGDRLTVRAGEAIIGVGKLAVQDAWSQGGPREEARDAQAEIGWTIHPTHADQGYA
+TELAGALLKLAFTGLGVHRVEAEAFADNAPTLRVMEKVGLRHEGTFREESLHLTRGWVDG
+VTYAMLASEFLARV
+>3_403
+MATPLLDLAARRGVAFPLRTERLTLTPFTAVDAPAVWDFCRLEEVRTWTSGRAGSAAELR
+EEYLATGDRLTVRDGAGDVVGVGKLAVQDAWSQGGPHPDARDAQAELGWTVAPEHAGRGY
+ATEIGRALLDLAFRGLGVRRVEAGAFADNAPSLRVMAKIGLRHEGTFLGESLHLTRGWID
+GVTFALLASEYEGGAAASRA
+>4_159
+MAPPLLELAASRGVCFPLRARRLTLTPFRGLDAPAVWGFCRLEQVWSWTSGRPESEGALR
+ESYLAAGDRLTVRVGDVIVGVGKAAVQDAWSQGGPREEARDAQAEIGWTIDPRQAGQGYG
+TELARALLGFAFNDLGVRRVEAHAFADNAPSLRIMEKVGMRHEGTFKEESLHLTRGWVDG
+ATYAMLASEFHSPLTQE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000289.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000289.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7af42c04fbffd54e81db0ba3435b466e572f73c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000289.fa
@@ -0,0 +1,70 @@
+>0_172
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADPEAVDPRVIKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTE
+LLPAHRVWDRFPTTGRLAD
+>1_2119
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPSLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVSRLTD
+LLPAHRVWERFPTTGRLAD
+>2_211
+MTTQQPDIPGTPGPRTPDLEERTAPTSSDDAAMPAPDQRGPASVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GMFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDTEEQMFEGIDLLDPTKLVPEELVPVQPLGRMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLAQ
+QVADGLGIPVPAPTETPADVQPSPVLSQIGGVWPLDGRQVGVVVGESVDEKELDALVQGI
+HGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDEKAGA
+AASEAVDPRVVKVLQEMWRHSKAILALEPAEGVLAAAQVSGKGVESAADGASAVSRLTEL
+LPAHRVWERFGTTGRFAD
+>3_156
+MAEQPKIPGTPGPITPDLEEHTALTDPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAAQ
+GCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGAH
+GVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGTW
+DLVGNNMPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTIWN
+MSDRGIPRSFRMMEGFGVHTYRLIAADGSTVLVKFHWKPKLGVHSVTWEEALITNGADPD
+YHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELVPVQTLGLMTL
+NANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWTQLPINR
+PHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHALIEHPEPLPASVKERA
+HAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEETIRVRQLQNLGAIDPRLAQ
+QVADGLGMPVPAPADAPADVQPSAALSQVGGTWPLDGRQVGLVVGPQVDEKELGDAVQGI
+HGAGMVPLVIAPKGGPVAGEVVAQRAYLTAASIELDAVVVLGATPPAGDAQHGLDAKAAA
+DAPDAVDPRVAKLVQEAWRHAKAIVAVGEGTSVLDELGLTGTPGVLTVDAGADAVAQLKE
+LMPAHRVWERFPTTGRLAD
+>4_169
+MTTQQPDIPGTPGPITPDLEEHTALTHPDQPVAVPAPDQRGPAQVSPTGQDTGADPATAA
+QGCPYLTTAHGVRLQDSDHSLKAGRRGPTLLQDHHLREKLSHFDHERIPERVVHARGAGA
+HGVFRGYGTAAKISRAGLFAKDKETEVFVRFSTVAGSRGSMDLARDTRGFATKFYTDEGT
+WDLVGNNIPVFFVQDAIKFPDVVHSVKPHPDREIPQAQSAHDTFWDFVSLHTEAQHHTLW
+NMSDRGIPRSYRMMEGFGVHTYRLIAADGSTVLVKFHWKPMLGVHSVTWEEALLTNGMDP
+DFHRRDLADAIEAGAFPEWELGVQVFEDNEEQMFEGIDLLDPTKLVPEELAPVQPLGRMT
+LNANPSNYFAETEQVAFNPANLVPGIDVTNDPLLQGRLFSYLDTQLTRLGGPNWNQLPIN
+RPHAPVNDMLRDGFHQSAVHRGVAPYRPNSLDGGLPYETPADDHAFIEHPEPLPASVKER
+AHAASFDDHFSQARLFFLSLSEVEREHVAQAYTFELGKCYEQTIRERQLAHLAAIDTRLA
+QQVADGLGIPVPAPTETPADVQPSPVLSQIGGAWPLDGRQVGVVVGESVDEKELDALVQG
+IHGAGMVPLVIAPKGGPVAGEIVAQRTYLTAASIELDAVVVASPAAPAADAAPGLDQKAG
+AADSEAVDPRVVKVLQEMWRHSKAILALEPAEAVLAAAQVSGKGVESAADGASAVAALKQ
+LLPAHRVWDRFPTTGRLAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000293.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000293.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a4cc9655de4389210a9bc13ed3144392eba489f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000293.fa
@@ -0,0 +1,55 @@
+>0_176
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKNDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
+>1_2123
+MAEGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLQGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRVPMEATIRD
+>2_207
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVFRTNKWAPRVLIANSNLVGDWATWPEF
+RKLEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGACLIVDVSEGRLRRRMGKRYLDEVVTDIDKAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKRGEIEIDIVTDQTSAHDPLSYLPIEIDEADWQAEAEGDPETF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEIAAERGVRVPMEATIRD
+>3_152
+MAAGFTQHDPSRTIRAPRGTELNAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAFDAIVETLKDLEEDETLLVQSGKPVGVFRTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKKYDGTLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEERLRRRMGKRYLHEVETDIDAAIARVMQAKRDGEAVSV
+GLVGNAAEVFPELLKRQKAGEVEIDIVTDQTSAHDPLSYLPIEIEEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDEALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGLADGTELAAAKLTALLTNDPGMGVIRHVD
+AGYSRAVEVAAERGVRIPMEPTVRD
+>4_173
+MAVGFTQHDPSRTIRAPRGTELSAKSWQTEAPLRMLMNNLDPEVAERPEDLVVYGGTGRA
+ARSWEAYDAIVATLKDLEEDETLLVQSGKPVGVVKTNVWAPRVLIANSNLVGDWADWKTF
+RELEAEGLMMYGQMTAGSWIYIATQGILQGTYETFAAIGRKRYDGSLKGTLTLTGGCGGM
+GGAQPLAVTLNGGVCLIVDVSEDRLRRRMGKRYLDEVETDIERAVERVMQAKRDGEAVSV
+GLVGNAAEVFPELLERQKAGTVEIDIVTDQTSAHDPLSYLPIEIDEKDWHAEAEADPDTF
+TKKAQESMARQVEAMVGFQDIGAEVFDYGNSIRDEARKAGYSRAFEFPGFVPAYIRPLFC
+EGLGPFRWAALSGDPEDIRVTDAALKELFPENEHLHRWLDGAAEFVEFEGLPARICWLGY
+GERHKAGLLFNQLVAEGKVKAPIVIGRDHLDSGSVASPYRETESMLDGSDAIADWPLLNA
+LTATSSGATWVSIHHGGGVGIGRSIHAGQVGVADGTELAAAKLEALLTNDPGMGVIRHVD
+AGYSRAAEVAKERGVRVPMEATIRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000296.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000296.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c90567c6e383ed5fdd92da12e4c80d82e25903e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000296.fa
@@ -0,0 +1,50 @@
+>0_179
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>1_2126
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGEDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
+>2_204
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAWKSEGTEAEGH
+>3_149
+MTTTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGVSTG
+FGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVRPVV
+VETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGADGALRPAGEALAE
+AGIEPVELREKEGLALVNGTEGMLGMLIMALADLDELVDTVDLTAAMSVEALLGTDRVFV
+PELHLPLRPHPGQAASADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLRDTL
+AYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSERRTD
+RMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQEDH
+VSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGVPGP
+GPDQYMAPQLAAAEQALRDGSVLAAVAEALAGASADAEPQDLAEESAGAEAEGH
+>4_176
+MTTPPVTVTLGTSGATLDDVVAVARHDARVVLADDVLETVGAVRRHVEALAEAETPTYGV
+STGFGALADKHIPLESRAQLQKSLIRSHAAGMGPVVEREVVRALMFLRATTLASGRTGVR
+PVVVETFVAMLNAGITPAVREFGSLGCSGDLAPLSHVALALMGEGDVVGTDGALRPAGEA
+LAEAGIEPVELREKEGLALVNGTEGMLGMLIMALADLEELADTVDLTAAMSVEALLGTDR
+VFVPELHLPLRPHPGQATSADRMLKILAGSPIVASHKEGDSRVQDAYSLRCAPQVAGGLR
+DTLAYVRTVAERELAATVDNPVVLDDGRVSSNGNFHGAPVAYVLDFLAIPVADVASMSER
+RTDRMLDPARSHGLPAFLVDDPGVDSGMMIAQYTQAGLVSDMKRLAVPASVDSIPSSAMQ
+EDHVSMGWHAARKLRSAVENFRRVLAVELVAAARAIELRAPLQPSAATGAAVRVIREAGV
+PGPGPDQYMAPQLAAAEQALRDGSVLAAVAEALAGVSADAEPQDLAEESEGAEAEGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00ae6ee0a2f6882af6cb05d46e7ba51e227f95b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000297.fa
@@ -0,0 +1,36 @@
+>0_184
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTPQRDPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVAAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>1_2131
+MTSELPSPSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTVVSRHRTDASLLA
+>2_198
+MTSELPSPSLSSAWAGRTDGDAPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALVGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGEGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRVLFDTAREHGVTWVTDE
+QAQIADVTGVRRWVRSFIDAVDVLYLTVDLDVLPAAVAPGVSAPAGFGVPYEVIHACAVE
+AATSGKLALADVVELNPSLDVDGRTAKAAARLIHTIVSRHRTDASLLA
+>3_145
+MSGVVRPSLRTRPSMAWNGAMTADRASELPSAALSPAWTGRTDGDAPEHLRWHQVVRSAD
+GGAPAQTVDAAPARSTALVGFASDEGVRRNHGRVGAEDGPDALRGALASLAYLEGTGALV
+DAGDVSVDRGDDDAPGELEAGQAELATVVSGLLNAHDLAVVLGGGHETAYASITGLTGST
+RVAAGTRVGILNLDAHFDLREAPRPSSGTPFLQALRDAEEAEHQLSYAVVGISEANNTRA
+LFDTARERGVTWVTDEQAQTADVTGVRRWVRSFIDAVDVLYLTIDLDVLPAAVAPGVSAP
+AGFGVPYEVIHACTLEATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDA
+SLLA
+>4_184
+MTSELPSSSLSPAWTGRTDGDTPEHLRWHQVVRPADGRGEPTTTQRHPGAGAPTSGARST
+ALIGFASDEGVRRNHGRVGAEDGPEALRGALASLAYLEGTGALVDAGDVSVDRGDDDAPG
+ELEAGQAELGTVVSGLLNAHDLAVVLGGGHETAYASITGLTGSTRVGAGTRVGILNLDAH
+FDLREAPRPSSGTPFLQALRDAEGAEHQLSYAVVGISEANNTRALFDTARERGVTWVTDE
+QAQTADVTGVRRWVRSFINAVDVLYLTIDLDVLPAAVAPGVSAPAGFGVPYEVIHACALE
+ATQSGKLALADVVELNPALDVDGRTAKAAARLIHTIVSRHRTDASLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000301.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000301.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1935c90b650c4574b0ee9dc060858f25ed183abc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000301.fa
@@ -0,0 +1,20 @@
+>0_188
+MPDDVAVRLLLIADTHIPRRARALPAQVWAEVARADVVLHAGDWVTEDVLDDLDARAARL
+VGVWGNNDGPKLRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPDTANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVSVDRTP
+>1_2135
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
+>2_193
+MTTETRLLLLADTHIPPRARAMPAQVWDEVARADVVLHAGDWVEESVLDELEARSRRLVG
+VWGNNDDGALRARLPEVARVEIGGVRIAMVHETGAARGRERRMAEAFPDADVLVFGHSHI
+PWDTVAGPETANPGLRLLNPGSPTDRRRQPVCTLMRAVVRDGGLADVELVPVDRTP
+>3_141
+MTTRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDAQAARLVGVW
+GNNDGPRLRARLPEVARVEIGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHSHIPW
+DTVAGPETANPGLRLLNPGSCTDRRRQPVCTLMRAVVRGGRLEDVELVPVDRTP
+>4_188
+MPDDVAVRLLLIADTHIPRRARALPAQVRAEVARADVVLHAGDWVAEDVLDDLDARAARL
+VGVWGNNDGPGPRARLPEVARVELGGVRIAMVHETGPAAGRERRMAAAFPDADVLVFGHS
+HIPWDTVAGPETANPGLRLLNPGSCTDRRRQPVCTLIRAVARDGRLEDVELVPVDRTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000307.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000307.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6883bc6c778256cb52edf99e259ac0798a7760a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000307.fa
@@ -0,0 +1,30 @@
+>0_201
+MRQRQTQTRRTRRGLSLAALGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDAVDISGPVDGSSMRYVSVYKDDGLITRDESRIVDGTAYSRFTVERVGA
+SGEDHPAYAERWTATPYEGDPSATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>1_2145
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVELTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGGVDPVQAPPA
+DEVLKQDG
+>2_172
+MPRQNPTGRARRGLPLAALGAAAALVLTGCGASGEDASAAWDRARTQLEETDSVRMVTEL
+RSDAPQAGNRTPESVDLSGPVDGSSMRYVSTYEDGDLITRDESRVVDGTAYSRFTVERRG
+ASGEDRPAYVERWTAAPHTGDPRATGMGAMVSSLLGSLPESGGLEDVAVDADGIRRSGQD
+AVRYVLDEPLSVADDGVAMTAFTVSEEDGRLLTVETESAGTKAVVTVSEMGDVEPLQAPP
+SDEVLPQQQGQGAPGAVPPGGAPQDGTAPGGTPAEPVPPTDG
+>3_118
+MRPTTPRTPAPHGGARRRALSLAALGAAAALSLSACGASGEDASAAWDAARTQLQDASSV
+RLTTEARNDSGAAPGTPDGVEIAGDVHSSDLSYTGVFRTDGYITRDESRTVGGQRYERFT
+LEQPGGVSGEGRPAFAEKWKKAEPLPGDASMRSILDGVLTAVPQAGALQGADVRATDIRR
+QGRDATRYVLDTPVKGGTTDSSLTAFTVADDDGTLLTVETTGPGTRGTVTFSDWNAVEPV
+TAPATEDMAQDTATAK
+>4_201
+MRQRQTQTRRTRRGLSLAAVGAAALLLTGCASGDDAPGAWDRARTQLEEADSVRMVTELR
+SEAPSNGRAVPDSVDISGPVDGSSMRYVSVYQDDGLITRDESRIVDGTAYSRFTVERAGA
+SGEDRPAYVERWTATPYESDPRATGMGAMVSSLLGSLPESGGLDDVEADADGIRRSGQDA
+IRYVLDEPVSGPQEGVALTAFTVSKEDGRLLTVETESAGTKAVVTLSEMGEVDPVQAPPA
+DEVLKQDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000311.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000311.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96fba9212986d9b65cb82b79a401d8d9afa2625a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000311.fa
@@ -0,0 +1,15 @@
+>0_205
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>1_2149
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGKVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
+>2_163
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDAVLDQAR
+RAAEELLSNPVIEDVVNVAVLDEAEGAR
+>3_112
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTEEVLAAAR
+TAAEEMLSNPVIEDVVNVAVLDEDAA
+>4_205
+MPIIVVDVMPKPEILDPQGKAINGALPRLGFTEFSQVRQGKRFELTVEGEVTDEILAQAR
+TAAEEMLSNPVIEDVVNVAVLDEAEGAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26320cca95dc941312964fa097c3a51b3ca97c99
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000325.fa
@@ -0,0 +1,39 @@
+>0_225
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPASDADTSASVSTMPITSTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAAEGSRSAEPAAPAAPADVEGDVVTVESIS
+DGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGDTVVLRYDR
+RLYDRYDRLLAGVYADGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQARANGVGRF
+SGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSGIYHMPGQQ
+HYGKTNARHCYASASAAQAGGYRAARR
+>1_2189
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESAADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSSAAQSSRAAASSSSGAAESRAARAAEESRTAEGSRSAEPAAPAAPADVEG
+DVVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETRHPSKPVECMGPEATAALKSMISPG
+DTVVLRYDRRLYDRYDRLLAGVYADGVLVNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQ
+ARANGVGRFSGECGAAAEPIPEAAPAPAPEAAPASGDAGPVRGADSVCPDSHPVKANDNS
+GIYHMPGQQHYGKTNARNCYASAAAAQADGYRAARR
+>2_128
+MTPRLFPRAGLVAAAALSLVLTGCTPAASGDDVAAPASAGAPSSGAAATTAAPAVSSTAS
+AEAADRSRAAESSRAAAQASEAEQSRRAEESRAAEARRAEESRAAEASREAERSRRAEES
+RAAAAAAAEEEDLDAAGSAEDAAWGGTAGVEGDVAVVQSVADGDTLRVSLDGVSTPVRLL
+NIDTPETVHPSKPVQCQGPEATAALKSMIGPGDTVVLRYDRRVYDRYDRLLAGVFADGRL
+VNAEMARLGLGEPVVFDGNVRFLPEVEAAWEQARADGVGLFSGECAVEEAPEPVEDEAPT
+AVAEPAPAPAAGSGPVPGADFVCPDDFPVKGNDNSFIYHVPGQQHYGRTNARNCYASAAA
+AEVDGYRAAKR
+>3_93
+MPSSRPPAPRVRTRLLVSAALVLLAATGCTASPATSSSTSSTSSAAPAALAASASPPASG
+ASSAAAVEGDAATVVRVVDGDTVDVRRGAEDVRVRLLNIDTPETKHPSRPVECLGPEATR
+KLEELLRPGDEVVLQYDEERFDRYGRTLAGVVEGETLVNAEIVRAGLGVPVVFEPNRRFL
+PPVEAAWAEAQREGAGLNQPGLECSLQTLQESVAQDPAPAAVSELAQALEAVEAEGQEWM
+KVHYAAVIPLAVSLVQQHGGRADVPSAGAASVAPRASTAPAVPAAPQAPAVGAGSDAAER
+DRQRAAEAQAAADRAERKRQAEARAEAQRQAQAQEQVQARERAAQASREAEAAASAREKQ
+KGASSGSSTAKGFADTSARDTSSGSPSSSGGTSQKAPNRCYAPGGETFVYCGEGSTGSSS
+GGSSSSASAGASSSGAGTSSGGAGGPVSGADGVCPAGYPVKVSSSGKYHVPGGQYYDDTS
+AKRCYASTAAAAADGAVASKR
+>4_226
+MPLARLRAALPAAALSLLLLTGCTATDDGVTPESDADTSASVSTMPTTPTPSVDAAATSR
+AAASSLAASSAAQSSRAAASSSIEAAQSRAARAAEESRTAEGSRSAEPAAPAAPADVEGD
+VVTVESISDGDTLRVTLGEVSTRVRLLNIDTPETHHPSKPVECMGPEATAALKSMISPGD
+TVVLRYDRRLYDRYDRLLAGVYAEGVLLNAEMARLGYGEPAVFDGNDRFLPEVEAAWEQA
+RANGVGRFSGECGTAAEPIPEAAPAPAPEAAPAAGDAGPVSGADSVCPDSHPVKANDNSG
+IYHMPGQQHYGKTNARHCYASASAAQAGGYRAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000333.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000333.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7009a760131e174a2bc8f319097031a753ab24f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000333.fa
@@ -0,0 +1,43 @@
+>0_237
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPVNRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>1_2200
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYAEVLPLLEVMGARIVHCGAAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
+>2_114
+MSEKTATTTTAPVIPHFVHGERVDGSSGRHSDVYHPATGQVEGRVPLASVEEIDAALASS
+EKGFAAWSALNPQRRGRILLKWVDLINENVDELATLLSQEHGKTVPDAKGDIQRGVEVVE
+FAAGAPHLLKGEFSSNAGSGIDVHSIRQPLGIAVGITPFNFPAMIPLWKAGIALAAGNAF
+VLKPSERDPSVPVRLAELALEAGMPAGALNVVHGDKTAVDALIEDPRVKAVGFVGSTPIA
+QSIYAHAGRMGKRAQCFGGAKNHAVIMPDADLEMAADALVGAAFGSAGERCMAISVAVPV
+GEETADRLVALLSERIRRLKVGPSLDESSDFGPVVSKDAKERIEGYIAAGAAAARRPGRG
+RPRRRRRGPRGRLLRGRHPLRPRHRGHEHLPRGDLRPGALRGPRRGLRGGAHPRQRARVR
+QRRGHLHPRRRRRPRLRHPRGDRHGGRQRADPRPDRLLHLRRLEGLRLRRPEPARHRRPE
+VLHQDQDHHHALALGRARGRQLRDARRLLTAVHPLPQEDPMTTVLFLGLGHMGGPMAANL
+AAAGHRVLGFDLVPEALEKARMAGIETVTDTAAAAAEADVVLTMLPNGRLVLDVYRGREG
+APGLLDAARPGTVFLDCSTIDVAEAREAAQAAEAAGMRAADAPVSGGQVGAEAGTLAFMV
+GAADEVYAEVLPLLEVMGGRIVHCGGSGLGQAAKICNNMVLGVTQIAVAEAFVLGERLGL
+EHQALYDVMSKASGQCWALTTNCPVPGPVPGSPANRDFQPGFAGALMAKDLGLALAALDE
+QGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHTDRSEA
+>3_83
+MSQSQTPSASLPGTVAFIGLGNMGGPMAANLVAAGVTVRGFDLVPAAVEAARATGVEIAD
+DAASAVPGADVVITMLPNGALVRGVYEGTADAPGLLGAADPDTLFLDCSTISTSEAQEVA
+ALAEAAGHRAADAPVSGGVVGAQAGTLAFMVGGSVEVFEEIRPLLEVMGSRIVHCGGNGL
+GQAAKVCNNMLLAISQIGVAEAFVLGERLGLEHQVLFDVMSEATGRCWSLTANCPVPGPV
+PTSPANRDFEGGFAGALMAKDLGLALKALDEQHVGAEMGRLAQRTYAAYADGEGARKDFS
+GIIETVREAGKDTAA
+>4_237
+MTTVLFLGLGHMGGPMAANLAAAGHRVLGFDLVPEALEKARAAGVETVTDTAAAAAEADV
+VLTMLPHGRLVLDVYRGEDGDGGLLAAARPGTVFLDCSTIDVAEAREAAAAAEAAGMRAA
+DAPVSGGQVGAEAGTLAFMVGASDEVYTEVLPLLEVMGARIVHCGGAGLGQAAKICNNMV
+LGVTQIAVAEAFVLGERLGLQHQALYDVMSKASGQCWSLTTNCPVPGPVPGSPANRDFQP
+GFAGALMAKDLGLALAALDEQGVAADLGRLAQAKYAEYAAGEGAARDFSGIIEDIRASHT
+DRSEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000340.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000340.fa
new file mode 100644
index 0000000000000000000000000000000000000000..063e0edc97668def08e88262525c4e80c6e16266
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000340.fa
@@ -0,0 +1,20 @@
+>0_252
+MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF
+GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG
+ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA
+>1_2216
+MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAILAVVPGLQAF
+GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG
+ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA
+>2_97
+MGLNGFLVAWLLPNLVMAALVAVLAVLPGLQAFGSLTPLLTVVGIAGLVVGLPLCLLVNF
+AFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAGILPMLIPVIGFPAAVLMALGRMAARPL
+VQVVTPGQEAEARSAAQTASPADPEPSERAARGA
+>3_67
+MTTPAPVKSTARARRKAARAVSGPRPRLRMGLNGFLVAWLLPNLLMAAVVLALTLIPSLQ
+RFGTLTPLLTVVGIAGLVIGLPLCLLVNRAFRHVLNQWVHVLAYALVGMLYGLVVLAQGV
+GGVLPMLIPVIGFPAAVLMGLGRLAARPLVDVVPGAEPRS
+>4_250
+MTTPAPVASAARARRRAARSGPRPQLRMGLNGFLVAWLLPNLVMAAVVAVLAVVPGLQAF
+GSLTPLLTVVGVAGLVVGLPLCLLVNWAFRHVLNQWVHVLAYALIGMLYGLVVLTQGAAG
+ILPMLIPVIGFPAAVLMALGRTAARPLVRTVTPEPSPAEPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000341.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000341.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3423d4fdc5565534cdbc50825aaf6abbe2d68c50
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000341.fa
@@ -0,0 +1,35 @@
+>0_253
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG
+GAVAAVALRTAGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>1_2217
+MKLPSPAPSAPGEVHHSASSVPVDGVEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTVLAAETANALHTAAIADGEVAPSPAARALRGLGGLAVG
+GAVAAVTLRATGLNDRIDGALVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDPVDEVEPEATAELPVEVRVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVASVAEAIREAGEVPDWVPLVVQTDDDVRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLAFHVDGDRRA
+>2_96
+MRQNSPVPGSLPARYVDDPAAAFPALRQRALAPGGRPYGLLAAAVVGALTLVDPHRMGAA
+ERRGLARTEAAASGAFVAAEAASSLRLAGLPGRVGPAAGGLAAGAATAALALSTVPLNDR
+IDGALVRFLERAGASAPRAVLAGTAALSVLAGNESVRRERRNALEEAAWPAWDDLSEEEQ
+SEPTAPLPVEVRVLLETLLDPALAEGRELPGAAALRAQLPHVRTVASMAEAIRDEDEVPD
+WTPLVVETDGPVDRAVPHDHVWPVRGRFAVGEDGHEVELRLQVIDGELGALVITLPADED
+ADPDAWDAFQELEAFPGVEDLTFQVDGERRD
+>3_66
+METPRTPETRTDPPADRLAEPQHPAHADAPVVHDTAVPESERIERTVSTRTGETRPPVVR
+TVVTESERIERPVVEVRDARVPGRLLWWIGGGTLAAGSLAALVRVLRERLATPEPTPLER
+LADAGRGAGLPLALSLAGTAAGVGVSLRARRRRRTEEVLAAPAVPFLLGEAVSAEAGEDD
+VDGLPPVNEASDAYPAGALETEALPLEVVVLLDTLLDPSLDEGRELPGAAALRAQLPHVR
+TAASVAEEIREDGKVPDWTPLVVEEETGVARAIPNDMVWPVRGRFTTEDGHELELRLQVI
+DGELGALVITLPEDVEDGVAAWDAFQELEAFPGVEELTFTVDGDRRP
+>4_251
+MKLPSPAPSVPGEVHHSASSVPVDDAEAVFPALRQRALAPGGRLYGLAAAAAVGGLTLLD
+PHARRGRERRALAELEAAVSGTFLAAETAGALHTAAIAEGEVAPSPAARALRGLGGLAVG
+GAVAAVALRATGLNDRIDGAVVRGLQRVGVPAPRVALAAAASLAMLLANEDARRTRRDAV
+ELAVTGPAGLDEDAVDEVEPEATAELPVEVCVLLETLLDPALAEGRDLPGAEALRSQLPH
+ARTVTSVAEAIREAGEVPDWVPLVVETDDDIRRAVPNDCVWPVRGRFASGSAGGHELELR
+LQVIDGEIGALTVTLPADAEADSDAWDAFQEIESFPGVEDLTFHVDGDRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e6140a25b74d414c275e3452ff6f2b74b312f15
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000349.fa
@@ -0,0 +1,45 @@
+>0_261
+MPDTPQPPAVPAHPDHFGFEVTHRLETPGHDGAPLGRTGVITTPHGRIQTPAFIPVATQA
+TVKAVLPESMKDLGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>1_2227
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
+>2_78
+MPDTSPGPAPSSSSSGAPAHPSHFGFEVTHRLEAGGVDGAPLGRTGVISTPHGQIQTPAF
+IPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTD
+SGGFQVMSLGSGFKKVIDMKGPSAPDGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRH
+RFTPEVSVGIQHRLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVR
+AARPYQALFGVIQGAQYEDLRRKACRDLAAMRADFPSAGELDGVTSGFDGYGVGGALEKE
+NLGTIVGWCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDG
+RFNLPGAKYRRDFGPLDPACDCYTCAHYSRAYIRHLFKAKEMVAHTLISIHNERFTVSLV
+DRIRAALQDGTYAELKEETLGRYYAPKG
+>3_55
+MPETSAPGTAGPTSSSAVTSDPAHPDHLGFEVRERLDAPGADGIALGRTGVLRTPHGEIQ
+TPAFIPVATQATVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGP
+TFTDSGGFQVMSLGSGFKKVIDMKGPAAPEGQGADDAVAPGKERLANVDDDGVWFKSHLT
+GDRHRFTPERSLQIQHNLGADVMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARL
+TAERAGRPYQGLFGVIQGAQYEDLRRKACRDLSGMTAEFAAAGERPATAHGFDGYGIGGA
+IEKENLGTIVGWCAQELPEDRPRHLLGISEPDDLFRAVENGADTFDCVSPTRVARTGAFY
+TRDGRYNLPGATYKRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLISIHNERFT
+VSLVDRIRASIQAGTFAELKAETLGRYYAPKG
+>4_259
+MPDTPQPPAVPAHPDHFGFEVTHRLETGGADGAPLGRTGVITTPHGRIQTPAFIPVATQA
+SVKAVLPESMAELGAQALLANAYHLYLQPGDDLLDEAGGLGAFMNWPGPTFTDSGGFQVM
+SLGSGFKKVIDMKGPGAPEGQGADDAVAPGKERLANVDDDGVWFKSHLTGDRHRFTPEVS
+VGIQHNLGADIMFAFDELTTLHNSRGYQEEALERTRRWAQRCLDEHARLTGVRAARPYQA
+LFGVIQGAQYEDLRRKACRDLAGMRAEFPAAGELDGVTSGFDGYGVGGALEKENLGTIVG
+WCAQELPEDKPRHLLGISEPDDLFTAVENGADTFDCVSPTRVARTGAFYTRDGRYNLPGA
+KYRRDFGPLDPECDCYTCAHYSRAYLRHLFKAKEMVAHTLLSIHNERFTVSLVDRIRAAM
+QDGTLAELKAETLGRYYAPKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfaeea08710a049a39a1e5a5c1663a2abd151fc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000353.fa
@@ -0,0 +1,15 @@
+>0_271
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>1_2237
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGLGR
+>2_64
+MPSYRARLQIGDLLPGHRPEEVMDLAEAAVQATHVLAAKDIEVVARVPRIVLRFTVPGSH
+RAGEDAEAAEVARRMAEAVSGVAATGRLDVLRRDGGRWVPVPAGPGR
+>3_50
+MPSYRARLQIGDVLPGHRPEEVLDTAEAAIGATHEVAAKDVEVVARVPRIVLRFTVPAAH
+RAAEDAEAAAVAGRMAEAVADVATVGRLDVLRREGGRWLPVSAR
+>4_270
+MPSYRARLQIGDLLPGHRPDEVMDLAEAAVQASHVLAAKDIEVVARVPRIVLRFTVHGSH
+RAGEDAEAAEVARRMAEAVSGVAVTGRLDVLRRDGGRWVPVPAGPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000354.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000354.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e03accf657cb52f402fe7a39dffb6578ef6cd8b7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000354.fa
@@ -0,0 +1,74 @@
+>0_272
+MQDASSESRAALERLRAASAPRPDDAETRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RSETAAERRVREDHRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRAAEHERPVAEAAAAAQARDAA
+RARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEEKARAAAEAEA
+RRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAERRRQAAEAERR
+RLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLHAERALAQARL
+LEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADRPLLSDPEERL
+TDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIPGYTPAPPEEP
+AGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLTADGRHGPGAS
+VFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLALALWFPLAVL
+APGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLLAGAPTAVGAA
+LHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLLCLALPRLLPS
+PLGAQQSVWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>1_2238
+MQDASSESRAALERLRDASAPRPDDDATRAPAERPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAQQRPRRDLSEILDRLGSPDLARFTDPLV
+GTVERILPAPGRDPEKAAEAARRRTAAEERRRARLRAGRERAAEAARRRAAEHERPVAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAYTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVRAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTAADRRGQALLTVVWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGRGQGASPRHRRIRGAIAGALLA
+LALWFPLAVLAPGGFDVVPWLLALVLMLRVVRRLGARPAARRVARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVGWFPTELLALLVLVALLLAALRLVLGGRGRMGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
+>2_63
+MQDPSSESHAALERLRGAPKPVPAPEEAAGAPRTPDQDDDGAATAEDPVPAAARTPADDP
+APAPSPSPPQDAETAPAPDASPASDADAPADVEADVEAPRPARRATPPRPRRPRPDLPPR
+PAPPRARPAHRLSPRRPMRGACARAAARTSTRRWSGRAPPAPPRSSAPRRDLSDILDRLG
+SPDLARFTAPLVGTVERILPAPGADPQKAAQAARRREEAEARRRARLQSGRERAAESARR
+RAAEHDRLAAEAAEREAALRDDDARSEARRADEEAAAAKEACRQERLRERRTAGRAAAEE
+RARLAAEAVEADRERERREAEEAAAAAAREEAALQARLQEEARARRERAEQEERLAQERA
+AEEARLAQAARIARRRREEERERQRREAERRRRLAQEAKARAAADQEKRRQQEQERRRRE
+AKVAEERARVQAERRAREEAELAERERRRLEAEAEAERRRQAQEAERRRREAERAEAERR
+ARAEEAERRRREAEEAARRAAEARRLHAERTRAHTVLHAERALAQARLLEDRARDAERRA
+AEEEARRLREHQDRESRALYRAARELEGPEVIPAASQRPLLARPEEGLTDEELVARARQA
+LPEWRHRQRLATKARAVGAETAAGRSAGPPTGPVPLIPGYTPAAPEEPAGPATVRDRRGQ
+LVLTLAWAAFVLAGVWGLGLFRFVPGLDALDAGPYPAAGDGRHGSGATVFSLFPLHPVIW
+PVLWLLTGLHVARQWGPGQGAAPRHRRTRGPMAGTLLALALWFPLTVLVPWGLESVLWLV
+ALALMLGAVRRLGARPAAGRLARLAEDGAPGALLGTLLAGAPTALAATLHAWGVHVGRFP
+TELVAALVLLTLLPGAVRLVLGGRGRMGVAVGMAWTLLCLALPRLLPSPLGAQQSAWVGF
+AAAFGALLLLTAAAVRRSWVRQIERDAARRPPPAVA
+>3_49
+MTSQDDDAPRPAPPAPRHAARPRRALAEPGRLAPEQLERHTRRLRGEPLPPETPEEAAAR
+AGRRHDLAAALDRLPAESAPAAPRPRADLSDLLDRIGTPDLARFADPLLGTVGRILPSGP
+SPERAAAAARRRAEHEGRRRAERAAGRARAAEAARRRAEETARREAEAAERARAARTVEE
+SRAEAVRAAEDAAREAERHRAERLRERREAARAAAADKARRVAEAAERARVEEEALLAVE
+ADAQAREVAAAQAEPDALARERRERADQEERRRRAALLARRRRDEERRRRRREAERARRE
+AEEQRERAARAERSAAEAARRRQAEEAAEAERRQMAVEAARARAEAERLAQEAARERRRR
+IAAARALPRTVAARHIAAGTAAEDRRRQAAARASEEAARVLAAHHDRETRALMAAARELD
+GPDVVPPAHLRPLLADPAEGLDDAALLERARAALPQWRRTGRLLTKADAVRAQTAHGAAD
+GTGPATGAFPIVPGYVPPSGPPEPRAPATREDRRHQLELTGAWLLFVLASAWGLGLFRLV
+PGLRVVDQGSYTAAHGGRYAFTTSVLSLFPLHPAVWPVLWLALGVYVAHQWGPGQGAAAR
+QRQTRRSVAGALALTALWFPLAVLVPWGLEFMVWLAALALMIRVMRGLTAVPARTRAAQT
+CTDGVLGGFLGLLLAAAPTTLASPVAATGVFWGWFPSALVAAALLWAVVLTGARLALQDR
+GRLGLALGMAWTLLCLALPRLLPSPLGAWQSAWVGLSAVAGGLGVLLLVVVRRTWVREIE
+EQAAAAPQGVPAGRVNGR
+>4_271
+MQDASSESRAALERLRGASAPRPDDDATRAPAARPRRALAAPGEISRRDLRRHERALRSG
+RPETAAERRVREDRRADVHRAMDRLRTPGAPAEQRPRRDLSEILDRLGSPDLARFADPLV
+GTVERILPAPGRDPEKAAEAARRRAAAEERRRARLRAGRERAAEVARRRAAEHERLAAEA
+AAAAQARDAARARDAAALQARLDEEARRAQAARVARRRREEEKQRRRREAERRRRVAAEE
+KARAAAEAEARRREREERRRREAEVAAERARVQAERRAREEAALAERERLRLEAEAEAER
+RRQAAEAERRRLEAERVEAERRRRAEEAERRRREAEEAARLEAERRRRQAARVRAHTVLH
+AERALAQARLLEDRAREAERRAAEDAARRRREHEERESRALARAARELEGPEVFPAAADR
+PLLSDPEERLTDEELFARARVALPEWRRRQRLSTKAQAVQAEATAHSSAGPVTGALPLIP
+GYTPAPPEEPAGSPTRADRRGQTLLTVAWALFVLSGAWGLGLAGRVPGLGALDAGAYPLT
+ADGRHGPGASVFGLSPLHPAIWPVLWLLTGMYVLRQWGPGQGASPRHRRIRGAVAGTLLA
+LALWFPLAVLAPGGLDVVPWLLALVLMLRVVRRLGARPAARRLARVAEDGALGVLLGTLL
+AGAPTAVGAALHAWGVHVDWFPTELLALLVLMALLLAALRLVLGGRGRLGVALGMAWTLL
+CLALPRLLPSPLGAQQSAWVGLAAAFGALLLVTAAAVRRSWARQIERDAARRPHPAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b935e49e0f8b1643619b95abe6655a9a0aea18d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000356.fa
@@ -0,0 +1,47 @@
+>0_275
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDLAAEGWPLIT
+NPHQAPPAWVAPDARVSGSLLSPGCRIAGEVSDSVVGPGVVVAAGATVRGSLLLGDCEVP
+AGAVLDTVVVDVGGAVPAREVTGRAAPAEEVVVLTPQDRGPAEDETTGSGRPGRSD
+>1_2248
+MADPFPTDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHARSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
+>2_60
+MPEGDSLVRLAHRLRPVLAGRALTHADLRVPQHATADLTGWTVVEVEPRGKYLLMRLTPP
+AGRPAARPLTLVSHLKMEGRWLVSALDARWGAPAWQVRAVLETADHRVLGAQLGMLTLVP
+TDREDTVLGHLGPDLLDPAWDGSEEAAAALLAEGTRRLTARPERPVGLALLDQRTTCGIG
+NIYRCESLLLAGIDPHRPVGAVPDVPGLLTIARDLLRANVPPAAPFLGWPRTTTGVRANP
+DRPYGIEVVVADRGFPPGLPAAVGSGTAADPAADPGADRTASGPALGRPPARPPADPGAA
+GRRRTGCTGTTAPPACAAAGACARRTSAPPRTTRGSCGGARPASGEPRPNRGPGGGAPYA
+ERRPSPQGRSARPPTPRRTRVADPFPDDPRSAVVALILAGGRGSRLAPLTDARSKPAVPF
+AGQYRLIDVALTTVAHSGLQDAWIVEQYRPFTLNQHVAGGRPWDLDGTRHGLRVLPPAQG
+RDEEGFAQGNGHAIHQQLAPLRRFGAKTVVIMSADHLYRMDLRPVLERHRERDAELTVVT
+TQVAEGASRFGVVSSDADGRVTAYDYKPDEPATDVVATEVFVADVDALTEVIESLLDSAS
+EEQVDDDDPAGAQLGDYGETIIPALVERGRVHEFRHEGYWKDVGTIDAYYQAHMALLRGD
+GLDLDDPRWPLISNFHPRPPAFIHPEAEVNGSMLCPGSRVRGTVTESVIGPGVVVEAGAT
+VHRSVLLGSATVPAGARLDAVIADVGARIPEGATGQTKPGPGNITVLTPDDRSTAEGDET
+TGHA
+>3_40
+MADPFPKDPAGSTVALVLAGGRGSRLDPLTAARSKPAVPFAGQYRLIDVVLSNLAHSGLK
+DVWIAEQYRPFTLNQHLAGGRPWDLDGTRHGLRILPPAEGREEEGFSAGNGHALAQQVPI
+LRSFGAERVVVLSADHLYQLDLRPVLAAHADSGAELTMVTTVTDEDPSRFGVVQADEDGA
+VTAYDYKPEDPEGRLVATEVFVFDVAALHEVVAELVAREKAAGEHADGEEDEDGDPVASS
+LGDYGETIIPAFVERGRVREHRLEGYWRDIGTLDAFYRAHMELLDGAGLDLAAPGWPLLT
+NPPAAPPARVGPRAEVSNALLSPGCVVKGTVEDSVLGPGVVVERGAHVRRSVLFGECIVP
+RGARLDAVIADVGAHIPAEEVGRSRPGPGNLTVLTPATRDPDSEDETTGGAAAKDG
+>4_281
+MADPFPKDPEGAVVALVLAGGTGGRLMPLTAARAKPMVPLAGQYRLIDVVLSNLAHSRLR
+DVWVVEQYRPFTLNQHLAGGRPWDLDGTRHGLRLLPPAQGRAEEGFARGNGHAIAQQLPL
+LEQFGAETVVVLSADHLYQLDLRPVLAEHTRSGAELTVVTTETDEDPSRFGVVQVDDDGA
+VTDYAYKPEDPAGTLVATEVFVFDVAALSEVVGDLVAGEDEAATKDEGETDEDGDPVGSS
+LGDYGESIIPAFVARGRVREHRLVGYWRDIGTLDAYVRAHREILDGTGLDVAAEGWPLLT
+NPHAAPPAWVAPEATVTGSLLSPGCRIAGEVTDSVVGPSVVVEAGAVVRGSILLGECTVP
+SGAVLDTVIADVGAAIPAEGATGRAEPADEVVVLEPGERGPASSDETTGSGAPVRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000357.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000357.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a24120ceb6a7a4e374c82426a0b4ffe5a7e62e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000357.fa
@@ -0,0 +1,20 @@
+>0_279
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>1_2252
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>2_57
+MSVRVLAIGKKHEAWVSEGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGTAFDSPGLARHLQSRFDVGAPVTVVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
+>3_36
+MMVLMAVRVVAIGKRHESWVSEGITRYEKRLKKPWDLTWQLLPHSSRQEDAARAEESERI
+LAKVGPDEQLILLDERGRGFDSPGLSAHLQGQFDLGRTVTLVIGGAYGVDASVHARADRV
+WSLSGLVFPHQLVRLILAEQVYRAQEIAGGRPYHHA
+>4_285
+MSVRVLAIGKKHEAWVVDGIDRYERRLKKPYDLSWRLLPHSARQEEAARTEESDRILGAV
+GADEHLILLDERGAAFDSPGLARHLQSRFDVGAPVTMVIGGAYGVDARVHARADRVWSLS
+PLVFPHQLVRLILAEQVYRAQEISAGRPYHHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000365.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000365.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09f8420eff951a4c760c206b9a54d51e5844ef41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000365.fa
@@ -0,0 +1,70 @@
+>0_288
+MDATSHPDAGPRLPETSVPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTALELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>1_5
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARDAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPGLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLRMPSPAARLAWLLDHLADLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHFGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPAV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
+>2_48
+MDTTQHPDAGPLPSESTAPIGPYGSGAAAPGAAAAREPELHAEALAVLRRLVDRPDAQFK
+DGQFEAIEALVAHRRRALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQV
+AAAARAGVRAVSVSSANATQWDEVRARLAADEVDVLLISPERLTNPRFREEQLPDLVARM
+GLLVVDEAHCISDWGHDFRPDYRRIRDLIGLLPSTGPRAVPVLATTATANARVVGDVVEQ
+LGVDSAQDVFVLRGSLARASLRLGVLRMPSPAARLAWLLDHLEDLPGSGIVYALTVSAAE
+DTARALREAGHEAVAYTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVH
+FGAPSSPVAYYQQVGRAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLQALA
+QHGGALSVAALEPAVRIKRTALELLLKVLAVDGAVERVGGGWRATGREWVYDAQRYARVA
+EARRAEERLMLDYQTTDTCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDTSARERAE
+AALRRTGVPIEPRRMWPSGMDRLGVPVKGRMAPEIQAEEGRALARLTDLGWGTVLRELLD
+KEDAPVPEDVLQGAVGVLAGWGWQTRPIAVVAMPSRTRPLLVGSFAEGIARIGRLPFLGS
+LEHARGGPTAGPGGNSAYRLGSVHGRFEVPEAMAHLLRTASDAGRHGPVLLVDDLVDSRW
+SLAEASRVLREAGAQGVLPLVLAQAG
+>3_26
+MSTSPQDPARPAAVADPALYAEALGVLRALVGRPDAEFKDGQYEAVEALVAHRRRALVVQ
+RTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAASLSSANATEW
+EDVRRSLEADEVDVLLISPERLTNPRFRDEQLPDLVSRMGLLVVDEAHCISDWGHDFRPD
+YRRIRDLIRLLPSSGPRAVPVLATTATANARVVQDVVEQLDVESRQDVFVLRGPLARASL
+RLGVLRLPSPAARLAWLLQHLGELPGSGIVYALTVSAAEDTARALREAGHEVVAYTGRTD
+PEQRARIEQDLKDNRVKAVIATSALGMGFDKPDLTFVVHLGAPSSPVAYYQQVGRAGRGT
+DHADVLLLPGQEDRAIWEYFATASMPDEVQARAVLEALEESGGAMSVAALEPVVSVKRTA
+LELLLKVLSVDGAVERVGGGWRATGSPWTYDAERYARVAEARRAEERLMLDYQTTQTCRM
+EFLARTLDDPTAAPCGRCDVCAGPWYPTGWDGAAREQADRALRRTGVPLEPRRMWPSGMD
+RLHVPVKGRISPAEQAEEGRALARLTDLGWGSRLRELLAAPDAPVPEEVLQAAVRVLAEW
+GWQERPIAVVAMPSRGRPQLVDSLARGLAGQGRLPFLGPLELVGGGPTAGPGGNSAYRLA
+SVHGRFAVPEGMARMLATAPDAGRHGPVLLVDDLADSRWSLAEAARVLRGTGAQGVLPFV
+LAQNG
+>4_295
+MDATSHPDAGPRLPETSAPGGDAALHEEALAVLRRLVDRPDARFKDGQFEAIEALVAHRR
+RALVVQRTGWGKSAVYFVASLLLRARGAGPTLIVSPLLALMRDQVAAAARAGVRAVSVSS
+ANATEWDEVRARLAADEVDVLLISPERLTNPRFRDEQLPDLVARMGLLVVDEAHCISDWG
+HDFRPDYRRIRDLIGLLPAEGPRAVPVLATTATANARVVADVVEQLGVASEQDVFVLRGP
+LARASLRLGVLHLPSPAARLAWLLDHLGDLPGSGIVYALTVSAAEDTARALREAGHEVVA
+YTGRTDPERRAEIEEDLKANRVKAVVATSALGMGFDKPDLTFVVHLGAPGSPVAYYQQVG
+RAGRGTDHADVLLLPGPEDRRIWEYFATASMPDEEQARAVLGALADHGGALSVAALEPDV
+RIKRTSLELLLKVLAVDGAVERVGGGWRATGREWTYDAERYARVAEARRAEERLMLDYQT
+TDRCRMEFLARTLDDPTAAPCGRCDVCAGPWYPTGSDGAARERAEAALRRTGVPIEPRRM
+WPSGMDRLGVPVKGRIAPESQAEEGRALARLTDLGWGTVLRDLLDREDAPVPEEVLRGAV
+DVLAGWGWRTRPIAVVAMPSRTRPQLVGSFAEGIARIGRLPFLGSLEHARGGPTAGPGGN
+SAYRLGSVYGRFAVPEAMAQMLRTAPDAGRHGPVLLVDDLVDSRWSLAEAARVLREAGAQ
+GVLPLVLAQAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8c78e329f8c3aaca4466d784ac91fa1fdbc2684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000368.fa
@@ -0,0 +1,30 @@
+>0_292
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPAQEPDATSAGA
+AGPVPADHEEPHRDDTAPAETPGPERPGQDSSGRGEPDAQTPDREPSDAVAEDDARQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMREHRGEG
+>1_9
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPGGHGEPHRDDAAPADTPGPKRPGQDSSGRGEPDAQTPDRETSDAVAEDDARQDSD
+HASAAPRPTAPSADELTTLTVPAEWTAAPAEEELPFEVEVMRGTESVRLSSRDLPPWLRD
+QLAAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
+>2_44
+MEYLVPVLAVVLIGALAFAVSRWMSAARDRQTAGPRTPSGRPLEIGPERARQAAALLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRSLKDAVMDVQSLAVHPQVYSVPATEQEAPEEAE
+VRDPRTRPTPPEPARDEAADGERQGTERADVVEEGADDPAADDEPRPEAESDLSAEEGRV
+DDGAASGTEPRPGTSEPARADELTALTVPADWSAAPAEEEPPFEVEVMRGMDSVRLSSQD
+LPPWLRDQLSAMVRDGNLESAAVQLSSHSQLSVPEAYELLRRMRERRGED
+>3_23
+MEYLVPILAVVVIGGITLLVARRLSGRSQAPTRSATGTGADTVEASPERARTAARRLDEA
+THRAVYGHIAQGRPFEAVRDYRRATGRGVRDAILDIQSLTLHPQVWSLPVQAEPADDASP
+AAADMPSGPPRGPSDGRGRDGESSARPRLRRAEPSEAGPAPDAEPAPGGDAAADPEADGA
+TSRRPGRQAPEELTTLTVPEGWTADPAPEEPPFEVEVMRGEESVRLASQDLPPWLRDQLS
+AMVRDGNLESAAVQLSSHSSLSVPEAFELLRRMKERREGRG
+>4_299
+MEYLVPVLAVVVIGALAFAAARWMSAGRARQAADQRTPSGRGLDIGPERARLAAGLLDED
+AHRRVYGHIAQSRVMEAVRDYRAHTGRGLKDAVMDVQSLAVHPQVYSEPVQEPDATSAGV
+AGPVPDDHGEPHRDDAAPAETPGPKRPGQDSSGRGEPDAQTPDREPSDAVAEDDAQQDTD
+HASAAPRPTATPADELTTLTVPAEWTAAPAEEELPFEVEVMRGTDSVRLSSQDLPPWLRD
+QLSAMVRDGNLESAAVQLSSHSELSVPEAYELLRRMRERRGEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000371.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000371.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7227917abd170c280d745b131273e790eb107b90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000371.fa
@@ -0,0 +1,84 @@
+>0_295
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTGQVTPTNAAATGGEPTPEPEPQPTPSERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAADGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGVVPGTKPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGASTNFMRSPGNQNPLPYLDADQPVRVGAGLEFSTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCGAYRDRAGTP
+VTTNGCLPRGAYTPEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPSARPALADEDVIRSAFIYQPAEVTPLGESVILDDQTNFDNARE
+PMAQLFRAADGTAEGAAGTEFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYVSQGALTGEYSYAFGGAVGS
+LDGIYASPSAAAAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPEPTPGETCDGVTDPRGVPGKPANSVREWLRCIGATPGHGGDHPGK
+GHGGDHPGKGRGPVRP
+>1_19
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGTP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
+>2_24
+MTQRTFRLSRPAVALAALTLLAPAVVAGPAHAAPTGDGLVINEVYTNGGSANAVFTHKFV
+ELYNPTDTPISLDGWSLQYRSATGTAAPNGVVALSGTVPAKGHFLIQGGSNGTTGAALPR
+PDLNAGGAFNPAGARGTVVLSDQAGALTALPVGSVTTGQAEGVADLLGYGTSNTFETAAA
+GAPSSNSDPKSLTRTDGVDTDDNAADFTVTAQVTPTSSTGEAPVDPIPDPEPDPEPAPAL
+TIAQIQGDGAATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGSAEDATPGASDGLF
+VYSPDTVGSVALGDHVQVTGEAAEHYGLTQVRVGAAGVTPVAEPAAVAPTAVDFPLSEAD
+REALEGMLLAPTGEWTVTDNYDLNQYGSLGIVPGTEPLPNPTSVAAPGAEAQAVAADNAS
+RLIVLDDGASTNFMRSPGNENPLPYLDADRPVRVGAGLDFTTGVILDYRFDAWSFQPLGH
+LTDATAAAVQPVAVEDTRPEEASPEAVGGNVSVGSFNVLNYFTALGQDFPGCRAYTDRFG
+EPVTTNGCLPRGAYTPEAFARQQEKIAAAIDGLDASVVALEEIENSAKFDLDRDRALAHL
+VDALNAQAGEQKWAYVASPADRPALSEEDVIRNAFVYQPAEVTPVGESVILRDEVNFDNA
+REPLAQHFRAADGTEAGVAGTDFVAVTNHFKSKGGSGAAGDNADSGDGQGAYNGDRTRQA
+QALVAFAEQVADDAGTDRVLLLGDFNAYEKEDPIRVLEEAGYVSQGALTGEYSYTFDGAV
+GSLDGVYASPAASAVVTGQDIWMINANESVALEYSRHDYVAEDLYAPDQWRSSDHNPLLV
+GLQLDAPVVEPEPQPGAGHPGKGKGLDKGAGHPGKGKGLDKGAGHPGHGRVPEAARP
+>3_20
+MPTPRLRLVRTAATLAAATLLAPAVLALPAQASPAGDSLVINEAYTNGGSAGALFTHKFV
+ELYNPTDQPISLDGWSLQYRSATGTTAPSTTVALSGTVPAKGHFLIQGGSNGATGAALPT
+PDLTTSFNPAGTKGTIVLADQAGTVAGLPTGSVVTDQVAGVADVLGYGATNTFETAASGA
+PAANSDPKSIARTGGADTDDNAADFTVAADVTPQNAAGGGTAPVDPVDPVDPTPAPAPSV
+TVAEIQGTGATSPLEGRRVSTTGVVTAVYSTGGYDGFYIQTAGTGGAEDATPGASDGVFV
+YAPAEVGSVTLGQTVTVTGDVAEYYGLTQVKAEAGGVRQAAEAGAPVTARELAFPLTEAE
+KEAHEGELLAPAGAWTVTDNYDVNQYGSLGLAPGTSPLPNPTSVALPGADAQAVAADNAQ
+RLIVLDDGASTNFFRSPGNQNALPYIDADAPARVGSAVDFRTPVILDYRYGAWSFQPLGH
+LTDANKAEVQPVDIADTRPAEAVREDLGGNVTVGSFNVLNYFTTLGEDVPGCGYYADKDG
+APVSTKGCLPRGAYTEEAFLEQQAKIATAINGMDTSVVALEEIENSEKFGLDRDHALAHL
+VDALNAQAGYAKWAYVASPTVRPALADEDVIRSAFIYQPAEVTPVGESVILDDQVNFANA
+REPMAQAFRVADGSAGGVVGTEFVAITNHFKSKGGSGATGDNVDTGDGQGAYNGDRTRMA
+QALVAFAEQMKVQAGTDRVLLMGDFNSYEKEDPIRVLEAAGYISQGAKTGEYSYTFDGAV
+GSLDGIYASPAADATVTGQDIWMINANESVAFEYSRDNYVGEEFYAPDQWRSSDHNPVLV
+GLQLDAPAAPVVPTPGTRPTPPADQCALITSPRGAKASAGFSASEWMRCAGVHPGKGRGR
+G
+>4_302
+MTPLPRFAARTAVTTAALALLAPAVALPSQASPAGDSLVINEAYTNGGSANAVYTHKFVE
+LYNPTDQPINLDGWSLQYRSAAGTAATQGTVALSGTVPAKGHFLVSGGSNGTAGAALPQA
+DLVAGGAFNPAGTKGTIVLARQAGTVTDLPVGSVVTGQVPGVADVLGYGATNTFETAAAG
+APSANSDPKSLTRTNGVDTDDNSADFTVTDQVTPTNAAATGGEPTPEPEPQPTPAERITI
+AQLQGTGTATPYAGRQVTTTGVVTAVYSTGGYDGYYIQTAGTGGDTPDATPGASDGVFVY
+SPDTVGSVTLGDHVQVTGEAAEHYGLTQIKVAAGGVLPVAEPGAVAPTPVEFPLEEADRE
+ALEGMVLAPQGDWTVTDNYSLNQYGSLGIVPGTTPLDNPTSVARPGAEAQAVAAANAQQL
+IVLDDGATTNFMRSPGNQNPLPYLDADQPVRVGAGLEFTTGVILDWRFDAWSFQPLGHLT
+DATAAAVQPVTIEDTRPAEAAPEAVGGNVTVGSFNVLNYFTTLGQDVAGCSAYRDRAGNP
+VTTNGCLPRGAYTSEAFARQQEKIAAAINGLGTSVVALEEIENSEKFGLDRDHALAHLVE
+ALNAQAGEQRWAYVASPATRPALADEDVIRSAFIYQPAEVTPVGESVILDDQTNFDNARE
+PMAQLFRAADGTSEGAAGTDFVAITNHFKSKGGSGATGDNVDAGDGQGAYNADRVGQAEA
+LVAFAERMKAETGTDRVLLMGDFNAYEKEDPIRVLEAAGYLSQGALTGEYSYAFGGAVGS
+LDGIYASPSAATAITGQDIWMINANESVALEYSRHNYVAEDLYSADQWRSSDHNPILVGL
+QLDAPVTEPTPEPEPSPGETCDGVTDPRGVPGKPANSVREWLRCVGATPGHGGDHPGKGH
+GPEHPGKGRGPVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000374.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000374.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62410b205ef5193d5c34290bc3595ae8cc485983
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000374.fa
@@ -0,0 +1,30 @@
+>0_299
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARSLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLAEHGVRAVPGAEEALI
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LEDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADHVLLAAGSDRVVPGLADVPDLV
+VRTR
+>1_23
+MSLPHAPRTPAPPAAASSAAPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEAAFDALLAEHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
+>2_20
+MSLPPRPPPRGRAPRADGPPAPPLRLAVVDMSGTSIVERGLQDAAFAHALETHGLAADAP
+AHADAVRVFRARRATSRTAVFAQVFPDRPAAAAAARTFEEAFDSLLAEHGVQPVPGAEEA
+LLRLRALGLRVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPFPDMILTALLG
+LDLDDVRGVLVVGDTAEDMTAGRRAGAGLVAGVRTGRDADAALLAAGAHHVVDGLADVPA
+LVGAGG
+>3_16
+MSLSTAVPALSVGTPVPLRLAVVDMSGTSVVEGGLQDRAFAEVVAARGLAEGSPEHERAA
+RLFRERRGTSRTAVFQALFEGRTAALEATRAFEAAFDRLLAEHGVTAVPGAEGALVRLRE
+AGLDLCLITGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMVLTALLALDHDDV
+RSVLTVGDTAADILAGRRAGAGLVVGVRSGQDTGGVLAGAGADQVVDSLAQVPDLVATLR
+G
+>4_306
+MSLPHAPRTPAPPAAASSAVPLRLAVVDMSGTSIVEHGLQDTAFARTLDQHGVPAGTPEH
+DDAARRFRALRPTSRTAVFPRVFADRAVAAAATRTFEATFDALLGQHGVQAVPGAEEALV
+RLRALGLHVCLCTGYARHTQNMILESLGWMGLADLSLSPDDAGRGVPYPDMILTALLGLD
+LDDVRSVLVVGDTAEDMTAGRRAGAGLVVGVRTGRDADDVLLAAGADRVVPGLADVPDLV
+VRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000375.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000375.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bed0320d1409a68141b95301f643f9c27bab188f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000375.fa
@@ -0,0 +1,40 @@
+>0_300
+MTASAPVPPVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQC
+EVADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRI
+FLMEDADRMTERATNVLLKAIEEPPARTIWMLCTPSPADVLPTVRSRCRLITLSIPAVEQ
+VAELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAM
+ALAATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRR
+RRAVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGTAGDSAEVLARI
+DAVTTTRERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>1_24
+MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV
+ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL
+MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA
+ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL
+AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR
+AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA
+VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>2_19
+MTALPDAVPAVFADLAGQGSAVEQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQ
+CEAPDPAARGCGRCHACRTVLAGTHPDVTVLATEAVTYRIEDVRSLVEAAQSTPATGRWR
+IFLMEDADRMTERATNVLLKAVEEPPARTVWMLCTPSPADVLPTVRSRCRLVTLSIPAVE
+DVADLLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLEATSVSDA
+MALAATLADVSKAEAESSAEARDAEELETLRRSLGLEPGEPVPPKLRQHVKRLEEDQTRR
+RRRSVRDSLDRAMIDVMGLFRDVLRVQLGAEGELINEHRRAEVEAYARGAAGDSAEVLAR
+IDAVATARERIAANVPEQLALEAMMLALLPRRVRTPRRR
+>3_15
+MTGAPDVYSDLAGQDAAVAQLRRAATEDRPTHAWLFTGPPGSGRSTAARAFAAALQCEQP
+DPANRGCGACHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAAQSTPATGRWRIFLM
+EDADRMTERATNVLLKAIEEPPPRTIWMLCSPSPADVLPTIRSRCRLVTLRIPAPEDVAA
+LLHRRDGLDEATALMTARISQSHVGMARRLARDPEALARREDVLSLPLQATAVSDAMAMA
+ARLAEVSHAEAESSAAARDAEELAALRRQLGVAEGEAVPPKLRQQVKRLEEDQSRRRTRV
+TRDALDRAMIDVIGLFRDVLRVQLGAGGDLVNEHRRAEIERYAAGAAGSSAEVVARIDAV
+HLARERLGQNVPEQLALEAMMLALLPARVRTPRGRR
+>4_307
+MTAPAPAVFADLAGQEAAVAQLRRAAAEDRPTHAWMFTGPPGSGRSTAARAFAAALQCEV
+ADPAARGCGECHACRTVLGGTHPDVTVLATEAVSYRIEDVRALVEAGQSTPATGRWRIFL
+MEDADRMTERATNVLLKAIEEPPARTIWMLCAPSPADVLPTVRSRCRLITLSIPAVEQVA
+ELLHRRDGLDRETALTTARISQSHVGMARRLARDPEALERRERILSLPLQATAVSDAMAL
+AATLAEVSKAEAESAAEARDAEELEALRRSLGLEPGEPVPPKLRHHVKRLEEDQTRRRRR
+AVRDSLDRAMIDVMGLFRDVLRVQLGADGELINEHRRDEIEAYARGAAGDSAEVLARIDA
+VTTARERIAANVPEQLALEAMMLALLPRRVRTPRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000384.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000384.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7b2e77babc9bf37912a0e4917682bc6a206bbd9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000384.fa
@@ -0,0 +1,45 @@
+>0_310
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLDLDAVVVLTPP
+AGADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASHALADLAPAGAPRRVLV
+HDAARALTPPSVFGAVTAALETGAVAAIPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG
+LVGIATALVIPAA
+>1_34
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLRHCLESVAAARAAGLGLDAVVVLTPP
+AEADAGRVAAEVDAGPRLDVPVHCVPGGAERADSVRAGLAAASGALADLAPAGAPRCVLV
+HDAARALTPPSVFGAVTAALGTGAVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPQEEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGLAVGNVAVQVVAPRPKVGARRAEMEAALSAALGGAPVSVSAATTDRLGFIGRKEG
+LVGIATALVIPAA
+>2_9
+MPTALVIAAAGAGTRLGAGMPKALVPLADGRTLLRHCLDSVAAARAAGAAVDAVVVLAPP
+AEEDAARVAAEVDAGPGLGAPVACVPGGAERADSVRAGLAAAADALNALGPAAGPRRVLV
+HDAARALTPPAVFAAVEAALDAGAVAVVPGIAVTDTVKQVAPGPGGAEVVTTTPPRAALR
+AVQTPQGFDLDALLAAHEAVRADPALDAAALTDDAMVMEAAGHPVAVVAGDAAAFKVTAP
+ADLELARLELARRADAPTPEEDPAMDQYGTAPGTGPEADAATDPAGPRPGAALPRVGVGT
+DVHRWAPEDAPRPLWLGGVHWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVD
+RPEMADASGTAMLAEVLRLLTEAGLAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAP
+VSVSAATTDRLGFIGRGEGLVGIATALVAPTA
+>3_5
+MPTALVIAAAGSGTRLGAGVPKALAPLTDGRPLLDHCLESVAAARATGLGLDALVVLVPP
+AADHARAVADVVARHETAVGAPVTCVPGGVERADSVRAGLAAADAALADRGHPAGQGVRH
+VLVHDAARAFTPPAVFEAVAGALVSGEVAAVPGLPLTDTVKEVTGADGREVVVATPARSA
+LRAVQTPQGFDLDVLLAAHAAAQADPAADAAALTDDAMAMEAAGHAVVVVPGDERAFKVT
+SPADLEAAARILAVRDAQSGPGTPSPAAVPAAPPLPRTGIGTDVHRWAPDDAPRPLWLGC
+VEWPGQNGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRWEMRGASGAAMLAEVLR
+LVTEAGCRIGSVAVQVVAPRPKVGTRRAEMEAAMSAALGGAPVAVSAATTDGLGFIGAGE
+GLVGLATALVVPAA
+>4_317
+MPTALVIAAAGAGTRLGAGLPKALAPLADGRTLLHHCLASVATARAAGLALDAVVVLTPP
+AEADAGRVAAEVDAGPRLDVPVHCVSGGAERADSVRAGLAAASYALADLAPAGAPRRVLV
+HDAARALTPPSVFGAVTAALETGVVAAVPGLPLTDTVKQVTPGRGGVDVVAATPARAGLR
+AIQTPQGFDLDTLLAAHEAVRTDPTLDAAALTDDAMVMEAAGHEVVVVTGDPAAFKVTAP
+ADLDLARLELARRAPREEAPMDQPARPAAAPAPLPRVGIGTDVHAWAPEDAPRPLWLGGI
+HWPGERGVAATSDGDVAAHAACNALLSAAGLGDLGAVFGVDRPEMADASGADMLREVLRL
+LTEAGVAVGNVAVQVVAPRPKVGTRRAEMEAALSAALGGAPVSVSAATTDRLGFIGRREG
+LVGIATALVVPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000389.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000389.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bc2f3cd8f6c832897c9655de07bfd8a076599307
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000389.fa
@@ -0,0 +1,21 @@
+>0_318
+MSWWPFPRPSASPSPDDDGAPAAAELEEAVAALRQLLRAERHRLRPDSWALAWEMVEQAA
+EYAPAWTRLQRTRPVETQELVLALTGRLEPLLCDFLALPDSEKPTHADAVHARLREQGTE
+HGRLRRRLTRALTARLRAGEEL
+>1_43
+MSWWPFLRSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLALPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
+>2_2620
+MAWWPFRGPSGAPRDDDASTAGRASLEAAVHSLRALMTAERHRLRPDSRDLAWTITERAA
+EYGPAWDRVSAQRPAEAQELLLLLSHRLEPALRDFLDLPDSQKPRHADELHGRLSELQTE
+AQRLGRRLTRALSSRLRARGEL
+>3_2431
+MAWWARRRLSSSGPAPLGKPPLVAAEELRRLTDELSEILQRESARIRPDAAAVLRSFLNR
+SRALLPAWDRTAPARSAEALAAYELLRDRVLPGLQDWLCLPDHLKPVHADDLLADAQAWE
+GDLSHHAARLTQVLTARGRAVRELDERQ
+
+>4_325
+MSWWPFLHSSASPSPDDDGAPAAAELEEAVAALRRLLRAERHRLRPDSWALAWEMVEHAA
+EYGPAWTRLQRTRPVETQELVLALTGRLEPLLRDFLAIPDSEKPAHADAVHARLREQSTE
+HGRLRRRLTRALTARLRAGEEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000397.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000397.fa
new file mode 100644
index 0000000000000000000000000000000000000000..041a381eb5be30f9ca1bfbfb5b07fad6ac4c9cbb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000397.fa
@@ -0,0 +1,75 @@
+>0_326
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDAVARAAHEAGMGVLVDIVPNHVGVATPQANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPAKESTAERARLARAVHDRQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAEAEPALAAVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRTRRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>1_51
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPRANPAWWDVLTHGPEA
+AHAAWFDVDWAAGGGSLLIPVLGDGPDGDADAELNRLVVDEGRLRYWDNVYPLAPGSLEA
+AEAETGLRAAEVFAEADPASEPTAEQARLARAVHERQHYRLVGWRRGDAELNYRRFFTVT
+TLAGVRVDEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEGYL
+VVEKILEPGEALPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVVRA
+KHDVATGSLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAVLE
+GALADAAAAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRWAN
+LNEVGGDPSHVALSLADFHSAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEPDR
+WAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTAPEEERILGFLQKASREAALATSW
+TEQDPEFEARLAALAAAVTSPEGPARGVLQAVADRLAEPGLVVQLGHKLVQLAAPGVPDV
+YQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAAVLRARRD
+RPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGETVVTVPAGRWED
+AVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
+>2_2566
+MSTSTERPVPSSTYRLQVGPDLPLESVAGLVPYLRRLGVGWLYLSPILEAEPGSDHGYDV
+VDPTRLDAARGGAEGLEAVARAAREAGLGVLVDIVPNHVGVATPEANPAWWDLLAHGSEA
+AHAPWFDVDWTAGEGRVLLPVLGDGPDGEAEAELDRLVVETGDDGGRLRHWDTRYPLAPG
+SLAAAEEETGLRAADVFAGAEPAHEPTPERARLARAVHARQHYRLIGWRRGDAELNYRRF
+FTVTTLAGVRVEDPEVFDAVHAEPARWVREGLVQGLRVDHPDGLADPAGYVRRLRSHVLP
+EGYLVVEKILEPGEELPADWDVDGTTGYDALGEVERVFMHPVAAGGPNEDERRRRDWDEV
+VAEAKRDVATGSLVAETARLVREVRGVHALGAHADEDVAAAFAAVLSRLPVYRTYLPVGL
+AVLERALADAGEAEPALAPVLADLGPELADPDSPVARRFQQTSGMVMAKGVEDRSFYRWT
+RWANLNEVGGDPAHVQLSLDAFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAE
+EPDRWAGELAGLRALHPLGDEGAERLLWESIVGVWPTDGTAPSTERILGFLQKASREAAL
+STTWTDQDPEFEGRLEDLARAVTAPDSPARGAVQAVADRIAEPGLVVQLGHKLVQLAAPG
+VPDVYQGTELPVPSLVDPDNRRPVDFHARADLLDRLDAGHVPGLDDADAAKLAVVAAVLR
+ARRDRPELFTRHRRLDVSGPAAEHAVAFDRGGALAVATRWPVHLAAAGGWGETVVTLPPG
+RWEDAVTGRPVHPDARGAVRLDELLSTLPVALLVPARAEEATP
+>3_2417
+MSHTDAVSAPASTYRLQVGPDLPLDSVAGLVPYLRRLGVDWLYLSPILAADPGSDHGYDV
+VDPARVDPARGGPEALAALAAAAHEAGMRLLVDVVPNHLGVATPLANPAWADLLAHGPEA
+AHAAWFDVDWEAGDGRVLLPVLGDGPEGDPRGAEAGLDQLIVDPSAGEHGVLRHWDTAYP
+LAPGSLAAAEEETGLRAAEVFAGADPAAPTDDAARLGRAVHDRQHYRLVHWRRGDAELNY
+RRFFTVTTLAGLRVEDPEVFDATHVEIGRWVSEGLVHGLRIDHPDGLTDPGAYLRALRER
+VLPEGYLVVEKILEPGEDLPAAWPVDGTTGYDALGELERVFMPADPDGPAADDAARAAWE
+ALIAEAKRDVATGSLAAETARLVREARAAVVLGAHSDEALTEAFADVLASLDVYRTYLPV
+GAERLAAAVARARAAHPEPADVLDDVARVLADPDSPVARRFQQTSGMVMAKGVEDRSFYR
+WTRWANLNEVGGDPAHLDLPLAGFHALQRARQASWPTTMTALTTHDTKRSEDVRARITAL
+AEEPASWEDALARLRTAHPLDAPGLEELVWESIVGVWPTDGTAPEADRLEEFLLKSAREG
+QEHTSWTAQDDAYEGRLRALAADVVAPDSAARAVVQEIADRIAEPGLTVQLGRKLVQLAA
+PGVPDVYQGTEIPFPTLVDPDNRRAVDFEARADLLDRLDAGHAPTLDEPEAAKLLVVSRA
+LRARRDRPELFHGYRPLDVDGPAAAHLIAFSRGGALALATRLPLTLAAAGGWRETVVSLP
+PGRWRCAVTGRAVTPDARGAVRVDDVLSQLPVALLLPEEETA
+>4_333
+MSTSTVRSAPASTYRLQVSPDLPLESVAGLVPYLRRLGVDWLYLSPLLEAEPGSDHGYDV
+VDPTRLDAARGGAEGLDMVARAAHEAGMGVLVDIVPNHVGVATPPANPAWWDVLTHGPEA
+AHAAWFDVDWAAGDGSLLIPVLGDGPDGNADAELDRLVVDAEGGRLRYWDNVYPLAPGSL
+EAAETETGLRAAEVFAAADSAKEPTAEQARLARAVHDRQHYRLVGWRRGDAELNYRRFFT
+VTTLAGVRVEEPEVFDAVHAEPARWVREGLVDGLRVDHPDGLADPAGYARRLRSHVLPEG
+YLVVEKILEPGETLPADWPVDGTTGYDALGEVERVFMHPEAAGDAAEDARRRREWDEAVV
+RAKHDVATGPLAAETARLVREVRAVHALGAHPDEDVAAAFAAVLARLPVYRTYLPVGLAV
+LEGALADAAEAEPGLADVLGDLRPELTDPDSPVARRFQQTSGMVMAKGVEDRSFYRYTRW
+ANLNEVGGDPSHVALSLADFHAAQQARQAAWPTAMTTLSTHDTKRGEDVRARIAVLAEEP
+DRWAAELAELRRLHPLGHPDAERLLWESIVGVWPTDGTTPEEERILGFLQKASREAALAT
+TWTDQDPEFEARLAALAAAVTSPEGPARGVLQAVADRIAEPGLVVQLGHKLVQLAAPGVP
+DVYQGTEVPFPTLVDPDNRRPVDFAARADLLDRLDAGHTPGLDDPAAAKLAVVAGVLRAR
+RDRPELFTGHRPLDVSGPAAEHAIAFDRGGALAVATRWPVRLAAAGGWGQTVVTVPAGRW
+EDAVTGHPVHPDARGAVRLDELLSTLPVALLVPAHAPSDRRERTAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000402.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000402.fa
new file mode 100644
index 0000000000000000000000000000000000000000..38b02623f790b8d9d470970de7b61c92cd17f0b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000402.fa
@@ -0,0 +1,25 @@
+>0_332
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAGGEQVLPAPEHILRAFRQSFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>1_57
+MEFIAPLDPGWEAALAPQAAAFEQVGEALRARRAAGEQVLPAPEHILRAFRQPFADVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGITPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLAAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
+>2_2552
+MELIAPLDPGWEAALAPQAAALEQVGAALTQRRAAGEQVLPAPEHILRVFRRPFEDVRVL
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLVNIHRELQDDLGIAPPAHGDLSAWADQGV
+MLLNRALTVRAGAPGSHRGLGWEQITEAAVRALCERGTPLVGLLWGADARRMAPLLTQAG
+AGVVESPHPSPLSAHRGFLGSRPFSRVNRLLEEAGAEPVDWRLPD
+>3_2411
+MDLISPLDPGWAAALADQEEALVRVGAELTARRAAGEHVLPAPEHILRAFRQPFADVKVL
+IVGQDPYPTPGHPIGLCFACDRHVRPLPRSLANIHRELHDDLGVPPAAHGDLSAWTDQGV
+LLLNRVLTVRAGAAGSHRGIGWEQITEAAVRALVARGTPLVGLLWGNDARRLAPLLTAGG
+AGVVESAHPSPLSASRGFFGSRPFSRVNALLEAAGASPVDWRLPD
+>4_339
+MEFIAPLDPGWEAALAPQAAAFEQVGERLRARRAAGEQVLPAPEHILRAFRQPFADVRVV
+VLGQDPYPTPGHPIGLSFAVDRHVRPLPRSLANIHRELHDDLGIAPPAHGDLSAWTDQGV
+LLLNRALSVRAGAPGSHRGLGWEQITEAAVRALCARGTPLVGLLWGADARRMAPLLTAAG
+AGVVESPHPSPLSAHRGFFGSRPFSRVNRLLEAAGAAPVDWRLPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000413.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000413.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c720ba4901064d4f9f4e1e763db631c4dcec25a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000413.fa
@@ -0,0 +1,20 @@
+>0_345
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>1_70
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>2_2539
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDAHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNALK
+ADRSLESMGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
+>3_2398
+MRTLVLNAGYEPVSVVSDRRALLLVATGKASVLEDGDAPMHSPTRAWGRPLVILLHQYVR
+VPHADAAAVSRKGVLRRDGHRCAYCGAHATTVDHVHPRSRGGQNTWENLVACCLRCNSAK
+ADRSLDALGWRLRVVPTRPCGVQWRLRELERPAPAWEGWLQFAA
+>4_352
+MRTLVLNAGYEPLSVVSDRRALLLVATGKASVLEDAGDPMRSPTRAWGRPLVILLHQYIR
+VPHTDAAPVSRKGVLRRDGHRCAYCGAHATTVDHVRPRSRGGENSWENLVACCLRCNGAK
+ADRSLEALGWRLRVEPVRPRGAQWRIRELERPAEAWRDYLRLAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000419.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000419.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f5685107941764734c4370c77a1880fa169dafc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000419.fa
@@ -0,0 +1,41 @@
+>0_353
+MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR
+WEADEEESV
+>2_980
+MTPPSPLAPEPVPDRAPAQDPGSGHAPSPASAALPPGHRPTGALPVAPGFDRDLHRLWWY
+TAAGLLSAVVVVAGFLVFVMARRLAVAEGPDASPLAVTVLVAGIAAAVAAAVGQTLATLR
+LRRAWEEEREPLRRTAVAALLPALLVALTPLAVPSLSAWPVLSLWLSVCLIAPQAAAHVR
+TAVLTSGAAATLGLTALALVRTPAGPADSAVGVLLWWAMVLLVVLPTVWVWRVAVRLEEA
+RAQAGELAVARERLRFAADLHDVQGHHLQVIALQAELAGRLLEKGRTDQAGAALRDVREQ
+AAEALGETRALVRGLRQVSVASEIENAREVLAATGAVVEVDVDPAAARLAREAARLVGLA
+VREATTNALRHAEPRRVRLALGPADGAAGGVRLTVTNDGARPPAAPPGTGLAGLAARAAE
+VSGRLSAGPDDDGGFRLELTVPSSSGATTRTDPTTTTGEDA
+>2_2532
+MTSEPTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWELTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GAAAGALVFVTDPPALWVYVGMGALLTGVACVTIPVSRTSFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAARRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEAAGITVTTDDDGDPRREEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGVAGAPAEDHTGGLDNLRSRLAGVGGRLDVSCGDGRFTLEAR
+WEADEEETV
+>3_1154
+MSPAGGPPAPARPTVGTAEHDPAVLPLHLWPSTMGFAGVWLISFGFVLVELLRRAFTPGD
+GRGEAILGVAAIAVFILVYLAAFVVPRPVRAWPAWANTVLTWFVLAGCVAVLTRILGVHA
+LLYSPFLVATWIFPHRLRVGLTGAGATMAAALATGLLFFPGDPALPVVLGNLAVLLVVLV
+GMRLAIARDDRVVEMTHELDLAGQRERLGRDLHDILGHSLTTINVKTQLVHRLIDTDPAR
+AKEEAAEVIALSRTALAEARAAVAELAAPELGGQLSLSVGALRDAGMAVEAPPPGAVTEV
+PQRRRALAAWIVREAVTNVLRHAGARRVRISLDAHHVAVLDDGAGLPAAVVAGVGPRTLA
+ERAAAEGARLEVGPGLGGAGTGVAVHWGGTTPEAARGVLPATEGRMDA
+>4_360
+MTSEHTSETRRLRSRTSFVLLAVFGVAAIVALLTSAVEPWPPLVLAPGLIAGLWLLSQWH
+REVAAPTRWAVLALGTLTWALSALWDLTPLGALAFALAGALEVMWSRHARAVVTLLVLTV
+GSAAGALVFVTDPQALWVYVGMGALLTGVACVTIPVSRISFDLMRLQDQRAEQERAASLD
+AERLRFSQDLHDIQGHALHVVKLKIAVAQRMLSTDTDAAQRELDEAQQTLRQTMAETKAL
+AQDGHTLTLRGELANSVALLEATGITVTTDDDGGPRGEEFEHVAGVVIREGTTNILRHSD
+ARRVEISLAPGHVVISNDGAAGVSAEDHTGGLDNLRSRLAGVGGRLDVSCVDGRFTLGAR
+WEADEEESV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0ab3069b59433e3efb086ffe4f8f828b4636c67
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000421.fa
@@ -0,0 +1,40 @@
+>0_358
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
+>1_91
+MSAAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRILLGEHAENPPRPSFRRVLLRWLARIFGSVFVLALAQRAESDTPYEKDQDAPE
+GMAADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGAALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>2_2520
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSVHRILLRWLARIFGSVFVLALAQRAESDTPYAKDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELTLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGYGA
+AAVTYVLGLLFGANVG
+>3_2392
+MSPAHAATPAALPEPTREQVRRWRRYLADEIAEGQIYRDIAASKDGVERDILIGLAEAEK
+RHEEHWRALLGEHAAHPPRPSVHRILLRALARVFGSVFVLALAQRAESDTPYAKDQDATE
+HMAADEQIHEEVVRGLASRGREQLAGSFRAAVFGMNDGLVSNLALVMGIGATGVASSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAEHLDLDRNELELVYLARG
+MTPEDAKHRALERLGYLSCDCNPQFSARPDGSKGPVDHSESFAEIGSAWGASLSSFCFFA
+SGALIPILPYLFGMTGLGALVVAAVLVGIALLFTGGVVGLLSGSSPLWRGLRQLMIGYGA
+AAVTYLLGLLVGGSIG
+>4_364
+MSPAHTATPAARPEPTREQVRRWRRYLADEIAEGQIYRDIAARKDGVERDILLGLAEAER
+RHEQHWRALLGEHAENPPRPSLHRILLRWLARIFGSVFVLALAQRAESDTPYAEDQDAPE
+GMVADEAIHEEVVRGLAARGREQLAGNFRAAVFGMNDGLVSNLALVMGIGATGVAPSVVL
+FTGVAGLLAGALSMAAGEYVSVRSQRELLEASSPTQITLEAAQHLDLDHNELKLVYLARG
+MTPEDAEHRALERLGYLTCDCNPQFSARPDGSQGPVDHSDSFAEIGSAWSASLSSFAFFA
+SGALIPILPYIFGMSGLWALGLAAAMVGVALLFTGGVVGLLSGSSPLARGLRQLAIGFGA
+AAVTYVLGLLFGANVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000424.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000424.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3bfa7830ded3d8c44b2e7909615bbe78627be2f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000424.fa
@@ -0,0 +1,40 @@
+>0_361
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPDQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLTVLSDILPTAFHGLV
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVSDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPVMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
+>1_94
+MTTENRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEVCETTNPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSTT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDVTRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+LVNPRVITLDEAPQAYAEFDQGSVEKFVIDPHGMIAR
+>2_2517
+MSPRGRSGSRLTQASLETEGNSFMTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHG
+VILKIVATNICGSDLHIYRGSFPVPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNV
+ACGRCRNCRAGRTEVCETANPEQACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQ
+AMEKILDLAVLSDILPTAFHGLMAAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVG
+DQDASRLELVRKHGCETIDLSVTENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEM
+QPIAAVNQVLDITRPGGATGIIGIYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQA
+PIMRYNRQLMMSILWDRMPYLTEMVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>3_2389
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+VPEGMVLGHEMTGQVLEVGSDVQFLKEGDLVSVPFNVACGRCRNCRAGHTEICETANPEQ
+ACAAYGFNLGNFQGGQAEYLFVPYADFQLLRFPDQEQAMEKILDLAVLSDILPTAFHGLM
+AAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDYVGSEAHGLGSESDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSVDKFIIDPHGMIAR
+>4_367
+MTTKNRAVAFHGIKDVRVDELDFPKLEMPDGSAAPHGVILKIVATNICGSDLHIYRGSFP
+APEGMVLGHEMTGQVLEVGSDVQFLQEGDLVSVPFNVACGRCRNCRAGRTEICETANPEQ
+ACAAYGFNLGGFQGGQAEYLFVPYADFQLLRFPGQEQAMEKILDLAVLSDILPTAFHGLM
+EAGAKPGSTVYIAGAGPVGRCAAAAARLLGASCIIVGDQDASRLELVRKHGCETIDLSVT
+ENLQDAVNDILGEPMVDCAVDCVGSEAHGLGSASDEMQPIAAVNQVLDITRPGGATGIIG
+IYGPDPIAETKAEQEGTFPVDFGKAWIKSPHIIGGQAPIMRYNRQLMMSILWDRMPYLTE
+MVNPRVISLDEAPQAYAEFDQGSLEKFVIDPHGMIAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba077196b7f294266a0dd002531496589ed670c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000430.fa
@@ -0,0 +1,41 @@
+>0_370
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRRSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDDRSTDEEAAR
+>1_103
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAPGQRDGRPADEEAAR
+>2_2509
+MSAVSDAAPVSPRRTRLAALGDPTPVENVATHLQEGWNRWHRSRALRAGHVPTIMAFTGY
+GSTSWVRILSRVVIAPDEEFLNGRRISKVVADGVRGWRNFVAPPMAYAEVEVEVGGTRTT
+VRTDRMGVVDAVLDVEMEPGWRTATLHVGDDEHVTMDLYICHPDARIGLVSDIDDTVVVT
+SLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRVAELEPKAPVLYLSTGAWNVAQTLTRFL
+GRNLYPLGALLLTSWGPTKDRWFRSGQEHKKTQLERLAEQFPDIKWILVGDDGQHDPEIY
+ADFAQRHPDRVAAIVIRQLTPSEALLAGGRAEDTRRSTPGIPWCYGPDGASLSNQLEDLG
+ILPVGFVDVQPEGWKEDILGDDEVLSAAEHGAAALGDEADAPDTAAEPRVPAGEAAVGDG
+AADEAEAAEAGGSR
+>3_2380
+MPASESASIAAQNDPARRQRLAAAGGPTPAENVATHLQEQWNRWHRSRALRRGFVPTVMA
+FTGYGTTSWVRVLSRVVLAKDEDFLNGRRLSKVVADGVHGWRNFVAPPMAYAEVEVEVGD
+LVTTVRADRMGVVDVVLDVELEPGWRTAVLRVGDEEEVTTDLYIASPDAKVGLVSDIDDT
+VVVTSLPRPLLAAWNSFVIDEHARTPTPGMAVLLRRIAAAEPMAPVLYLSTGAWNVAQTL
+TRFLGRNLYPLGALLLTSWGPTKDRWFRSGQEHKVTQLERLAQQFPDLQWILVGDDGQHD
+PEIYADFATKHPDKVKAIVIRQLTPSEALLAGGRAEATRHSTPGIPWCYGPDGAALSNQL
+EDLGILPVDFVDVHPEGWLEDILGEDEASAAGRDGDEHGVHGGRADQDEARDVDVSAQD
+>4_376
+MPAASDAPTPAPRRGRLAPSGDPTPVENVATHLQEGWNRWHRARALRAGNVPTVMAFTGY
+GSTSWVRILSRVVIASDEEFMNGRRLSKVVADGVRGWRNFVAPPMAYAEVEVQVGDLRTT
+VRTDRMGVVDVVLDVELEPGWQTATLHVGGQEEHAVMDLYICEPGARIGLVSDIDDTVVV
+TSLPRPLLAAWNSFVIDEHARTPTPGIAVLLRRIAELEPKAPVLYLSTGAWNVAQTLTRF
+LGRNLYPLGALLLTSWGPTRDRWFRSGQEHKRVQLERLAEQFPDIQWILVGDDGQHDPEI
+YAEFAQRHPDRVKAIVIRQLTPSQALLAGGRAEDTRHSTPGIPWCYGPDGATLSNQLEDL
+GILPVEFVDVQPEAWREDILGDDEAPATLDAAAQRDGRSADEEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d382689d8b45ff0b133d49e53adf8d440332ce96
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000435.fa
@@ -0,0 +1,46 @@
+>0_376
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVTTAMPTAPDHLITGTAWLVPWGLTLLPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGGGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLTGLLLLVPLALTSGTLGLGALTDLGSHVWAVSAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD
+>1_109
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTAHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAAVAVLALTGLNALLVAGRLAVEWTAVV
+TVAQAIGGGPLGGLLVALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPISAGVVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLAGLLLLVPLALTSGTLGLGTLTDIGPHVWAVCAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGLRDRPSPRRARD
+>2_2504
+MTALLSLLAVMIPTLVVWATGGFQRPTIEGALQVGGTLWLALHAVPVTVATVLPTAEGHV
+LSGTAWLVPWGLTLIPLLLSWRAGRRLARASYRDQAWQAFAGAVVGYALAGLTVAFLPGT
+PELRVSPWAAALLPALLFGIAALAGARREAGTWAHLIGLDLTERIARRSQYERWAGSYAW
+SVVRAAVVALLVLAALSALLVAVRLAVEWPAVVTLAQAIDAGPFGGLLLAVLQIGWLPTL
+TGWAIAWTAGPGFSVGSDSLYSVFGATPAAAPALPALGALPAAWAPWHPLFLAVPIAAGV
+AAGVWLLREGENHLDDWLDARTGHRAVSLALSTLALAVLTGLLAGLLLLVPLALTSGTLG
+VGTLTDIGANVWAVCAAVAGWVALGCAAGYLVALALAGRRFIPPAEAAVAAERPRPRRSR
+D
+>3_2375
+MSPRVPSLLRPVPLPLWLQGVVEALVTALTSLALVLVPTLAVWITGGFSSTRIEDVLQTG
+GALWLGLHAVPLAVTTVVAQADTPTVTGTVWLVPWALTALPVWLSWRAGRRLARASYREQ
+AWQALAGAVAAYAVVALACALLPGEGRITVHPLPSVLLPCLLFTTSAVAGARREAGTWAH
+LIGLDLTERIARRSQYERWAGTYAWSVLRGAGVGLAALAGLHALLVTVAVLVRWPRIIEV
+QQMVGAGPVGGLMLALLEIGWLPTFTAWAVAWTAGPGFAVGADGHYSVFGTTPAPVPALP
+LLEALPAPWAPWHPAFLLVPVLAGAVAGWWLLREGENHLDDWIDSRITARWASLTLSTLA
+LALLLGLVSGVAVLVPLALTNGTLGVGSMREIGSNAPLVALAVAGWMALGCALGYLVALA
+VVDRPVRGRRRISLPLPGSAPRAVTGRARRLPPRRLPRGVADAEADEPEVAAPAAAREEI
+PGRETPAQETPSEEPPAAARPAPRRAGAPRVPRVPRPAPRRARD
+>4_382
+MSSRPAAPRLLRPVPLPLWLQGVVEALVTAMISLLAVMVPTLAVWATGGFERPTIEGAVQ
+VGGVLWLALHAVPVTVATAMPTAPDHLITGTAWLVPWGLTLVPLALSWRAGRRLARASYR
+DQAWQAFVGAVGAYALVGLAVAFLPGTDELTVHPAPAALLPALLFGVAALAGARREAGTW
+AHLIGLDLTERISRRSQYERWAGSYAWSVVRAAVLAVLALTGLNALLVAGRLAVEWTAVV
+TVAEAIGAGPLGGLLLALLQIGWLPTFTAWSIAWTAGPGFSVGADSLYSVFGATPATAPA
+LPALGALPGTWSPWQLLLLAVPIGAGAVAGVWLLREGENHLDDWLHTRHGSRAVSLTLST
+LALAVLTGLLTGLLLLVPLALTSGTLGLGTLTDIGSHVWAVCAAVAGWVALGCAAGYLTA
+LAVAGHRDGTTTVPRSGDRASGPRDRPSPRRARD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b215281992117590c02098b81756f982f80709ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000444.fa
@@ -0,0 +1,81 @@
+>0_389
+MVPMPTPVDPVTVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADSHPGADPDARARLADA
+AVGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAKALEADPTVDALVFLPGVAEVETVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRTDPAVPRVVVATAVAESSLTVPGVRLVVDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLGAVDADGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWHREADR
+LERLARRHAHHAPETREPDEPGPEAATAPRHSAGLVAALAFPAWIARRAGEEGAYLLASG
+TRAALPRDAVGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRSLVERAGAGLRRTE
+DTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRDALAADGLARFDPRGRAERL
+RRRVHLLHRVLGAPWPDLSDTALPDLDTLVDGLAADLAAGRPLARLDAEALLRGALPWPE
+AGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVL
+HLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAVAEPTARTNRRAL
+>1_118
+MDPMPTPVDPVAVPSALSTALGRLSAGLTFAAALPELGSALDARGAAVVEAPPGTGKTTV
+VPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDARARLADA
+AVGYAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFAL
+LADLRQLRPELALVAMSATVDAAALAARWARGMGEAPLPVVSTPAVLHPLREEHAPFRGH
+RLTAEGRVDRAFLDHVAATAARAHAEALEADPTVDALVFLPGVAEVEAVAGRVAALAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAP
+VALAFTAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDP
+PLGHALLRAALWTGPRPAAEATAALALDLRAPGADLEALVASVRDGRHPEAGRWRREADR
+LERLARRHAHHSLETRAPGEPGPEATAAARRHPAGLVAALAFPAWIARRAGEAGAYLLAS
+GTRAALPRDAAGGGLAGQEWLAVAEVARVAGDAAGTGAAIRATAPIDRTLAELAGAGLRR
+TEDTADWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTE
+RLRRRVHLLHRVLGAPWPDLSDAALPGLDALVDGLAADLAAGRSLARLDAEALLRGALPW
+PEAGRLDELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPV
+VLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
+>2_2493
+MPAPSPHSSRPASVDTAVAPALSAALERLGSGLTFVAALPDLEAALDARGAAVVEAPPGT
+GKTTVVPPALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRSAVLDAADRTSAPDALADAA
+VGYAVRGDAVGGGASAVEFVTPGLLLRRLLADPGLDGVDAVVLDEVHERDLDTDVLFALL
+ADLRQLRPELALVAMSATVDAAALAARWARGMGEEAPLPVVSTPAVLHPLREEHAPFRGR
+RLTAEGRVDRAFLDHVAATAARAHAAALDADPTVDALVFVPGVAEVEAVAGRVAARAPDT
+EVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRD
+RGRGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGAAPAAPTPALAVVDLAP
+VALAFAAWGAPGGRGLTLPKDPPADAMAAAERTLASLGAVDTDGRITPHGAVLAELPLDP
+PLGHALLRAAPLTGPRPAAEATAALALDLRASGADLEALVAALRDGRHPESRRWRREADR
+LERLARRHAHRAPETREPDGPGPEAATARRHPAGLVAALASPAWIARRAGEAGAYLLASG
+TRAALPRNAVVGGLAGQEWLAVAEVARAAGDAAGTGAAIRAAAPIDRPLAELAGAGLRRT
+EDTADWRGDRLTGRRVDRMGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRAER
+LRRRVHLLHRVLGAPWPDLSDTALPGLDALVDGLAADLAAGRSLAHVDAEALLRGALPWP
+EAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGRELVV
+LHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRVR
+>3_2361
+MSTSSASHSTPDLRAALAAASARLGADLAFSASLPALEAALDARAGAVVHAPPGTGKTTA
+VPPAVALWLARRAESGGEGGRVLVTQPRRVAVRAAWRRLHGAVADALGPESGPDTGRLPD
+AVVGYAVRGDAVGRGASAVEFVTPGLLLRRLLGDPGLEGVGAVVLDEVHERDLDTDVLFA
+LLADLRQLRPELALTAMSATLDADALAARWATGMGEDPVPVVRTPSVQHPLTVEHAPFGG
+PRTTADGRVDRDFLDHVAATAARAHAEALDADPTVDALVFVPGVAEVEAVAGRVAALAPD
+TEVRVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRR
+DRGRGITGLATVQASRAAADQRAGRAARLGPGTAVRCHTAAALGAAPAAPTPALAVADLA
+SVVLAFAVWGAPGGDGLVLPEDPPADAMAAAERTLASLDAVDTDGRITPHGTVLAELPLD
+PPLGHALLRAAPLTGPRSAAEATAALALDLRAPGADLEALVAALRDGRHPEAGRWRREAD
+RLERLARRHAHRAPETREPDEPGPAATATARRHPAGLVAALAFPAWIARRAGEEGAYLLA
+SGTRAALPRDAVGGGLAGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRPLAELAGAGLR
+RTEDTAEWRGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRVALAADGLARFDPSGRA
+ERLRRRVHLLHRVLGAPWPDLSDATLPGLDALVDGLAADLAAGRSLTRLDAEALLRGALP
+WPEAGRLDELAPERLPVPSGRGVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREP
+VVLHLLSPAGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTDRTNRRA
+R
+>4_392
+MPTPVDPVSVPSALSAALGRLSAGLTFAAALPDLEAALDARGAAVVEAPPGTGKTTVVPP
+ALAVRLADHGGGRVLVTQPRRVAVRAAWRRLRTAVLAAAADAQPGADPDAQARLGDAAVG
+YAVRGDAAGGGASAVEFVTPGLLLRRLLADPGLDGVGAVVLDEVHERDLDTDVLFALLAD
+LRQLRPELALVAMSATVDAAALAARWARGMGEDAPLPVVSTPAVLHPLREEHTPFRGHRL
+TAEGRVDRAFLDHVAATAARAHAEALDADPTVDALVFLPGVAEVEAVAGRVAALAPDTEV
+RVLHGRQEPADQDAALAGRADPAVPRVVVATAVAESSLTVPGVRLVIDSGLAREPRRDRG
+RGMAGLVTVQASRAAAGQRAGRAARLGPGTVVRCHTAAALGTAPAAPTPALAVVDLAPVA
+LAFAAWGAPGGRGLTLPEDPPADAMAAAERTLASLDAVDADGRITPHGAVLAELPLDPPL
+GHALLRAAPWTGPRPAAEATAALALDLRAPGADLEALVAAVRDGRHPEAGRWRREADRLE
+RLARRHAHHAPGEPGPEAAATVRRHPAGLVAALAFPAWIARRAGEAGAYLLASGTRAALP
+RDAAGGDLTGQEWLAVAEVARVAGDAAGTGAAIRAAAPIDRTLAELAGAGLRRTEDTADW
+RGDRLTGRRVDRLGALVLAETPAPVAPDAAAQAVRAALAADGLARFDPSGRTERLRRRVH
+LLHRVLGAPWPDLSDAGLPGLDALVDGLAADLAAGRPLTRLDAEALLRGALPWPEAGRLD
+ELAPERLPVPSGRAVVVDYPAVHEDTPPVVAAKLQEFFGARVTPAVADGREPVVLHLLSP
+AGRPLAVTADLPSFWAGPYAQVRAENRGRYPKHPWPEDPAAAEPTARTNRRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45ef8441d93b0570cb5cf4f54cf1e5db233e0e51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000454.fa
@@ -0,0 +1,49 @@
+>0_403
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAGESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAAVAALDVVRRRRAARAA
+>1_133
+MTPRPPHPADPASGAFTPDQRRILTALLMPLFLALMSVSVVNVALPAIESGLDATSADLQ
+WVLAGYTLTFGTVLVAAGRAGDLWGRKNLFLAGITLYMLGSLLSGLAGDTLLLNAGRLLT
+GLGAGVFNPQVIGFIQSNFHGRARGRAYGLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWR
+STFLMNVPVGLAAVAMGALWLPPPTRVHGLPPAPGPRGIAALDPVGALLLGAGGVSLMVP
+FIVPGTAWLLVLAAALVTAWWLWEKRVKARASATGVQPMVDPALFRRPSFTIGALESTIY
+LATMPAVFAIVAIFLQRGMGFTPLEAGLVGLPGAVVVASLSPWVGSMVQRRGPVLVLLGA
+LVGLVSLGVLALAFERSAAGAWSPWIVGVGLIVQSASQALLLTSTQVLMMDDVAGHEAGA
+AGGVAQTAQRLGTALGLSVVTGAFFAALAGAAAESAGPPSAAAYAHAASTAMGMVAVCWA
+LTAVVAALDVVRRRRAVRAA
+>2_2477
+MGGPVAATARRPANRRAGPVVVRAYPEAVTPRPRSADGDAAPAAFTPEQRRILTALLMPL
+FLALMSVSVVNVALPAIESGLHATSADLQWVLAGYTLTFGTVLVASGRAGDLWGRKSLFL
+VGIGLYVAGALVSGFAADPLMLNAGRLVTGVGAGVFNPQVVGFIQSNFSGRARGRAYGLF
+GTVIGLGVAVGPMLGGLLLGALGPEWGWRSTFLMNAPVGLAAIVMGVLWLPAPTRVHGLP
+AAPGPRGIAALDPVGALLLGLGAVCLMVPFIVPGTAGLLVLAAALVTAWWLWEKRVKARA
+SATGVQPMVDPALFRRLSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGLVGL
+PGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVGVGL
+IVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAALAGA
+AAEGAGPPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAVRAA
+>3_2347
+MTLPSPAAAESGAFTADQRRILTVLLIPLFLALMSVSVVNVALPSIEGGLGASSADLQWV
+LSGYTLTFGMVLVAAGRAGDLWGRRPLFLAGIALYVLGSLLSGLAPDPLWLNAGRLLTGL
+GAGVFNPQTIGFIQSHFTGRARGRAYGLFGMVVGLGVAVGPLLGGLLLGALGPDWGWRST
+FLMNVPVGVLAIVMATAWLSPDTRVKGAAGRSGGPRGIAALDPVGALLLGGASLCLMVPF
+IAPGTWALLAGAAVLGVGWWLWELRVKRRAAATGVEPMVDPALFRRASFSIGAAESTIFL
+SSMPAVFAVTAVFLQQGMGFSPLASGLATLPGAVVQAVASPWAGSKVPSQGARMVFGGGV
+VGLASLAILALAFERSAAGAWSPWIVGAALAVMAVSQALILTTTQVLMMEDVAGHEAGAA
+GGVAQTAQRMGTALGLSVVMGAFYAALAGAAGPGGAPSAAGFAHAASAAVLMVGACWLVT
+TAIAAADLVRRRRTAR
+>4_406
+MPLFLALMSVSVVNVALPAIESGLDATSADLQWVLAGYTLTFGTVLVAAGRAGDLWGRKS
+LFLAGITLYMLGSLLSGLAGDTLLLNAGRLLTGLGAGVFNPQVIGFIQSNFHGRARGRAY
+GLFGTVVGLGVAVGPLLGGLFLGAFGPEWGWRSTFLMNVPVGLAAVAMGALWLPPPTRVH
+GLPPAPGPRGIAALDPVGALLLGAGGVSLMVPFIVPGTAWLLVLAAALVTAWWLWEKRVK
+ARAWATGVQPMVDPALFRRPSFTIGALESTIYLATMPAVFAIVAIFLQRGMGFTPLEAGL
+VGLPGAVVVASLSPWVGSMVQRRGPVLVLLGALVGLVSLGVLALAFERSAAGAWSPWIVG
+VGLIVQSASQALLLTSTQVLMMDDVAGHEAGAAGGVAQTAQRLGTALGLSVVTGAFFAAL
+AGAAAESAGSPSAAAYAHAASTAMGMVAVCWALTAVVAALDVVRRRRAARAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000458.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000458.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2130af87ee1b561b39c5787be0e64b6b01dec03
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000458.fa
@@ -0,0 +1,30 @@
+>0_407
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAERARRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>1_137
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAAKCDRRVELQDGVVIA
+DERVGTERDGARA
+>2_2473
+MHTVQQAAGAHAPAGREPVLETENLVKVYGRGESRFDALKGVTLQIQAGESVAIVGKSGS
+GKSTLMHLLALLDRPSAGVVAMDGRPVQDVSPAEVARLRNETFGFVFQQFFLNPAQTVLE
+NTVLPLKISGVPRAERRERGMAVLERLELADKAGNKATDLSGGQKQRVCIARALVNRPTV
+LFADEPTGNLDSATSAAVEDILFGLHRDEGITLVVVTHDDDLAARCDRRLVMQDGMIVDE
+TTTAGAQA
+>3_2343
+MSTVHTHPPETQASRGEEPVLETENLVKVYGRGASRFDALKGVTLQIHRGESVAVVGKSG
+SGKSTLMHLLALLDVPTSGVVAMDGRPVSQLKAAEVAHLRNERFGFVFQQFFLNADQTVL
+ENVVLPLKIAGVPRHEREARGREVLERLEIADKAKNRANDLSGGQKQRVCIARALINRPT
+VLFADEPTGNLDSATSRSVEEILFGLHRDEGITLVVVTHDDDLAAQCDRRLVMQDGVIVA
+AEGAGRAVAAGTGARA
+>4_410
+MSTAVPIPAVAEVPPGAEPVLETENLVKVYGRGASRFDALKGITLQIQRGESLAVVGKSG
+SGKSTLMHLLALLDQPSAGVVAMDGRPVSQLKAAEISQLRNERFGFVFQQFFLNPNQTVL
+ENTVLPLKIAGVGRAQRTRRGMAVLERLELADKAKNKATDLSGGQKQRVCIARALVNNPT
+VLFADEPTGNLDSATSAAVEDILFGLHRDDGITLVVVTHDDDLAAKCDRRVELQDGVVID
+DERVGTEQDGARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a0e6d6ad9e2e3636c69c57956dfc46ec7ce86908
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000477.fa
@@ -0,0 +1,27 @@
+>0_428
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTASPKADAPTPTPEATTPTPAATGAEVIDL
+HSVQERRQAGHHGHLDGHPDADRADTAPAAPASPSAPPRRTAPARPAGRRTRPAPRRAAS
+AAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEI
+ATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETETETDTEAED
+TPAARADEVVNTRLPWAEGLWDSAVRAGLE
+>1_158
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSIQERRQAGHPDVDRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPRGAASAAA
+TAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAAREEIATM
+QAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATETEDTPAAG
+ADEVVNTRLPWAEGLWDSAVRAGLE
+>2_2451
+MAARRRAPLPDPVPARQITGRSLLVVAVLLVAAVLVAPTLRAFLNQQLEIAAAEEEIAAM
+QAQREDYEERIRLWDDPGYVTQQARERLQLVMPGETLYSVTGVPEEAPRDPRPEAPAGEP
+VNTRLPWAEGLWDSAVRAGPRVSPGPRPDPGSGPARP
+>3_2323
+MSARRPRVPRVAVPDTAPERATPAVVEPVVVEPAPVAPAAPEAPAPPAPPGPQVIDLQEA
+AQRRRHEATRPSPRPDAERAAAQRVARLREERRRATVREHAAARRRVPLPEPVPARQLTG
+RSLVVLAVLIIAAVLVAPTARLMLNQQLEISAAQQDIAEQQRRKAEYEEQIRRWDDPGYV
+AQQARQRLELVMPGETLYTVTGLPDESGAVPADSVPQEKVNDRLPWVEGLWDSAVRAATE
+>4_431
+MSPRRPRVPRVDPTTGAPRRTAVAAPAAPTTAFPEADTPTPTPAAPTPAPAATDAEVIDL
+QSVQERRQAGHPGHLDGHPDADRADTAPAGDTAAPASPSAPPRRTAPARPAGRRPRPAPR
+RAASAAATAARRRAPLPEPVPARQITGRSLIVVAVLLVAAVLVAPTLRAFLNQQLEISAA
+REEIATMQAQREDYERRIQLWDDPAYVTQQARERLELVMPGETLYSVTGRPSETDTATET
+EDTPAAGADEVVNTRLPWAEGLWDSAVRAGLE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000479.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000479.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3c3cd61a03e9502cdf2343c0a3605f510704c52
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000479.fa
@@ -0,0 +1,45 @@
+>0_430
+MSLTPELSPKPRLLIVGGGYAGFQLAKELQTKVKDRGGVVTVVDPLPYMTYQPFLPEVVG
+GHIVGRNVVVDLATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFELPYQDIAMTAGAT
+TRVFPIKGLGEHGIGLKTVEEAVTLRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+IETVGEMEHLIRTAVARNPRLSQSEVRIVLVEAMGRIMPEVGEDQAVGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANAVAKQTDFPVEERGRIEV
+TPTLQVKDGENGVFEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYMAVR
+HGEGEVQEYVHKSLGAVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>1_160
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVEHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
+>2_2449
+MSLTPELSPKPRLLIVGGGYAGFHIAKELQKKVKDAGGVVTVVDPLPYMTYQPFLPEVVG
+GHIDGRNVVVDHATHLKDAEVLRGTVVKVEHARRVATVRGEDGHEFEVPYQDVVMTAGAT
+TRVFPIAGLGEHGIGLKTVEEAEALRNQILERLDAASLMVDAEARRRALTFVVVGGGFAG
+VETVGEMEHLIRTAVSRDPRVSQSEVRIALVEAMGRIMPEVSEDQAAGVVEHLKDRGIEV
+LLNTSLGDATDGIMTLVDMKDKSEKEKFGADTLVWTAGVAANSVAKQTDFPVEERGRIEV
+TATLQVKDGQGGVLEGAWGCGDVCAVPDLTGAGPGGFCVPNAQHAGRQAKQLAANYLAVR
+HGEGEVQEYVHKSLGTVAGLGFFKGVGNPLGVKISGPAAFLAHRGYHAYAMPTLDRRFRI
+FAGWVAETLFGRDSTSVEGQDRPFNAFRRAAGVELEPGRFERKRALESSKG
+>3_2321
+MSITPDLSPKPRLLVVGGGYAGFHIAQTLQSKVKDRGGVVTVVDPRPYMTYQPFLPEVVG
+GHIEGRHVIVDLQTHLKDTEVVRGAVTKVEHARKVAVVRGEDGAEFEVPYQDIVMTAGAN
+TRVFPIPGLAEQGIGLKTVEEAVALRNQILERLDAAALMTDAEQRRAALTFVVVGGGFAG
+IEAIAEMENLIRTAVSRNENLSQTEVRIVLVEAMGRIMPEVSEDQAQAVVAHLKGRGIEV
+LLNTSLGDATGGVMKLVNMADKSEADSFRADTLVWTAGVAANGVAKQTDFPVEDRGRIEV
+TPTLQIKDGEGVLEGAWACGDVAAVPDLTGAGPGGFCVPNAQHAGRQAAQLAKNYMAVRH
+GEGEVQEYVHKSLGAVAGLGFLKGVGNPMGVKLFGVPAFLAHRGYHAYAMPTLERRFRIV
+SGWIAETLFGRDSTSVDGQETPFNAFRVAAGAEPVPSTLEKKRAGELAAK
+>4_433
+MSLTPELSPKPRLLIVGGGYAGFHVARELQKKVAERGGVVTVVDPRPYMTYYPFLPEVVG
+GHIEGRHVNVDLQTHLKDAEVVRGAVVSVDHAGRTAVVRGEGGDEFEIPYQDIVMTAGAV
+TRVFPIPGLGEQGIGLRSVEEAVQLRNQILERLDAGSLMTDAEERKRALTFVVVGGGFAG
+IEAIAEMENLIRNAVERNERLSQSEIRIVLVEAMGRIMPEVSEEQAQGVVGHLKDRGIEV
+LLNTSLGDATDGVMKLVAMPSKEEAETFAADTLVWCAGVVANSVVKSTDFPVDDRGRVEA
+TPTLQIKDGEAGALEGAWACGDVSAVPDLTGAGPGGFCVPNAQHAIRQAKRLAANYMAVR
+HGEGEVQEYVHKSLGTVAGLGFGRGVGNPLGTKIAGIPAFLAHRGYHGYAMPTLERKFRI
+LSGWVAETLFGRDSTSVAGLDTPFNPFRRAAGVELEPGRFERQRALESSKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f2d8e16b39870734df1fe5a2333ab9870760debb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000482.fa
@@ -0,0 +1,40 @@
+>0_436
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAELGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVSLGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDETAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>1_163
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGVAAALLCVLLLVVVVVGLMGLAGQQIVQGFAQLGDQLGQAVDD
+TIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATVMNSAVTFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTGHALEPGGAEDEAAGSHRYRPSAHDDAALASEADAGTRHGDDA
+>2_2434
+MSSTLAAQTKINKDVPYGLTVAAAWSWRLVAVLVGLGILWWLLSFVSLVLIPVLVAALLA
+TLLAPLFEGMRRIGIPGIAASLLCVVLLIVVVVGLVVVAGQQIAQGFSDLGDKLTQAVDG
+AIAWLASIGVELPTAGGGLEGLWQTLRDNSGTLLDSAMTFGSTAVNIGAGFFIALFSLIF
+FLYDGDRIWRFILVFVPKAHRATVGRAGQTGWRALGNYVRVQIFVAFVDAVGIGLGALIL
+GVPLAIPLAVLVFLASFIPMIGATVTGAIAVLFALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSAVLGLAGAVFAVPVLAFVNSFIRALTADPPEQLTD
+RSDQALAPGSAADEAVGSHVFEPTKHDDAALASEDDAGTSGDLR
+>3_2318
+MSSTLSTDAKLEKDIPYGLTVAAGWSWRVIAVAAMLWVVWHFAGFASLVIIPVLVAALLA
+VLLAPIYRALRRARIPGVLAAVLSIVLLLAAVVLLAWVAGLELVQGFSDLSDQLGASVEH
+LVTWVQGMGVPVSFDAAALDNVWSTVKDNSGVLVDGALAFGSTAANVLTGLFIALFTLIF
+FLFDGERIWRFLLAFVPHTSRSRVDVAGRTGWNALGSFVRVQIVVAFIDAVGIGLGAWLL
+GVPLALPVAVIVFLFSFVPTIGAIASGALACVLALTANGLVNALLMLGVVILVQQIESNL
+LQPLIMGRAVSLHPLAVFLGVAAGGVALGLVGAVFAVPLLAFANAFVQALRAKGPGEEIL
+PGEKVFRPSDEVIAAARRDAKLDPKLDPTSFDDDSGPDGDVEDGRTGSTRTELKP
+>4_436
+MSSTLAAQTKIDKDVPYGLTVAAAWSWRLVAVVIGIGVVVYLLGFVSLVVIPILVAALLA
+TLLAPVFQAMRRIKVPGIAAALLCVLLLVVVVVGLMGLAGQQIVQGVAQLGDQLGQAVDD
+AIAWLAGVGVEIPRSGAGLEGLWQTLRDNSATLMNSAVSFGSTAVNIGAGLFIALFSLIF
+FLYDGDRIWRFLLIFVPKAHRATVGRAGRSGWQSLGSYVRVQIFVAFIDAVGIGIGALIL
+GVPLAIPLAVLVFLASFIPMIGATLTGAMAVLLALMSNGLVNALLMLGVVLLVQQIESNV
+LQPLVMGKAVALHPLAVFLAVAAGSTVLGLAGAVFAVPVLAFVNSFVRALTADTPEELTE
+RTDHALEPGGAEDEAAGSHRYRPSTHEDAALASEADAGTRHGDGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000492.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000492.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4223beda33232971e03b46b8e74b54ea35f160fb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000492.fa
@@ -0,0 +1,20 @@
+>0_447
+MSGVGWAWTHGAPATAVLWSLGLVWFAVCAGVLVRTDLREHRLPNRWTLRLALGGLTMMT
+GGALLAGRGDLTLCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>1_174
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
+>2_2424
+MDGVGWAWAQGLPATAVLWSAGLAWFAVCAAVLVRVDLREHRLPNRWTLRLALGGLAAMA
+GGAALAGRADLVLSSVLGGLGYAAAMLVLHVLSRGSLGMGDVKLAAGLGAYTGVLGGSAV
+VAAGLGAILLGGAVAAVLVAARRASRSTALPFGPPMILAAAAVLAFAPAGG
+>3_2307
+MTWWTGAWEAGERLTAMLWAAGLVWFLLCSVVLARTDLREHRLPNRWTGRLALGGVVAMG
+GGAVLGGLWSVVASCLLGGLGYALAMLALHVLTRGGLGLGDVKLAAGLGLYCGVAGLAAV
+LAAAVLAVLLGGVVAVVLVLARRADRHTALPFGPAMVAGALGVLLLA
+>4_447
+MSGVGWAWTHGAPATAVLWTLGLAWFAVCSGVLVRTDLREHRLSNRWTLRLALGGLAMMT
+GGALLAGRGDLALCSLLGGLGYTVAMLALHVLSRGGLGMGDVKLAGGLGVYTGVLGPTAV
+LAAGVGAILLGGVVAGLLVLAGRATGRTALPFGPAMVAAAAGVLVLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..719f7c87f639afac770d1472355f6da2643d1aa0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000495.fa
@@ -0,0 +1,25 @@
+>0_450
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>1_177
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATIPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDQVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+QAVLEDLAHGVAKETR
+>2_2421
+MLTVSSTHPTDPTDPNAPAPRPVLTAKQAQRARQPWIGMVLSVVALLALVAVVLILNPEP
+PQRPREDRVDVAAAAATVPHDDGVLPALAPEVPESWYANFARLQTMDGVSTWDVGWVVTD
+TVFAGMQQAHDVDPTWVTLRVDSVPATETLEIDGLAWDLHADPRAPEKRLVTEVEDTTVV
+LTTTGDRAVLEDLARGVAKETR
+>3_2304
+MPGMSSPDPAAPPAPRPVLTPKQAQRARAPWIAMVLSTLAVLGIVLVALMVNQPPPAPAQ
+ADRVDVAAAASTVPHDDGALPALAPDVPEPWDSTYARVERLQGVDTWDVGWAVNDAVFAG
+LKQTSRADPTWLALRVGSAPAVGTVDVDGITWDHYAPQDSKDQHLVAEVRGSTLVLTTSG
+DQAVLEDLARAVAKEIR
+>4_450
+MLTVSSADPHAPAPRPVLTATQAQRARQPWMAMVLSLAALLAIVAVVLLLNPEPPQRPRE
+DRVDVAAEAATVPHDDGDLPALAPEVPESWYANYARLQKLDGVSTWDVGWVVTDTVFAGL
+QQAEDVDPTWVSLRVDHVPTSETIEIDGIAWDLHADPKKPERRLVAEVDGSTVVLTTTGD
+RAVLEDLAHGVAKETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e327e8de1ed24676568a6d3fe91c0a74da6b3c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000499.fa
@@ -0,0 +1,43 @@
+>0_455
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>1_182
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLTLDDADDARASAADGTLAAWLGAGIAPLLAEALVPFSRELSA
+QVARTPSGEVAVYPIVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVVALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
+>2_2416
+MMAGPAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRVLQEVGVAVRPGPEALQHAQDKLVMRAAVERLGLPNPAWAAVRDLDEVLAFGDEHG
+WPMILKTPRGGYDGKGVLKLDDADDARASASDGTLGTWLGAGIAPLLAEALVPFTRELSA
+QVARTPSGRVAAYPVVDSVQVAGVCDLVVAPARDLDPAVAEAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQINELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGDTAPRGAG
+VVMKNLLGGAREDLHAGLADALAAHPQAKVHLYGKAVRPGRKVGHVNVVADHGLTLEQAV
+RAAESAAAVLRDGAAPDAVDASPSSPATPHPAGGPPMTATPQNPAQPLQDDAPVVSVVMG
+SDSDWPVMSAAAEALRELDVPVEVGVVSAHRMPHEMVEFGARAHERGIRVIVAGAGGAAH
+LPGMLASVTPLPVIGVPVKLKSLDGLDSLLSIVQMPAGVPVATVSVDGARNAGLLAARIL
+ASADTEEGERLRAALTEHAAELNAQAQAKGARLRERMAADR
+>3_2299
+MIGGGQLARMMAGPAAELGVPFRVLAEAPDASAAQVAPHMVGDHASLEDLRAFAATVDVV
+TFDHEHVPTEHLRTLEAAGVAVRPGPDALQYAQDKLLMRGLVERLGLPNPAWAPVSSLEE
+VIAFGDEHGWPMILKTARGGYDGKGVLKVDSADDARSGAADGTLGTWLGAGIAPLLAEAM
+VPFARELSAQVARRPSGEVAAYPVVASLQTQGVCDVVTAPAPDLAPAVAEAASGAAVRIA
+EELDVTGMLAVELFETPGTDAGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDMPL
+GGTAPRGDGTVMKNVLGGAHEDLHSGFSEALAAHPEAKVHVYGKGVRPGRKVGHVNVVAE
+HGLSLADAERIAESTAAVLRDATAPSAPTPKA
+>4_455
+MMAGAAAELGVPFRVLAEAPDASAAQVAPHVVGDHTDLADLRAFAATVDVVTFDHEHVPT
+EHLRALQEAGVAVRPDPEALQHAQDKLVMRAAVERLGLPNPAWAPVDDLEAVLAFGDEHG
+WPMILKTARGGYDGKGVLKLDDADDARASAADGTLAAWLGAGITPLLAEALVPFSRELSA
+QVARTPSGEVAVYPVVDSVQVAGVCDLVVAPAQDLDPAVAAAATAAAVRLAEELDVTGML
+AVELFETPGVGPGFQVNELAMRPHNSGHWSMDGAVTGQFEQHVRAVLDLPLGETAPRGAG
+VVMKNVLGGAREDLHAGSVAALAAHPQAKVHLYGKDVRPGRKVGHVNVVADHGLSLEEAV
+RTAESAAALLRDDAPTTGTETEARP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9242923c1e6f7592b24f4852b869d76835108e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000501.fa
@@ -0,0 +1,25 @@
+>0_457
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP
+>1_184
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFTGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPATDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGTDVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP
+>2_2414
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPGEHGAVDQRIELSGRVTVNWAAKTAGLL
+ADEGLGPGDPVALDLPAHWLSHALALGVLCAGAEPADDGAAPAAVLTDRPERWTDPATAV
+FAVALPRGLELPTGGAVADPSVVDVAAEILGQPDALPGPVDHVRPEALPAADVAAADGDA
+RTDEDQDDDGPRPRLTWAGMRAVLQAWDAGRAVQVRP
+>3_2297
+MVSLSAPRPDGPLVTRLASSPRPALVQEPAPAGEAAGAAHGAVDQRIELSGSVTVNWAAK
+AAGLLLDEGVAPGDAVLLDLPDHWLSRALALGVLCAGARPAFVAGPADRAQEAPDDAAAV
+LTDRPEHWDDPVLTVVAVRLPRGIEPDFGDDDAGDPSVVDLAAEIRAQPDALPGRVDHVT
+VDAVPADPADAAGPLTEGGVGVGRARLDAPALRASLEAWDAGRAAHVPA
+>4_457
+MVSLSAPRSTGPLVLRLASSPRPALVQEPGAPDEPGAVDQRIELSGRVTVNWAAKFAGLL
+GAEGIGAGDAVALDLPVHWLSHALALGVLCAEAEPALEGDSPAAVLTDRPEAWPDPSVAV
+FAVALPRGLEPEFDGPAVDPAVVDVAAEIRAQPDALPGPVDHVRPASIPAGADVAPDDDG
+PRPRLTWAGVRAALEAWDAGRAVTVRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000504.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000504.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba9237a5b73a05b6efaa20397c4d52c2d347d292
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000504.fa
@@ -0,0 +1,16 @@
+>0_460
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>1_187
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
+>2_2411
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRLAEPHTYDLCAEHARRTTAPRGWEVLR
+LELPGHYEAVAPDGTVHTVPTAPRAVPAAPPADVASRPSLAAPRPAPAVPPVDADEPEAP
+APPTRPGLRLVRDDDPLPPA
+>3_2294
+MRRCSKTGCQEPAEATLTYNYAGSQVVIGPLAQRAEPHAYDLCAAHAARTTAPRGWEVLR
+LAPAAPAAPGVAAPTHPALRLVTDPVEGTAG
+>4_460
+MRRCSKTGCQSPALATLTYNYADSQVVIGPLSRRAEPHTYDLCGEHARRTTAPRGWEVLR
+LELPEHYEAVDADGGVRTVPTRPMAVPPARPGLRVVRDGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000505.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000505.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb799d7ae607c483fc339f6880edc4ada54800d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000505.fa
@@ -0,0 +1,50 @@
+>0_461
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLGGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>1_188
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPFKADHYRY
+>2_2410
+MTETPAESRTPDVDPAYANRATVPGAAFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGESQPLAGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNETLEDYWWTASQILTWPGAAEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGQGDLFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDAGTDSERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKSQAEYLGVDVAGPYKADHYRY
+>3_2293
+MTETSSARPTPDVDPAFANRSTVPGATFDFAVRDLSLAEAGRHQIRLAEHEMPGLMALRE
+EYGESQPLKGARIAGSLHMTVQTAVLIETLTALGAEVRWASCNIFSTQDEAAAAIVVGSG
+TPDAPAGVPVFAWKGESLEEYWWTASQILTWPGAAEDPDRGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLAEDPQRWTRTASTLRGVSEETTTGVLRLYQ
+LAQEGTLLFPAINVNDSVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVEQGDLFVTTTGGKDIIMAED
+MLRMKDKAIVGNVGHFDNEIDMAGLGRVDGVVKTEIKPQVHEWTFDTGTEDERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELYDGSTGQGALTGEHYEKQVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
+>4_461
+MTETSAEFRTPDVDPAFANRTTVPGASFDFTVRDLSLAEAGRHQIRLAEHEMPGLMSLRE
+EYGEAQPLKGARIAGSLHMTVQTAVLIETLIALGAEVRWASCNIFSTQDEAAAAVVVGSG
+TPEDPQGVPVFAWKNESLEDYWWTASQILTWPGADEDPERGPNMILDDGGDATLLVHKGV
+EFEAAGAVPSATEDDPEEYRIILETLRRSLARDPQHWTRTAGTLRGVSEETTTGVLRLYQ
+LAQEGRLLFPAINVNDAVTKSKFDNKYGIRHSLPDGIMRATDVLIGGKVAVVCGYGDVGK
+GAAEALRGQGARVIVTEIDPICALQAAMDGYQVARLEDVVGEGDIFVTTTGGKDIIMAEH
+MAAMKDKAIVGNVGHFDNEIDMAGLARIPGVVKTEIKPQVHEWTLDGGTEAERSIIVLSE
+GRLLNLGNATGHPSFVMSASFTNQVMAQIELFGGSTGTGALTGEHYEKRVYTLPKVLDEK
+VARLHLDALGVGLTELTKAQAEYLGVDVAGPYKADHYRY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..655fac8862212fd25c95dece9a60fa6123935fd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000509.fa
@@ -0,0 +1,30 @@
+>0_465
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVAEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
+>1_194
+MTGRIVLAATPIGNLGDASARLRELMAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHHE
+HNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVTT
+ALALSGLPTDRFAFDGFVPRKDGDRRRWLTSLLTEARTVVAFESPQRLADALAVVVEVLG
+AERPVCVARELTKLHEEVVRGTAADVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEASE
+ADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARS
+>2_2405
+MTPRPTDLPSPSGRIVLAATPIGNLGDASARLRELLAEADVIAAEDTRTARRLCQGLGVT
+PAGRVVAHHEHNEAASTQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVT
+CAPGPSAVTTALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLAD
+ALAVVVEVLGAERPVCVARELTKLHEEVVRGTAAEVHAWAAERHAGEGIRGEIVLVIGPA
+SPDAASAGGATEADAVAEVGVLVDSGTRLKEAVATVAAAHGLRSRTLYQAVLAARG
+>3_2288
+MSLPAASGRIVLAATPLGNLGDATGRLRELLATADVIAAEDTRNTRRLCQGLGITPAGRL
+MAHHEHNEAASAAGLLERVRAGETVVMVSDAGMPTVSDPGFRLVEAAVAAGLPVTCAPGA
+SAVTTALALSGLPSDRFAFDGFLPRKDGERRRRLEEIRTDPRTVVYFESPQRTASALAVI
+AEVLGGARPVCVARELTKLHEEVVRGTADELVAWAVEREAGEGIRGEVAIVVGPAAPDAG
+AGADEADVLAEVAALTDSGTRLKEAVAAVAAAHGLRSRELYQAVLDARRG
+>4_465
+MPEGRIVLAATPIGNLGDASARLRDLLAEADVIAAEDTRTARRLCAGLGVTPAGRVVAHH
+EHNEAASAQGLLDQVRGGATVAVVSDAGMPTVSDPGYRLVAAAVSAGLPVTCAPGPSAVT
+TALALSGLPTDRFAFDGFVPRKDGERRRWLTSLLTEARTVVAFESPQRLADALAVVVEVL
+GAERPVCVARELTKLHEEVVRGTAAGVHAWAAERHAGEGIRGEIVLVIGPAAPGAEGEAS
+EADAVAEVAVLVESGTRLKEAVAAVAGAHGMRSRELYQAVLAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000517.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000517.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52e42fe211ecdada03bba9602e363d122a25ab48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000517.fa
@@ -0,0 +1,30 @@
+>0_478
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGAADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVIGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH
+>1_208
+MAERVEPAHGEDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPSGS
+MENTLEVGDRMLVNRTAYPDGMADAQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLTGI
+GRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPVDEPYIHNDLPFIRDELDCESEVMS
+ARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQAGDCARFVTREDIVGEVFVTVW
+PPTHWGGH
+>2_2395
+MAERVEPVRGEDGDDGSVAAPERRRSRLPGWASVLLNVVVAIAVVAVVQALWVKVYSVPS
+GSMEQTLEVGDRMLVNRTAYPDGMAASQDVVVFNANEDWAQPLPPEGPVENAVRTFGDIT
+GIGRSHDQALVKRVVGTEGQTVECCTSEGRVTVDGQPLDEPYLHNDLPFAPGRLDCESDV
+MSARCFGPITVPEDSMLVLGDHRSNSADSVIGCRGLPAEQAEGCARFVTREDVVGEVFVT
+IWPPSNWGGH
+>3_2278
+MAHTPDAVPARDEAACDEAVRDDAAPAPASSAAAPGRRRRVQLPFWASVLLNVAVALLVV
+SVVQALWVKVYSVPSGSMEQTLQVGDRMLVNRTAYPDGVAERQDIVVFDANETWGVDTVG
+EEGPVEGAVRTFGDLTGIGRSHENALVKRVIGLPGETVECCTSQGAVTVGGTPLEEDYLY
+EDLPFVPGTLDCTTTPRSSRCFGPVTVPERSMLVMGDHRSNSADSVYQCRGLTAEQAGDC
+AHFVRDEDVVGRVFSTVWPPSNWSGH
+>4_477
+MAERVEPAHGDDVDGGAVAAPQPHRPRLPFWASLLLNVVVALAVVAVVQALWVKVYSVPS
+GSMENTLEVGDRMLVNRTAYPDGAADSQDVVVFTANEDWAHPMPPEGAVENAVRTFGDLT
+GIGRSHEQALVKRVVGTAGQTVECCTAEGAVTVDGEPLDEPYIHNDLPFIRDELDCESEV
+MSARCFGPVTVPEDSMLVLGDHRSNSADSVIACRGIPADQVGDCARFVTREDIVGEVFVT
+VWPPTHWGGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000519.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000519.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d984c797f26cecf1319683edeff048d00270d299
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000519.fa
@@ -0,0 +1,35 @@
+>0_481
+MAAQSTTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVVAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGQRR
+>1_210
+MAAQSPTAAVTVVIPHYGDPAPTLALVDRLLTDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDAEITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGTPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAATRSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNVLRQARGVDVDARAVLRDEHAL
+VWKGKRR
+>2_2393
+MAAQSTAAAVTVVIPHYGDPAPTLALVDRLLADPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLSEVDTDLALVLNSDALITGEQIDALVAAAAPFQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQGVEWLTPLARFRHLPLLHEAVGHDVAAARSAAPVAVDWVM
+GAVMLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRDRGVASIVVPSVRVEHGMHGSSDPL
+RRRGWLVDSRFRYARKFGRPRALKAVLTAATGVNYAVNRVRQARGTDVDAAAVLRDEHAL
+IWKGTRR
+>3_2276
+MPASRIAPSVTVVIPHYGDPEPTRALVDALLAAPGRSVAGVVVSDDASPEPYPQPAPGRE
+GLTVVRREANGGFGANVNTGLAEVRTELALVLNSDAEITGEQIDALVEAARPYQPAVVSP
+QVVNEDGSPQWSGRHFPTVTHQTVEWLTPLARFRHLPALHEAVGHDVRAAEADSPVAVDW
+VMGAVMLLPMAEVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSVVVPSVRVVHGLHGSSD
+PLRRRAWLVDSRFRYARKFGRPRLLRGALTAATGVNWAVNRVRQTRGTDVDANAVFRAER
+DLIWKGTRR
+>4_480
+MTAQSPTAAVTVVIPHYGDPAPTLALVDRLLSDPGDALAAVVVSDDASPTPYPEAHDPRL
+TVVRRERNGGFGANVNTGLAAVTTELALVLNSDADITGAQIDALVAAAAPYQPAVVSPQV
+VNEDGSPQWSGRHFPTVLHQTVEWLTPLARFRHLDVLHEAVGHDVAAARSASPVAVDWVM
+GAVLLLPMAQVRAVGGFDEEYFMNSEEVDLQRRLRERGVPSIVVPAVRVPHGLHGSSDPL
+RRRGWLVDSRYRYARKFGHPRVLKAALTAATGANFAVNALRQARGVDVDARAVLRDEHAL
+VWKGRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000521.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000521.fa
new file mode 100644
index 0000000000000000000000000000000000000000..473e310ec223eececba953142c6eb4d2b8aafbfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000521.fa
@@ -0,0 +1,40 @@
+>0_483
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLLL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLPGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPRD
+ATLYAFTSADADWWTQGRADVEAVAVGSALLEQARRAAPAPSDTAGDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA
+>1_212
+MTDAPLFWRSGDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALARRGSTGDDVPRLLL
+PPGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAAGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARVGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSALLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWRRYGMTRWRPGRVPEPTPPLASPTTDP
+AAAIAEHVWKESA
+>2_2391
+MSGVGSGDVPLFWRPEDLPAWQRWQRAQWPASRRLADTARRLARAGRGALAAGRGAAPAP
+ESGLRLVLPAGDVHTLVGVESAAPTQRAALVEPVRALAEGRAGHAAADAARTAAGVGWVV
+PADVVAAQLPDLPGSDALSVHAVDDVMVAERLGGLRCVLVAGEYLPAGRAAVRWARERGA
+RVGVVQHGLLAVSTPPVPRDVALYAFTDHDAHWWTQGRTDVQAVAVGSALLEAARRMASH
+AVADAVPRAAGPGVFLGQLHGAELPRTDFARAAQEYVRATGAAYRPHPAERDRLSLAQHE
+AWRKAGMRIDATAGPLASTAGPVAAVFSTGILEAAQAGRPAWAVHPDPPAWLEGFWERYG
+MTRWRPGVETEPTPPLASPSADPAAAIAAHLWKETA
+>3_2274
+MTRAVAQPPLFWRAEQLDAWRRWQRTQWPLARRAADLVRGGVARSRGAVQAPDAGLRLLL
+PAGDVHTLIAVESAGPTQRAALVEPTRALAEGRTGLDAAARTRLLGGVAWVVPADVAGAL
+LPDLPAAAQLTGHAADPDTVGTRLAGLERVLVAGEYLPAGRAAVRWAHERGASVHVVQHG
+LLAVSTPPVPRDATLYAFTARDADWWTQGRADVRAVPVGSALLEAARRGAASADPTATGS
+TGPGPGLFLGQLHGAELPRAQFAAAAEQYVRTTGAVYRPHPAERDRLSRAQHARWEGAGI
+AVDRSGAPLTQTAGPVAAVFSTGILEAAQTGRPAWAVHPDPPRWLVEFWDRYGITRWMPG
+ADPTPTPALVAPTADPAAAIARDLWKEHA
+>4_482
+MTDAPLFWRSEDLPRWHAWQRAQWPLTRRAADTARSTVRGVAGALTRRRSTGDDAPRLYL
+PAGDVHTLVALESFGPTQLAALASPVAALATARPEAAAGVGWVLPAGDAPALPGAVGHRE
+HAATADVVTDRLSGLRRVLVAGEYLPSGRAAVRWARQRGARIGVVQHGLLAVSTPPVPQD
+ATLYAFTSADADWWTQGRADVEAVPVGSVLLEQARRTAPALSGAGDDGPGVFLGQLHGAE
+LPRRDFAAAAEQYVRATGAAYRPHPAERDRLSRGQHAAWRRAGVRIDDAGAPLVATRGPV
+AAVFSTGILEAAQAGRPAWAVHPEPPAWLEGFWRRYGMTRWRPGRTPEPTPPLASPTADP
+AAAIAEHVWKESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de1c63a8b2d62ddded2cf28c1cc9d67fbcb7250d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000526.fa
@@ -0,0 +1,40 @@
+>0_490
+MTDMTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRKDPRRALPLLPLASSLLHVKEPVAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRNSIKGRIARALRPGLRRWDRAAVRRRSRYVANSTVVKERIEDVYGLD
+GVDLVFPPHSVSTDGPQEPIPGAERLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHAIALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGTFVLDASIDAVGEGIKKLQAARWDTAAMRRHVEKFSEREFA
+LRIRALVEGLPGA
+>1_219
+MSEQTPATIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFEDAHIVTS
+PLNRVGVLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEDGRNSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKKRIDDVYGLD
+GVDLVFPPHSVSTDGPQGPIPGAEQLAEDGFLLSVARLMPYKHVDVAIEAAARAGRPLVV
+IGKGPEEARLRAMAGEDVVFGQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVDGVNGVFVEEPTVDAVAGGVERLLAHDWDRAAMQAHAERFSEAQFG
+RRIRALVAESPAGPAHRGRQ
+>2_2385
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGVLRRDPRRALPLLPVASSLMHVKEPVAVVSTSGWAHGFRYHGDTLVYCHTPARW
+VYLLEDYLGEEGQKSMKGRVARVLRPGLRAWDRAAQRRRTRYVANSTVVKERIEEAYGLT
+DVPIVFPPHSVSTDGSQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPDEARLKAMAGDGVVFAQDLTDAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTITEGVNGVFVEAPTVEAVTDGVEQALARDWDPPAMRAHAERFSEDQIA
+RQVRTQLGQLQNHARNKGAM
+>3_2267
+MKIHASRPLSARRASQPGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYNPEGTF
+PEFKKARIITSPLNRVGVLRSDPRRALPLLPLASSLMHVKEPLAVVSTSGWAHGFRYEGD
+TLVYCHTPARWVYLLEDYLGEGGQRSLKGRVARALRPALRAWDSAAQLRRTRYVANSTVV
+KRRIEEVYGVANVDLVFPPHSVSTDGPQAPIPGAEDLAEGGYLLSVARLMPYKHVDVAIR
+AAERTGRRLLVIGKGPEEARLRALAGQGVVFAQDLTDAQLRWAYAHAVALIAASHEDFGI
+TPLEASAWGVPTVALRAGGYLDTIVEGVNGVFVPEPTVEAVTDVVEQVLAQDWDRGAMQA
+HAEHFSEVAFRERLARLLDDPHGAV
+>4_489
+MTDTTRGRIAIAHDYLTQKGGAERVVLALHRMWPDAPIYTTFYDPEGTFPEFKDARIITS
+PLNRVGLLRKDPRRALPLLPLASSLMHVKEPIAVVSTSGWAHGFRYDGATLVYCHTPARW
+VYLLDDYLGEGGRDSIKGRIARVLRPGLRRWDRAAVRRRSRYVANSTVVKERIEEVYGLI
+DVPVVFPPHSVSTDGPQEPIPGAEHLAEGGYLLSVARLMPYKHVDVAIRAAERTGLRLLV
+IGKGPEEARLKAMAGDGVVFAQDLTEAQLRWAYAHATALIAASHEDFGITPLEASAWGVP
+TVALRAGGYLDTIVEGVNGVFVNGTSVAAVAGGIEWVRAHNWDRAAMRSHARRFSEFEFG
+QQVQAQLGWIGISR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000531.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000531.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1cd9e7029d1bc642a2e78531e7d76c93f9d0af1c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000531.fa
@@ -0,0 +1,20 @@
+>0_506
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGALRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
+>1_236
+MAFSAQQSIPHPPAAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRAGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVDRQARALSSWLERDGGAARS
+>2_2370
+MAFSAQQSIPHPPAAVAAALASEEFHRSVVEQLGGSLVSFRVEGSPEGPMTVTTVRSAPA
+DRLPEMARKFIGSSLQVEQVERWEAPAADGSRVGTTTITVPAAKATAEGAQRLTAAGEGS
+QYSVDGTVTCKIPLVGSKLAAKAEPMVGKVVNRQARALTSWIGRDGGAAGA
+>3_2251
+MAFSAQQTIPHPPAAVAEALFSEDFHRSVAESLGGGLVSFARQDQADGGVELTIVRSGPT
+DRLPDMVRKVVGENLNIEQVERWSAPAADGSRTGTTTIRVPKAKATAEGTLRLAAAPAGT
+EYGVNGDLQVKIPLVGSKMAQMAEPMVGKVVARAGREVSAWIDRGGRG
+>4_506
+MAFSAQQPIPHPPSAVAAALASEDFHRSVVESFGGSLVSFSVEGSPEGPMTVTAVRSLPA
+DRIPDRVPDMARKLIGSALQVEQVERWDAPAADGSRTGTTTITVPSAKATADGSLRLTAA
+GEGSQFSVDGTLVCRIPLVGSKLAAKAEPMVGKVVNRQARALSSWLERDGGAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000534.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000534.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66f2b5cad77af8a75bf81140bdacd05ef6617d91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000534.fa
@@ -0,0 +1,16 @@
+>0_509
+MTVETTEGWTLAPNIAWARTAGGQAAVMTLEAGQPLLLGASGDVIWDVLVGGRTPEDDLV
+ADPPASLSTTDVTVQVAEAFGLAPADVAADVHAFLEMLEAHGVLVRVRTA
+>1_239
+MTVETTEGWALAPDIAWARTAGGQTAVMTLEAGQPLLLSASGDVIWDVLVGGRTPADDLV
+ADPPAPLSTTDVTVQVAKAFGLYPADVAADVHAFLEMLEAHGVLVRVRTA
+>2_2367
+MAADRLPAPFGMTSERGSAWAVAPGVAWALTDGGDAAVMHLEHGVPLLLSPTGHAVWDVL
+VGGRTPEDDLTAAPPIPLPEEAVAAETAAAFGLAPEDVAADVGAFLAMLEQHGVVVRVGG
+VLPRP
+>3_2248
+MSDAEHPPFAQAPAARAWRVAPTTAWVRSGEHQVTVMDLDEGNPQVLSPTGSAVWELLLD
+GRTPEDDLAADPPKPVEEEALCGAVAEAFGVDVEVVAADTRAFLGMLAGHRLVVPAVLP
+>4_509
+MTVETTEGWALAPDIAWARTAGGQAAVMTLEAGQPLLLSASGDVIWDVLVGGRTPEDDLI
+ADPPVPLSTTDVTVQVAEAFGLDPADVAADVHAFLEMLEAHGILVRVRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000537.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000537.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a1a53705477beceed8ce8c32e6a66431eef1111
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000537.fa
@@ -0,0 +1,35 @@
+>0_512
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQP
+HVRRHRTLIGVGLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+ERLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>1_245
+MVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVWGRFRSLMVPYLVWAAL
+MSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVLRRFLERFPSAV
+AWAVGLAGLAWAHLVPDSAIARTPLGVGLALPCLLFVLSGEMFRRRVQPHVRRHRTLIGV
+GLVLLGMVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTVERLLRSFARRT
+GTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALALSWLAGLALLAT
+PLSKPFTGARRRWHPVHRLRHVEPPHPVTSALPRVTTASERTHP
+>2_2361
+MDALRLVSIAAVVLGHAYLADLTFSRYLEIWRMPLFFFLTGYFWTRGRPVARDARGRFKA
+LMVPYLVWAVVMSAAALAWFGDDPERLQRLMAAGWYGGADQEPPWWAFWFISVLFFATVL
+RRFLERFPTAVAWGVGLAGLAWAYLVPESAIARTPLGVGLALPCLLFILSGEAFRRRVQP
+RIRRHRTLLGLALVGLGLAAVALGLEPHNIKFGGFGTPLLTPLVGVLMSAGMVLVFGAAV
+ERILREFARRTGSGQALRRVITALVRTGTVVVLLHGWVLMWVMRQGVEDNLLKFVLALGI
+SWLVGLALLATPLSKPLTGARRRWFPLHRLRGEEPPHPPTSALPRVTTASERTHP
+>3_2242
+MDALRLVSISAVVLGHAYLADLTFSPYLEIWRMPLFFFLTGYFWTRGRPWAADALSRFRS
+LMVPYLLWSVLMTLVVLSWSRRSQIDGVTLADLVSAGWYGGADQPPPWWAFWFISVLFFV
+ALLRRALERAPSWAGWAVALAGLAAAELVPESAIARTPLGIGLAAPCLFYVLAGEAFRRR
+VQPRIRRHRTLIGVALVAAGVGAVALGLPPHNIKWGGFGLFPWTPLTGIAMAAGMVLVFG
+AFVERRLRAFARDTGTGRAIRAGITALTRTGTVVVLLHGLVLMEAMRVGIEDNLMKFVVA
+LTVSWAVGLALLATPLARPLTGVPQQWFPFGREAGA
+>4_515
+MDALRLVSIAAVVLGHAYLTDLTFSRYLEIWRMPLFFFLTGYFWTRGRPWATDVRGRFRS
+LMVPYLVWAALMSVAAFAWFADDPDLLRRLMITGWYGGADQEPPWWAFWFISVLFFTTVL
+RRFLERFPSAVAWAVGLAGLAWAHFVPDSAIARTPLGVGLALPCLLFVLSGETFRRRVQP
+HVRRHRTLIGVGLVLLGLVAVRLGLEPPNIKFGGFGTPVLTPAVGVLMSAGMVLVFGSTV
+EGLLRSFARRTGTGQALRRAITALVRTGTVVVLLHGWVLMWVTRHGVEDNAAKFALALAL
+SWLAGLALLATPLSKPFTGARRRWHPVHRLRRVEPPHPVTSALPRVPTASERTHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000538.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000538.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3ca4eafda03b6fd2ec746d5fc9d343210469fa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000538.fa
@@ -0,0 +1,25 @@
+>0_514
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
+>1_247
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELADS
+DVLTCTVIGFPLGANTSEVKAFEARQAIDAGADEVDMVLDIAAARAGDRARLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEDIGVKASGGVRTREDALAMIEAGATRIGASSALAILGSD
+>2_2359
+MTRTLSTAELAQYIDATALKTETSEADVRRLVAEARQAGVKSVCVNPRWVPLVSAELAGS
+DVLTCTVIGFPLGANASEVKTFEARQAIEAGAHEVDMVIDVAAARAGDRARLVEDVRAVA
+EAAHAAGPAGQGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGEHVGVKASGGVRTREDALAMIEAGATRIGASSALAILGTD
+>3_2241
+MSETPQLTTAELAKHIDHTLLKPEASREDILRVVAEAREAGVKSVCVNPRWVREVRAGLE
+GSDVLTCTVIGFPLGASSSAVKAFETTQAIADGADEVDMVIDIAAARAGDRARLEEDVRA
+VVAAAHASGPAGRAGTLVKVIIETALLDDAAKVLACEAAVAAGADFVKTSTGFSTGGATV
+EDVALMRRTVGPEIGVKASGGVRSREDALAMITAGATRIGASSALAILGDD
+>4_517
+MTVSLTTAELAKYIDATALKADTSEADVRRLVAESREAGVKSVCINPVWVPLVAAELAGS
+DVLTCTVIGFPLGANASEVKAFEARQAIDAGADEVDMVLDVAAARAGDRDRLVADVRAVA
+EAAHADGPAGDGGALLKVIVETALLDDDAIVLACEAAVEAGADFVKTSTGFSTAGATVEH
+VALMRRTVGERIGVKASGGVRTRADALAMIEAGATRIGASSALAILGSD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02dd1d32f6f6afb5bbc026ef86b81649af8b96ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000542.fa
@@ -0,0 +1,45 @@
+>0_518
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLSEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNGPLMVAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVSYVGYYLAAASAITVIALVLSPETRHTDLDTVTSARERRAAR
+>1_251
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTNPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQKFDVAYVGYYLAAASAITVIALALSPETRHTDLDTVTSARERRAAR
+>2_2355
+MSRTTTPADGTAAGLEAAAEVPRGRVITASLVGTSIEFYDFYVYATAAVSVFPLIFFPGD
+DQTTALLASFAVFGTAFVARPIGSVLFGHFGDIMGRKVTLIGSLLTMGIATFLIGLLPTA
+FQIGLWAPAMLVVLRFCQGLGLGGEWSGAALLATEYAAEGKRARAAMWPQLGAPIGFFLA
+NGLFLALVIGFGHDSTNPDHDGAFLNWVWRLPFLLSIVMVAVGLYVRVKLEETPVFQRAI
+ANDTRVKAPLGEVFKRNWWELILGTFIMYATYVLFYLMTTWILSYAIGKTENGMLGVPYA
+EFLVLQLIGILFFAAFVPASGWLADRFGRKPTLLTVSALMVLFGLSFGLWLSAERMGTGA
+GVNVPLMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGISYNVSSILGAALTPFL
+AAWLVKEYGVAYVGYYLAAASVITMIALALAPETRHTDLDGVTSARERRAASV
+>3_2237
+MSHTTARSAEAPSVEDVPKSRVILASLVGTSIEFYDFYVYATAAVSVFPLIFFPGDDPTT
+ALLASFAVFGTAFVARPIGSILFGHFGDRMGRKVTLIGSLLTMGIATFLIGLLPTAFQIG
+LWAPAMLVVLRFCQGLGLGGEWSGAALLATEYADHGKRARAAMWPQLGAPIGFLLANGLF
+LILVRAFGHDSTNPQLEGSFLTWVWRVPFLLSIVMVAVGLYVRVKLEETPVFQRALEDDT
+RVKAPLGEVFKRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKTQNGMLGVKYADFLV
+LQLVGILFFAAFVPVSGWLADRFGRKPTLLVVSGLMVVFGLSFGAWLSPAAMGQGDALNV
+PSMLAFLAVGMALMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGAALTPFLAGWL
+VKEFGVATVGWYLAIASVITMAALALSPETRHADLHEVTSARERRAAAR
+>4_521
+MSHSTPPVNPGAPTDLTSDAVATAEEVPRSRVIIASLVGTSIEFYDFYIYATAAVSVFPL
+IFFAGGDDNTALLASMATFGAAFIARPLGAVVFGHLGDRVGRKTTLIGSLLTMGIATFLI
+GLLPTYFQIGLWAPAMLTLLRFFQGLGLGGEWSGAALLATEYAKDGKRAQAAMWPQLGAP
+IGFLLANGLFLALVLGFDHDSTSPVLDGPFLTWVWRVPFLLSIVMVAVGLYVRVKLEETP
+VFQRALDRDQRVKAPLGEVFRRNWWELILGTFVMYATYVLFYLMTTWILSYAIGKPANGF
+LGVPYAEFLVLQLVGILFFAAFVPVSGLLADRFGRRPTLIVISVLMVLFGLSFGLWLSPE
+NMGVGAELNVPLMLAFLATGMTLMGLTFGPMSAVLPELFPTNTRYTGSGIAYNVSSILGA
+ALTPFIAAWLVQRFDVSYVGYYLAAASAITVIALALSPETRHADLDTVTSARERRAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51699bd7d44fea9b63e3560ecea4b8d65100a64c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000546.fa
@@ -0,0 +1,50 @@
+>0_523
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>1_257
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLAVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
+>2_2348
+MSDPDLTTTAGRLADLHRRLEATAAPGGEGAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPETTDEDLALDEIVPDSANQPYDMLEVIGAIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKAARFVRFCDAF
+NIPILTLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATQDAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGALIRALRATLHKREARPAKKHGNMPL
+>3_2231
+MSAPELSTTAGRLADLHRRLEATAAPGGEAAVERQHSRGKHTARERIDLLLDEGSFVELD
+ALATHRTTAFGMDAKHPAGDGVVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVMASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNSTTGTAHYMATSEE
+DAIAYVQDLLEYLPSNNLAEAPVFEAESLEETEQDLALDTIVPDSANQPYDMLEVIAALV
+DDGHLLQLQEMYAPNVITGLARLDGMSVGVVANQPQQLAGTLDIAASEKASRFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGPQGAVNILYRRELAAAEAAGEDVEARRAQIVADYEAELLN
+PYQAADLGYVDAVVPPRQTRAHLVRALRATFHKREARPAKKHGNMPL
+>4_526
+MTDPDLTTTAGRLADLHRRLEATAAPGGPDAVERQHARGKHTARERIDLLLDEGSFVELD
+ALAVHRTTAFGMDAKHPAGDGLVSGFGTVDGRQVAVYSQDFTVFGGSLSERNGQKIVKVQ
+EFAARNGCPVIGILDGGGARIQEGVASLAQFADIFRNNVLASGMIPQISLIMGPSAGGAA
+YSPALTDVVVMVDQTSHMFITGPDVIKTVTGEDVDMETLGGARSHNATSGTAHYMASSEE
+DAIAYVQELLELLPSNNLAEAPTFEAADPEPTDEDLALDEIVPDSANQPYDMLEVIASIV
+DEGHLLQLQELYAPNVITGLARLDGMSVGVVANQPMQFAGTLDIAASEKAARFVRFCDAF
+NIPIITLVDVPGFLPGTDQEFNGIIRRGAKLIYAYAEATVPKLTVITRKAFGGAYIVMGS
+KKLGADLNLAWPSAQIGVMGAQGAVNILYRRDLKATAEAGGDVDARRAEIVADYEAELLN
+PYQAAELGYVDAVVPPHATRGQLIRALRATLHKREARPAKKHGNMPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000555.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000555.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07da0dde708b23a11f10ba6389c1fdca9821ca71
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000555.fa
@@ -0,0 +1,36 @@
+>0_534
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLASALAERDVSWAVPVALSDPVSAG
+PGAAVLQRFLPGGPYPPHEGDPDVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPAR
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALTDAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWGPALNVAYLALWHGEQKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>1_268
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAALADAVTTWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDLACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
+>2_2333
+MASDPVDSELELVHRALGRLRPHVSPADARALHEADWSAGTVEEGGQFNRVLVCAGAGVL
+RMTRAHEVGAAPAARWSPERDPARQLGRRMALLDGLDAALAEQGVAWTVPVALSDPVPAG
+TGAAVLQRYLPGGPHPPHEGDPAVLRRLLDEIAAVDVADPRIAPHLGRPFSFRGPWTAQR
+AEHVAGIPGRLAPRLGAWPGDDVDARTGADAWADAVARVTRAVTAWTEEPPVPPSLVHGD
+LAGHNMRWRAMPAADDAPGEVRWELAGVLDWDLACAWDPALNVAYLSLWHGEDQVERLAV
+DAGEAARARVWLGAMALETLDDAAARDELVGGLPNGSWRRLLRKALPRVARALTALG
+>3_2216
+MASDPARSELDLVAAALQRLRPGLDDGVAARLRGADWSAGRVEEGGQFHRVLVLEDVGVL
+RMTRVHEAGAAPAARWTPERDPAVHLPRRLALLDGLAAVLAEAGVRWSLPTALSAVVEDG
+PGAAVLQRYVPGFPHPPHEGDPAVLRGVLADLAAVDVADPRVAPHLGRPFTFRGPWTPER
+AAHVAGLPARLAPRLGAWPGDALGHAGDETAAGEAAVRLRADAWGESVTALTGVVSAWTR
+EPPVPPALVHGDLAGHNMRWRVVPAAATPDAEVPDAPVRWELAGVLDWDLACAWDPALNV
+AYLGLWHGEDLVEAIAADPAEARRARVWLGAMALETLDDAGARDVLVGGLAESSWRRLLR
+KTLPRVGRALAAAAA
+>4_537
+MVSPPAPSELELVHRALQHLRPGLDPALARRLRTADWAAASVEEGGQFHRVLVLEDVGVL
+RMTRAHEVGAAPAARWAPERDPAAHLPRRLALLDGLAAALAERRVPWTVPIALSDPVPAG
+PGAAVLQRFLPGGPHPPHEGDPAVLRGVLDDLAAVDVTDPRIAPHLGRPFAFRGPWTPER
+ARHVAALPGAVAARLGAWEGHDVDARLGAEAWPDAVAAVTDAVTAWTAAPPVPPSLVHGD
+LAGHNMRWRAVPEDEDPRAPLRWALAGVLDWDFACAWDPALNVAYLALWHGEEKVPDLAR
+DAAEARRARVWLGAMAMETLDDAAARDAIVGGLAAGSWRRLLRKTLPRVARALTALDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62c597a5dadd1c3b6d2e22d2e5bc89de295dba16
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000563.fa
@@ -0,0 +1,45 @@
+>0_542
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAGQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPTTQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>1_276
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPAEDRAHYSDGTIDLEYDFGFTGGDGWGELMGIANRTDYDLGQHTTH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRGLWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
+>2_2325
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHKRHRQDHLLEAFEAKKGRPSASMD
+EIVCPDCGTKGAWTEPQMFSGLVKTFLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDTWVEACWDWFID
+LGIDPENLRRLDVPEEERAHYSDGTIDLEYRFGFGGGDGWGELMGVANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGTDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQALAAELRALWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQAVTIRERDTMSQERVALSQVKSYLLERLVK
+>3_2208
+MAAKSPLDNVINLAKRRGFVFQAGDIYGGSRSAWDYGPLGVELKENIKAEWWRTFVRSRE
+DMVGLDSSIILPRQVWEASGHVATFTDPLVECQQCHRRHRQDHLLEAFEAKKGRAAAGME
+EITCPDCGTTGKWTEPQMFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGASRK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKEHFDTWVEACWDWFID
+LGIDPANLRKFDVPEEERAHYSDGTIDLEYRFGFAGGDGWGELMGVANRTDYDLTSHANA
+SGAKLQYFDQANDVHYTPYVIEPSFGLTRSMMAFLVDAYTEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKLELQEPSQRLAAELRAHWNIETDDSGAIGRRYRRQDEIGTPFCI
+TVDFDTLEDQSVTIRERDTMSQERVALAQVRAYLAERLTK
+>4_545
+MAAKSPLDNVINLAKRRGFVFQAGEIYGGSRSAWDYGPLGVELKENIKAEWWKTFVRSRE
+DMVGLDSSIILPRAVWEASGHVETFTDPLVECTQCHRRHRQDHLLEAFEAKKGRPAEGMA
+EIVCPDCGTQGAWTEPQLFSGLVKTYLGPVDNEEGLHYMRPETAQGIFVNFLNVLGAARK
+KPPFGIGQIGKAFRNEITPGNFIFRTREFEQMEIEYFVPPAEAKQHFDRWVEDCWDWFID
+LGIDPAHLRKFDVPADERAHYSDATIDLEYDFGFTGGDGWGELMGIANRTDYDLGRHTEH
+SGTKMQYFDQANNEHYTPYVIEPSFGLTRAMMAFLVDAYAEDEAPNAKGGVDVRTVLKLD
+PRLAPVKAAVLPLSKKPELQPATQSLAAELRTLWNIETDDSGAIGRRYRRQDEIGTPYCI
+TVDFDTLEDQAVTIRERDTMAQERVALSQVKSYLLERLVK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000569.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000569.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b748823baab3d441b61779727c1990cc2fb65282
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000569.fa
@@ -0,0 +1,34 @@
+>0_555
+MADPHPVLAASAPVLADPHPVLAASAPDLDPDALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDARTGLWERFSAEELATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPGLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECWAPADVDPGAPADEATAGSE
+ADLEAMLREAPPACTVCGDGLIRPGIVWFGEMLPAEPWDRAFAALEDCDLCVVVGTSGIV
+QPAASLPFVALGAGAAVVEVNPVETELSGAVTHVLRGPAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>1_296
+MADPHPVLAASAPVLAASAPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVKTELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
+>2_2302
+MPVEPGRDDVGPAGEAGRAVVGAGQRRRVVNPVAATPPSYLGRHYPVPMSHPSPGDLSET
+VPTADLDAVRALVAQARRPVVLTGAGMSAESGIPTFRDAQTGLWERYSPEQLATEDAFLA
+DPDLVWSWYRWRARMVRARRPNPGHDAVAHWQRAVPGLEVVTQNVDDLHERAGARVLAHL
+HGSLFEHRCAECGAPADVDPGAPADAEAAGSEADLEAMLREAPPTCPACGTGRIRPGVVW
+FGEMLPQEPWERAYEALERCDLALVVGTSGLVQPAASLPFVALGAGAAVVEVNPVETELS
+GAVTHALRGSAGAVLPALVAGV
+>3_2195
+MSPTQPSDPAALGAVRRLILEAERPVVLTGAGVSAESGVPTFRDAQTGLWERYSPEQLAT
+AEAFAADPSLVWSWYLWRARMVRAVEPNAGHRALAAWQARTPALRIVTQNVDDLHERAGA
+DVLSHLHGSLFAFRCAECDTPADVDPSAVVALAESAAPGSEAGLEALMHLEPPLCAACRR
+GRVRPDIVWFGELLPERAWGDAQAALEECDLCVVVGTSGVVQPAASLPFLALGAGAPVVE
+VNPDRTALSDAMTHVLRGPAGTVLPALLG
+>4_556
+MADPHPVLAASAPVLADPHPVLAASAPDLDPGALDAVRALVAAAERPVVLSGAGMSAESG
+IPTFRDAQTGLWERFSAEQLATEEAFLADPALVWSWYRWRARMVRARRPNPGHDAVAAWQ
+RRTPDLEVVTQNVDDLHERAGARVLAHLHGSLFEHRCAECGAPADVDPGAPSDVDAAGSE
+ADLEAMLREAPPACPACGTGRIRPGVVWFGEMLPQEPWERAYEALERCDLALVVGTSGLI
+QPAASLPFVALGAGVAVVEVNPVETELSGAVTHALRGSAGAVLPALVAGVWPGPSGALST
+ARHVTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8ff6ece47e4873b0bc938eb9716eb026de45a61
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000570.fa
@@ -0,0 +1,50 @@
+>0_556
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWAGLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSRRAEDPAPLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLDPTTAEAGADRWAADVRRALAAARRALETAAGDAVVPPPQDAVPGPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGSRRWAVVSASPERFLSGREGRYSTKPIKGTAARLADPAGDAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYASVHQLVSTVTGTARAGIEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGLPTTAPDIA
+>1_298
+MPTAPAPSVAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRTPSPGPRLVRHDDPADPDRAWADLAAAAAPRPVVGGE
+GLPLRGGLVGWLGYELGLADLGVTPPSPRPGDPASLPAQFWVRPSRYVVADHAAGVLHCC
+VVSLAPTAAETGADRWAADVRRALAAARRALETASGDVVVPPPRDAGPGPQADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVDPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGRAGRYSTKPIKGTAARLADPVADAEAARALAADPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVDVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDVA
+>2_2301
+MAAVYAHAVQRGAGSFWLDSALPDPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHADP
+ADPERAWSDLAAAAAPRRVVGGEGLPLRGGLVGWLGYELGLADLGVRPPSRRAGDPAALP
+AQFWVRPSRYAVADHAAGTLSCCVVALDAAAAEAAADRWAADVRRALDAARRATQAAADD
+AAASEVRADVAPEAGTGEAAGAWREDRAAYDEHIARCHAALHAGDSYELCLTTRFDADPA
+LRVDPLALFLELAAHQPAPYAALMEHGTGPRGWAVVSASPERFLAGRDGRYSTKPIKGTA
+ARLPDPAADAEAARALAADPKTRAENLMIVDLLRNDLSRVCEPGSVQVPSLMAVESYATV
+HQLVSTVTGTARAGVAPVDVVRSLFPGGSMTGAPKRRSVELLAQWEDSPRGVYSGALGLL
+GADGAVSLSIVIRTAVLAAGRWGIGAGGAIVADSTAEAEHEEVLLKARGLRRALARADGT
+ARTTTAPPRSR
+>3_2194
+MPTAPGRPDASPAPLHVAVRTLDIATLAAVGHTAATAAGAVYAHAVQRGTASFWLDSALP
+DGGEARWSMVGDGVDVLGEEEGRIPSPGLRLIRHGDPADPDRAWADLAAAAAPREVHGGE
+GLPLRGGLVGWLGYELGLADLGVTPPPPRPGDPAALPAQFWVRPSRYAVADHVAGALSCC
+VVSLDADAAEAAADRWEADVRRALEAARTSTEEVEVDVDAPEAPGVWREDGAAYAEQIAR
+CRAALHAGDSYELCLTTRFDADPALRVDPLALFRDLAAHQPAPYAALMEHGTGAERWAVV
+SASPERFLSGRDGRYSTKPIKGTAARLPDPTEDAAAAAALAADPKTRAENLMIVDLLRND
+LSRVCEPGTVQVPALMAVESYATVHQLVSTVTGVARAGVAPVDVVRSLFPGGSMTGAPKR
+RTVELLAAWEGSPRGVYSGALGMLGADGTVELSIVIRTAVLSPTTPDAPARWSVGAGGAI
+VADSDAHAEHEEVLLKARGLRRALTRAAGTA
+>4_557
+MPTAPAPSEAAATPLHVAVRTLDAAALAAAGHTAATAVAAVYAHAVVRGAASFWLDSALP
+DPAEARWSVAGDGLDVLGEEQGRVPSPGPRLVRHDDPADPDRAWADLGAAAAPRSVVGGE
+GLPLRGGLVGWLGYELGMADLGVSPPSRRPEDPAPLPAQFWVRPSRYAVADHAAGVLHCC
+VVSLDPTAAEAGADRWAADVRRALAAARRDLETAAGDAVVPPPEDAGPEPRADEEAPGTW
+REDRAAYAEQIARCRAALHAGDSYELCLTTRFDADPGLRVNPLVLFHELAAHQPAPYAAL
+LEHGTGARRWAVVSASPERFLAGREGRYSTKPIKGTAARLPDPAADAAAARALADDPKTR
+AENLMIVDLLRNDLSRVCEPGSVEVPSLMAVESYASVHQLVSTVTGTARAGVEPVEVVRS
+LFPGGSMTGAPKRRSVELLAAWEASPRGVYSGALGMLSADGTTSLSVVIRTAVLAGGRWS
+VGAGGAIVADSDPAAEHDEVLLKARGLRRALARAAGTGVPTTAPDIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000572.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000572.fa
new file mode 100644
index 0000000000000000000000000000000000000000..caf29289bec2f0a2c8947cd889c721e46758f5e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000572.fa
@@ -0,0 +1,25 @@
+>0_560
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPEVDASSSLASTPATDDASGS
+ATSSSASSASASSTAAAAGSDSATGQADDPAYAVIDAVLEKYGDGIIVAVDADDDDTTWE
+VDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTLDE
+MDLDDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDEH
+>1_302
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSVSPEVDASSAVASTPATDDASTT
+SASASSSASSTSASSTAAAASSGSGTGQADDPAYAVIDAVLEKHGDGIIVEVDANDDDTT
+WEVDVVVGEEVKELDVTADGDITETDRESDLEDVQKAKDAEVTAQQALDTAREGRDGVTL
+DEMDLEDDNGTLQWEVGFDREDGSDGPEVEIDATSGEVLTVDER
+>2_2298
+MNATSLARKTALTGTGLLAALALAACGTADDDTAANPQETAVQQSPTQAATTAPASASGS
+ASASASGSASASASGSASPAAASGSVERQGDDPAYAAIDAILGLHDDGVIVEMDLDDDDA
+KWEVDVVVGDDVKEYDVTTGGQVSEGVRPQIDDDVRRAGEAQVTAETAISTALQGRTDQT
+VDEVDLDEEGGTLVWKVELDRENGEDGAEVKIDAKTGDVIEVEEG
+>3_2192
+MTITTLTRKTALTGTGVLAALALAACGTTADNGDDGSASLEVDASSAVASTPATEDASTT
+SASASSASSAPASSTAAAAGRDSATGQADDPASAVIDAVLEKYGDGIIVGVDANDDDTTW
+EVDVVVDKEVKELDVTADGDITETDRESDPEDVQKAKDAEVTAQQALDTARKGRDGVTLD
+EMDLDDDNGTLQWEVEFDREDGSDGPEVEIDATSGEVLTVDEH
+>4_561
+MTITTLTRKTALTGTGMLAALALAACGTTSDNGDDGSASPGVDASSAVASTPTTDDASGS
+ASSSASSASASSTAAAAGSGSATGQADEPAYAVIDAVLEKYADGIIVAVDANDDDTTWEV
+DVVVGEGAKELDVTADGDITETDRESDPEDVQKAKEAEVTAQQALDTAREGRDGVTLDEM
+DLEDDNGTLQWEVRFDREDGSDGPEVEIDATSGEVLTVDER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000575.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000575.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fb22c368971bb9c8e837ed0a87838d4d2290b51
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000575.fa
@@ -0,0 +1,25 @@
+>0_609
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATAASSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>2_390
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>2_735
+MSTETSAAGRAGHSVRLVVLATVIVLILGAAGWALGRLTAPVTSFPSAASPEAGFARDMQ
+VHHLQAVEMSFLVRDRTEDPEIRQLAYDIARTQQHQAGQMYGWLSIWGLPQASPEPAMAW
+MDEDAGHSSPHDTGQQSTAMPGMATAAQLEALTDAEGSEAEQLYLELMISHHQAGTTMAQ
+AVLDRTDNEAVRALAQSIATSQQTEIRYLEQLLRTR
+>3_2143
+MKRTMTLTALALASALTLTACGTGAQDENAGAEASATATSSAPAATPAATATATPSTTAT
+GSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVIDAQGPEI
+KRMNSMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARLYLEQMT
+AHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
+>4_572
+MKRTMTLTALTLASALTLTACGTGAQDENAGAEASATATGSAPAATPAATDTATPSATES
+ATSSATGSAEEVSAEHNDADVMFAQMMIPHHQQAVEMSEMLLAKDDVPAEVAAFAQKVID
+AQGPEIERMNAMLTAWGQDPVDTDGMDGMEGMDHGGMSGMMSEEDMTALDQAQGTEAARL
+YLEQMTAHHKGAVDMAKDEAKDGQNPQAVQLAEQVIADQEAEITEMQQMLDKL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d638ff637a69cf947e73d20025749c205dd7afc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000577.fa
@@ -0,0 +1,20 @@
+>0_612
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>2_1952
+MTHHVNAMLDTHPKDLGGIDRQKLAECIEACFACAQTCTACADACLSEDMVAELRQCIRL
+NLDCADVCAATGAVLTRQTGEDASTVRALLEACRAACRSCGEECASHAGMHEHCAVCAEA
+CRRCEQACADLLAALG
+>3_2139
+MTHHVSAMLETYPKEVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCAEVCAATGRVLSRQTGTNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>4_569
+MTHHVSAMLDTYPKNVGNIDRQKLAECIQACFECAQTCTACADACLAEDMVADLRQCIRL
+NLDCADVCAATGRMLSRQTGNNVETTRALLEACRAACKTCGDECESHAQMHEHCKVCAEA
+CRRCEQACADLLVTLG
+>4_860
+MTHHVSAMLETHPKDLGGVDRRKLAECIEACLACAQTCTACADACLSDDMVAEMRRCIRL
+NLDCADVCGATAAVLTRQTGEDASTVRALLEACRTACRACGDECASHAEMHEHCKVCAES
+CRRCEQACADLLASLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ad4612bbd25758cff8f5f83a7f06af29b1130346
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000598.fa
@@ -0,0 +1,44 @@
+>0_644
+MTHGSLTDYTLPAPAPAHDGGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>1_390
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPTRLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPSPRPVLFTGPCAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLSGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
+>2_2242
+MTHGSLTDYTLPAAGAPSASNAHDDGAPRAVALIGSTGSIGTQGLDVIAQDPARFRAVAL
+SGGANTGLLAEQAVRFEVQAVGSATATEDELRAAIADAAARLGLKPAPRPALFTGPTAAE
+RIAAWKGADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAAAPGQLVP
+VDSEHSALAQALRGGTADEVRRLVLTASGGPFRGLDRAALAEVTPAQALAHPTWDMGRVV
+TTNSASLVNKALEVIEAHLLFDVPLERIDVVVHPQSVVHSMVEFTDGSTLAQASPPDMRL
+PIALGLAWPARVPGAAAGCDWTRAATWAFEPLDEDAFPAVRAAKEAAAASPTHMAVFNAV
+NEEAVDAFHDGRIRFDAIVDTVRAVVGEYEPARVLGAAGHGHVAQDLTVEAVLAAEDWAR
+TAARARW
+>3_2103
+MTHGSLTDYTFPADHGPGASDGACRAVALVGSTGSIGTQGLDVIAQAPERFRAVALSGGA
+NTALLAEQAVAHGVEAVGSAAASEEELRAALADAAARLRRPDPRPALFTGPEAAARIAAW
+EGADTVLNGITGSIGLAPTLAALRAGHRLALANKESLIVGGALVKAAAAPGQLVPVDSEH
+SALAQALRGGTAGEVRRLVLTASGGPFRGFSAAQLAEVTPAQALAHPTWDMGRVVTTNSA
+SLVNKALEVIEAHLLFDVPLERIDVVVHSQSVVHSMVEFTDGSTLAQASPPDMRLPIALG
+IGWPHRVLGAAAGCDWTQAAQWTFEPLDEAAFPAVSLAKEAAASSDTHMAVFNAANEEAV
+DAFHGGRIRFDQIVETVRAVLGEYRPDGVLAAAGADPDELTVEAVLAAEDWARAAARGRW
+>4_614
+MTHGSLTDYTLPAPAPADDDGAPRAVALIGSTGSIGTQGLDVIAQDPARLRAVALAGGAN
+TTLLAEQAVRFEVEAVGSAAAGEEELRAALADAAARLGRPAPRPVLFTGPRAAEQIAAWP
+GADTVLNGITGSIGLRPTLAALHAGHRLALANKESLIVGGALVKAAARPGQLVPVDSEHS
+ALAQALRGGTADEVRRLVLTASGGPFRGLDRAALHAVTPAQALAHPTWDMGRVVTTNSAS
+LVNKALEVIEAHLLFDVPLDRIDVVVHPQSVVHSMVEFVDGSTLAQASPPDMRLPIALGL
+CWPRRLPGAAPACDWTRAATWTFEPLDEEAFPAVRAAKEAAAASPTHMAVFNAANEESVD
+AFHAGALPFDGIVDTVRAVVADYAPEHVLAAAGHDPAPTGLTVDAVLAAEAWARRAARAR
+W
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000601.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000601.fa
new file mode 100644
index 0000000000000000000000000000000000000000..997849e9b62b26b0e2cc1074c9b0f4d445890284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000601.fa
@@ -0,0 +1,34 @@
+>0_647
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHTGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>1_393
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGALRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPHVVQAQP
+HDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIHAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAASAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
+>2_2239
+MTRLPPVPRWSPSTDRQVRAATGGRVRLLTDADTPALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDAGEGRDDDGAPVAGLRAALWVGSNVVPVAAAETPDAGWAPGDAE
+ALGAAAVALRRRYGSLYGPAEPVLAVGSALAAAGHRARSVREDQPLLVLGADGAAETSPH
+VVQAHPRDFERVLPASAAMFEEELGFSPFLGGAAQYRDRVERLIRAGRVFIDPGPADAGG
+PLRFKADIGLLSSRCAQIQGVWMAPAARGRGLAAAAMAAVVEYVRLQAPVVSLYVNAYNT
+PALRTYERVGFERRGTFATVLY
+>3_2100
+MDLAAASDGRVRVLTDADTPALTALAAADPVANVHAASLLEAGRLAGPRGGRADGTLFLG
+VEDPDRPGALRSACWVGSTVVPLAGHDDDVPALAASVAALRRRFASVYGPAVTVLAVGRT
+LRDAGHRPRAVREEQPLMVHARTPGDLVPDPAVRAAAPGEWESVVPASAAMFEEELGFSP
+FLTGAAQYRDRVRRLVADGRVFTAPGEPVVDDPTSGVRFKADIGLLSASCVQVQGVWLHP
+SRRGRGEAAPAMAAAVALMARRAPAVSLYVNGFNTPALRTYERVGFERVGTFATVLY
+>4_617
+MTRLPPVPRWSPSTDREVRAATGDRVRLLTDADTAALAALSARAPVSNVFVDSLLEAGRL
+AGPRGGAAGTLFLGIDDDAPGAGGLRAAVWIGSNVVPVAASEAPDAGWAPGDAEALGAAA
+AALRRRYGSIYGPAGPVLAAGEALAAAGHRSRSVRPDQPLLVLGTAGGIDPNPSVVQAQP
+RDFARVLPASAAMFEEELGFSPFAGGAAQYRDRVERLIQAGRVFIDPGPRDAGGPLRFKA
+DIGLLSSRCAQIQGVWMAPAARGRGLAVSAMAAVVDYVRLQAPVVSLYVNAYNTPALRTY
+ERVGFERRGTFATVLY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..390568f185b25a4a9d797e28f3aaa663206bc67f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000604.fa
@@ -0,0 +1,25 @@
+>0_650
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>1_396
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGTAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSVDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
+>2_2236
+MDSTDRHDDAASLRARVEEALASADVVVEEVRVAGAAAHPTVEVVVDRASGTEGLSLDEL
+AGLSGRVSAALDALGDHVPGVGAGEYLLELTTAGVDRPLTQPRHFARNVGRLVEVAVDGG
+EPFTARLLAADEDAVELAEVRPGAKKGMKAKELPAQRVELARLGPAVVQVEWTPAQQAAD
+AAAAGEQTAEHTEA
+>3_2097
+METVPAALTELVEGAVSHRGVVVESVRVAGAADAPTVEVVLDRLEGTEGLSLDEVAELSG
+LVSDALDACGDEVPGVGAGEYLLEVSTAGVDRPLTGPRHWLRNVGRLVEVSIDAALPVTA
+RVLGVEASGVELEVVRPGAKKGMPAKVLPAEHVDFSRLGPGQVQVEWSTAAEQSGAEQTA
+EQTEA
+>4_620
+MDSTDRRDDLAELRTRVEEALAADDVVVEQVRATGAAEHRTVEVVLDRASGTQGLSLDDV
+ARLSGRVSAALDALGDHVPGVGAGEYLLEVTTAGVDRPLTEPRHFARNVGRLVEVSIDGA
+APVTARLKDVTDDDVELAVVRPPAKKGMKAKELPAERVALDRLGPAIVQVEWSPAQQAGD
+ADAAAGEDTAEHTEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2035d3250946c79b388630d84a897c1dde2fe0ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000622.fa
@@ -0,0 +1,25 @@
+>0_670
+MSAAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPVVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>1_416
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWGGDSLVARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRGA
+>2_2208
+MSTGGEAERVSAWNLPNILTSVRILMVPLFAWALWAGGPWGGDSATARWIAVALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGAALVLFSLLGELWWWVTVVILVREWGIT
+LMRFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVVGGWWPWVGWTVIGAATVLTV
+LTGLEYVKDAWILRRDALAAPRGA
+>3_2078
+MNAQPERVSAWNLPNILTTVRILMVPFFVWAVWAGGPWGQDSLTARWIAVALFAAAMYTD
+KLDGDIARSRGLITDFGKIADPIADKLLTGSALVLFALLGELWWWVVIVILVREWGITAM
+RFVVIRYGVMPAGRGGKLKTVLQAVGIGLLLMPLAPVLGGWWPWLGWTVIGAALALTVVT
+GVEYVRDAVRLRADWLASHPEARR
+>4_640
+MSTAGGAQHVSAWNLPNILTSVRILMVPFFAWALWAGGPWSGDSLLARWVALALFAAAMY
+TDKLDGDIARARGLITDFGKIADPIADKLLTGTALVLFSLLGELWWWVTIVILVREWGIT
+LMRFVMIRYGVMPAGRGGKLKTVLQTVGIGLLLLPLAPLVGGWWPWAGWVVIGAATVLTV
+LTGLEYVKDAWVLRRDALAAQRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b01ad4f9d2c564ea5050b90142c831836af9ea6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000624.fa
@@ -0,0 +1,17 @@
+>0_673
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>1_419
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
+>2_2205
+MMRHPVQAHGITRWVDDQPRPRATTPDIKERSMPLLRHEIGDVLRDVRQLQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICQALEIPLSYLLREVSDRLVDQEGIQVPDTLPE
+DLTDAADPSLGTLAGR
+>3_2076
+MMRHPVQAHGITRWVDSQPRPSQPTPELKERSMPILRHEIGDVLRDVRQRQGRTLREVSH
+DARVSLGYLSEVERGQKEASSELLASICDALQIPLSFLLREVSDRLAEQEGVVVPDTVPA
+DMAEDGAADVAPLAVR
+>4_643
+MPLLRHEIGDVLRDVRQLQGRTLREVSHDARVSLGYLSEVERGQKEASSELLASICQALD
+IPLSYLLREVSDRLVEQEGMVVPDTLPDDLTDPSLGSLAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..18b2a924f9cd422df0e908d993d875b775ed700d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000631.fa
@@ -0,0 +1,25 @@
+>0_683
+MVAVSSASHYFDADPSAPERRRTVRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPARGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNLVALRP
+EDVPEGAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVARAR
+>1_426
+MVAVSSASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
+>2_2196
+MVAVTSPAHYFSPDPGTPERRRSVDVELAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALASPEAEVTGVEVNERSLALARDNAAAVGASNARFLTP
+EQIPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIA
+GMLQEQAPGEFTATRAATVKGFRILRISRAAESSS
+>3_2068
+MDAVTSPAHYFSPDPGTPERRRRVDVEIAGRRVTLQTANGVFSPDGIDKGTAALLSAVPA
+PPARGAFLDVGAGWGPLALTLALTSPEAEVTGVEVNERSLALARDNAAAVGAQNARFLTP
+EQVPDDARFDLIWSNPPIRIGKAALHDLLAQWLPRLAPGGEAWLVVQKNLGADSLLPWIS
+GMLQERAPGEFTATRAATVKGFRILRISRAAESSS
+>4_650
+MVAVSPASHYFDADPSAPERRRTLRTRLAGRDVEVQTANGIFSPDGLDKGTAALFSAVPA
+PPATGRFLDVGAGWGPIALTLALRSPEAEVTAVEVNDRSLQLTRDNAAALGLDNVVALRP
+EDVPEDAEFDLIWSNPPIRIGKPALHALLERWLPRLAPGGEAWLVVQKNLGADSLLPWIG
+RMLEERAPGRFTAERADSVKGFRILRVVRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000632.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000632.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30320e917cd53f279fc23ffb60f6168522ab2c28
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000632.fa
@@ -0,0 +1,37 @@
+>0_684
+MGRTQWPLTDEFAGQRVVIVGMGVSATQLLAEISTVADTLWVTRREPRWQDSAAPGALAE
+SVRGVDERTRAGLPPGSVVGATGMHRSSWVREAESRGVLVRHPMFTAVEPDGVRMPDGSF
+EPADVILWATGFRPAIRHLAPLRLRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANR
+AGRDAVRAILADLAGPASG
+>1_427
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
+>2_2195
+MRTILAADRRRRHPSPVGEHAPAVPTLGRMTPHPDRHVTVLVVGAGQAGLSAAHHLRRRG
+FQPVGPGEAPRPAPEGSPGTFAVLDAEDRPGGAWLHRWDTLTMGSVNHIHELPGHPVPPA
+DPAARANAVLPAYFAEYEERFDLRVHRPVRVSRVERIGEPGAAEGFRVHTDAGTWTCGFL
+VNATGTWTSPHWPAVPGRREFRGRQLHTHDYRDPEEFARRRVVVVGMGVSATQHLAEVSR
+VADTLWVTRREPRWIDDPDPGHLAESVEGVDERTRLGLAPRSVVSATGMFRSDWVREAQA
+RGVLERHPMFERIEPDGVRMPDGSLERADVILWATGFRPAVRHLAPLRLRTPDGGIRAAH
+GRALDEPRLFLIGYGPSQSTVGANRAGRDAVRAILADLRAAGAA
+>3_2067
+MTPHPDRHVTVLVVGAGQAGLSAAHHLRRRGFLPVGPGEAPGPAPGGSPGTFAVLDAEDR
+PGGAWLHRWDTLTMGSVNHIHELPGHPVPPADPDAQANAVLPAYFAEYEERFDLRVHRPV
+RVSRVERIGEPGAAEGFRVHTDTGTWTCGFLVNATGTWTSPHWPAVPGRREFRGRQLHTH
+DYRGPQEFAGRRVVVVGMGVSATQHLAEVSRVADTLWVTRREPRWIDDPDPGHLAESVEG
+VDERTRLGLAPRSVVSATGMFRSDWVREAQARGVLERHPMFERIEPDGVRMPDGSLERAD
+VILWATGFRPAVRHLAPLRLRTPDGGIRAAHGRALDEPRLFLIGYGPSQSTVGANRAGRD
+AVRAILADLRAAGAA
+>4_651
+MGVECTGRRVWATGAPAPGPLTTRTYPAGMTASPSPAPPRPGRTGRATVVVIGAGQAGLS
+AAYHLRRRGFVGLGPNDDGAAGVPDDAPGTFVVLDAETAPGGAWQHRWDSLTMATVNHIH
+ELPGDPVPPADPAAHANTLLPAYFADYEARFALPIRRPVRVRRVERIGEPGRARGFFVRT
+DGAPGTWRADFVVNATGTWTSPRWPSVPGMRSFRGRQLHTRDYVSKDEFAGQRVVIVGMG
+VSATQLLAEISTVADTLWVTRREPQWQDSAAPGALAESVRGVDERTRAGLPPGSVVGATG
+MHRSSWVREAETRGVLVRHPMFMAVEPDGVRMPDGSFEPADVILWATGFRPAIRHLAPLR
+LRTPAGGIRVAGGRALDEPRLFLLGYGPSQSTVGANRAGRDAVRAILADLAGPASG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000639.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000639.fa
new file mode 100644
index 0000000000000000000000000000000000000000..656e13ab74bde03f442cb0bc19b56888b2bc72f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000639.fa
@@ -0,0 +1,25 @@
+>0_694
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>1_434
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>2_2188
+MARPTSVPGVRPSVAVLDYGSGNVHSAVRALERAGADVELTRDPEAVQSADGLLVPGVGA
+FASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERAEGMGEWPGVVEA
+LPAEVLPHMGWNTVRPPEGSALFAGIEDERFYFVHSYGVLRWEFDQTISAMRPPQVTWAH
+HGADFVAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
+>3_2059
+MASPTSVPGVRPTVAVLDYGSGNVHSAVRAVEHAGARVELTKDPDAVLGADGLVVPGVGA
+FASVMEALRSSGGTRWIGRRVAGGRPVLGICVGHQVLFEAGVEHGVRTEGMGEWPGVVEP
+LPAATVPHMGWNTVRPAEGSALFAGIEDERFYFVHSYAVQSWEFDQGNEAMRPPQVTWSH
+HGADFIAAVENGPLSATQFHPEKSGDAGQALLRNWLETL
+>4_658
+MARPTTVPGVRPRVAVLDYGSGNVHSALRAVERAGAEVELTRDPQAVQEADGLLVPGVGA
+YASVMRALTEVGGTRWIGRRVAGGRPVLGICVGHQILFDAGVEHGERTAGMGEWPGVVAE
+LPAEVLPHMGWNTVRPAEGSALFAGIEDERFYFVHSYGVLEWEFDQTISAMRPPQVTWAH
+HGADFIAAVENGPLSATQFHPEKSGDAGLQLLRNWLETL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000641.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000641.fa
new file mode 100644
index 0000000000000000000000000000000000000000..970a16a08d7c1f98dd5fe7dd03846f1d6c01116f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000641.fa
@@ -0,0 +1,30 @@
+>0_696
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFGDRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>1_436
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
+>2_2186
+MTPNPAAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQRAGAEWIHLVDL
+DAAFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPAWT
+ARVIERFGDKVAVGLDVRGTTLAARGWTQEGGDLWEVLARLEDAGCSRYVVTDVTKDGTL
+KGPNTELLAQVCARTDKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQ
+ALAVAGGATVEQARAEQPGPVAE
+>3_2057
+MTETTPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPLTAALDWQDAGAEWIHLVDLDA
+AFGRGDNRDVLRRVVDEIGVKIELSGGIRDDASLENALAMGAARVNLGTAALEDPAWTAR
+AIERFGNRVAVGLDVRGTTLAARGWTQDGGDLWEVLARLEEAGCARYVVTDVTKDGTLRG
+PNRELLARMCAATDKPVVASGGISSLEDIAALAAMVPQGVEGAIMGKALYAGRFSLEQAL
+AVAAGATVERAREQHPFQAAP
+>4_660
+MTPNAPALELLPAVDVQDGQAVRLVQGEAGSATSYGDPVTAALDWQRAGAEWIHLVDLDA
+AFGRGDNREVMRRVVEEIGVKIELSGGIRDDASLENALEMGAARVNLGTAALEDPDWTAR
+VIERFADRVAVGLDVRGTTLAARGWTKEGGDLWEVLARLEDAGCARYVVTDVTKDGTLKG
+PNTELLAQVCAKTAKPVVASGGISSLEDVAALAAMTGQGVEGAIMGKALYAGRFSLEQAL
+AVAGGATVEQARSEQPGPVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99a5c97228f5ca02a71d7eaa6b60388672febc55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000647.fa
@@ -0,0 +1,25 @@
+>0_702
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>1_442
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPLAHLVRQFAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
+>2_2179
+MNTAFDAGRLGRTDVLTLQQVTSFMSNDMQVTGPDGQTVATVVTTGGGLGRMVLGSRTFD
+VVDGEDGRVLFRLADPATFGRDRYAIVDADGLPLANLVREFALFRTSVSVEVVDGTRFAV
+TGNLWDHDYTMTVGQAPIARATATFGGFMNALAGRSRYELRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRRNN
+>3_2051
+MTTFDAGRLALVNSLALQQVTSFLSNDMQVLGPDGEVVATVQTQGGGLSRMLMGSRRLLV
+CDGDDGRPLFELQDPATFGRDRFQVLDPAGLPLANLRREVAFFRTAVSVEVVDGTVFRVE
+GDLFDHDYRMIAGEVPIARAVSQWSGFGNALLGRSRYRLELDPAMPPVVRCAVLGTAIAL
+DLLRAKDARRND
+>4_666
+MSPAFDAGRLAHTDVLILQQVTSFLSNDIQVTDPDGRTVVSVVTTGGGLGRMLMGNRSFD
+VVDGDDGRVLFRLADPATFGRDRFAILDADGLPFANLVRQIAFLRTSVNVEVVDGTCFAV
+TGDLWDHDYAMTVGQQPIARVTARFGGVMNALAGRSRYEMRLDPGMPPVVRCAVLGTAIA
+LDLIRAKDRRSNG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000649.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000649.fa
new file mode 100644
index 0000000000000000000000000000000000000000..109f7b0860a29c0c006e91c07f48b155769124d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000649.fa
@@ -0,0 +1,25 @@
+>0_704
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLATARSYAATAEHPDRPADLFEYDTDRHLFMNSSTADFDADLT
+AVLVRRIHELLA
+>1_444
+MAQIVLFHHALGLTDGVRALAEQIAGGGHTVHTPDLYDGRTFATVDEGVAHAQHIGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGALALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
+>2_2173
+MAQILLFHHALGLTDGVRALAAQIEAGGHTVHTPDLYDGALFTDVEEGIAHVESLGGFDV
+IAERGMRAAAQHPQASVVAGISMGVVAAHKAAQAVPAFRACIDIAGIVPLDAFAPLWQPH
+TALQVHLATRDPWVMDEDLPLARSVAATEEDPDKPAVLFEYDTDAHLFMDSSTDGHDPAL
+TEVLVRRIHELLA
+>3_2048
+MAQIILFHHARGLTEGVLALAEQIEQASGHHVHTPDLFGGAVLPTVEDGLAHLQQIGQDE
+VMTRAMHACAEHKEASVVAGISMGVMPAWKAAQTAPGFRACIAMSSALPLDAYARLWQPH
+TSLQIHLAAQDPWVKDEDLPLARTYAATAEHPDRPADLFEYETASHLFMDSSTDQYDARH
+TEVMVERIRELLA
+>4_668
+MAQIVLFHHALGLTDGVRALAEQIASGGHTVHTPDLYDGRTFATVDEGVAHAQHLGFEEI
+GRRGMRACAEHQEASVVAGISMGVMPAWRAAQVVPGFRACIAMAGVLALDAYAPLWQPHT
+ALQIHLGTRDPWALEGDLETARSYAATAEHPDRPADLFEYDTDRHLFMDSSTADFDADLT
+AVLVRRIHELLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000672.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000672.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34e76972cdcefda03144591cbc739d33168bcb47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000672.fa
@@ -0,0 +1,36 @@
+>0_732
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>1_471
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMAALGVPSAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WTVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
+>2_2122
+MNEDVIGLLWLVVLLVANAFFVAGEFAVMGARRSQIEPKAEAGSRPAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVGPMTALGVPDAAADVTAFVLALLVVTFLHVTF
+GEMVPKNAAVSFADRAVMILARPLVGLSKLLHPIVTVLNWAANVVLRAFRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHTAGDVMVPLEKVVTVPEGITPHDFE
+WTVGRVGYSRFVVEDPDGGYTGYLHLKDVLTVGPSGHEEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGVLFLEDVLEELVGEINDVTQSPRRFRPA
+>3_2016
+MSQDVVGLLWLAVLLAANAFFVAGEFAVMGARRSQIEPRAEAGSRQAQVALFAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLAAPMEALGLPLAAADVVAFVLALLIVTFLHVTM
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPLIVVLNWAANTVLRAFGIEPKDEVASS
+FTLEEVQTIVAESTRSGTLEDESGVLHSALEFSSYTAGDVMVPIEKVVSVPEDVTPQQFE
+WAVGRVGYSRFVVEDSQGGYAGYLHLKDVLAGGPSRYADPVPVTRVRSLANVRVADEVED
+ALGLMQRTGSHLARVISEDGATVGVLFLEDVLEELVGEIHDVTQSPRRFRPTTGSHAAPE
+PTRMRDLPAR
+>4_696
+MNGDVVGLLWLVVLLAANAFFVAGEFAVMGARRAQIEPRAEAGSRQAQVALYAMEHVSQM
+LAVCQLGITVCSLLILNVSEPALHHLLVVPMGALGVPAAAADVTAFVLALLVVTFLHVTL
+GEMVPKNAAVSFADRAVMLLAQPLVWLSKLLHPVVAALNWTANLVLHALRIEPKDEVASS
+YTLEEVQSIVAESTRSGTLEDESGVLHSALEFSDHRAGDVMVPLERVVTVPEGITPHDFE
+WAVGRVGFSRFVVEDPDGGYTGYLHLKDVLTVGPSGHDEPIPLTRVRSLANVRLEDEVED
+ALALMQRTGSHLARVITPEGETAGILFLEDVLEELVGEINDVTQSPRRFRPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cadd202eab7597654731aa54d384e318cc6b6ef5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000673.fa
@@ -0,0 +1,35 @@
+>0_733
+MLRRRRLPALTGALAALTLSLAACGGTSGDSAGAQAAGASADSGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDAQVREILAGVPEDRRTLVTDHDAYGYFSDAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGNLPV
+IEVYESGVGPKDTPEADYAEAMLANARTLADALEG
+>1_472
+MLRRRRLPALTGALTALTLSLAACGGTSGDSAGEQAAGASAAAGSGSAAGAPVAVATTTQ
+LGSVLDRVVACADARSVTVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDERFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQEIAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLLNARTLADALEG
+>2_2121
+MHRTPRRRAAAALTLASALALAGCGADSGGDGQAGSGEPAAVATTTQLGSVLGDVARCAG
+ATTATVMGPGDDPHDFAPSSQQVAQMARAGLVFANGFGLEAGMASALENAAQDGAQVLEV
+APRLDPLPFGAGEGAADGHAGETADEHAAHAEEGSAGAHDGHDHGSQDPHVWMDVARMAR
+AAEVMGDALAEHTGEDRFADCGRQVRGELEATDAEVREILAAVPEDRRRLIADHDAYGYF
+AAAYGFEVAGVVVPGGSTDGEPSSQRIAELTQAVAEAGADALVTSAGGGAPTVETIAADG
+GGSTPVVELYEGGVGPADGEPAGYAEAMLHNARVLADALGE
+>3_2015
+MSRSSPTPRLAAPAVVAALGVALAGCSVADSSSPSAAEEGAVTASSSAAGPVVAVATTTQ
+LASVADRVARCGGGSVVSVMGPGDDPHDVAASSDQVAQMVHSGLVFTNGLGLEGGMDSAL
+DNARQDGAVVVEVAPRLDPLPFGEHDADHAGHEGADAHAGHEHGSQDPHVWMDVARMAAA
+ARVVGDELAAETGEQKYAECGATVEGELEETDRQVREILAAVPQERRTLVTDHDAYGYFS
+AAYGFTIEGVVVPGGSTDAEPSSRELAALTQQVKDHGAAALLTSTGTPNGLVETVAREAG
+GLPVVQLYEGGVGPVGTPEADYAQAMLHNARTLADALKG
+>4_697
+MLRRRRLPALTGALTALTLSLAACGGTSGDSSGAQAAGASADAGSGSAVGEPVAVATTTQ
+LGSVLDRVVACAGARSATVMGPGDDPHDFSASSAQVKDMVSSGLVFSNGLGLEGGMESAL
+ANAEADGATVVEVAPQLDPLPFGGHDHAEEGAGHEGHDHGSEDPHVWMDVARMARAAELM
+GDTLAQERGDEQFAECGATVRGELEQTDTQVREILAGVPEDRRTLVTDHDAYGYFSEAYD
+FTVSGVVVPGGSTDGEPSSQELAELARSIRDGGADAVITSVGARNSLVDTVAEEAGDLPV
+IEVYEGGVGPKDTPEADYAEAMLVNARTLADALEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29fadaf91099a0d6c44f139f7f6ca6c580a64b85
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000674.fa
@@ -0,0 +1,31 @@
+>0_734
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQRERETPVVALPGAEVAR
+>1_473
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAPR
+>2_2120
+MDWLIEPFLLGFQQRALVGGLIAAALCAVVGTWLVLRGMSFFGDAFVHGVMPGIALSVVL
+GFDAHLGAALAALVMLAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISLSDSYTGSLT
+AILFGDALGVTWEGIVRQAVIAALVLVLALVLYRPLMALSFSPAKARSLGMRPRLTHALL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALAVLLGAAGVTIGLVLS
+YHLGTAASATMALVPIAMFFVVLAGRAGLRALRSRRVRADRRRAVVETPSRRSVSP
+>3_2014
+MDWLIDPFLLGFQQRALLGGLIAALMCSAVGTWLVLRGMSFFGDAFVHGVLPGIALAVLL
+GGSPHLGAALAAVLMMGGISLVHRTTTLKEDTAIGLLFVGMMALGVVIISLSSSYTGSLT
+AILFGDALGVTPENLLVQAAIGVVVVVLALVLYRPLLALSFSEAKSQALGMRPRLTHTLL
+LVLIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRTVPQMMALSAGIGALSVVAGLVLS
+YHWGTAASATMALVPVVLFFVVLLGRSAVQAAAGRRRRTRGAASAPTPAGDDDAESRRET
+EGSPAR
+>4_698
+MDWLLEPFQMGFQQRALVGGLIAVVMCSVVGTWLVLRGMSFFGDAFVHGVLPGIALAVVT
+GGSPHLGAAVAAVVMMAGISLVHRATTLKEDTAIGLLFVGMMALGVVIISKSDSYTGSLT
+SILFGDVLGVSVDGIVTQAVIAVVVIALALLLYRPLLALSFSEVKARSLGMRPGLTHTLL
+LVMIGAAVIGSFQAVGTVLVFGLLVGPPATAALLTRSVPQMMLVSVVIGAACVVTGLTLS
+YRLGTAGSATMALMPILLFFVVLAVRAAVLALLGRHVRSRAQREQEAPVVALPGAEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000676.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000676.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d4c53728ec1ee5a10c27bc5d1b03059eed25223
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000676.fa
@@ -0,0 +1,36 @@
+>0_737
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQARVVPAPTAAPSSSHDAGGDPDADTDGV
+DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPEGPAYAQPGRCRPNRVILLDVRFRATAG
+GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV
+YDDDHGLSAARAWWLLRHAGLRDSMLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM
+PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP
+AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN
+AVAVGPEPDGASGRD
+>1_476
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV
+DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG
+GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV
+YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM
+PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNVPTAESIAEDGRLRP
+AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN
+AVAVGPEPDGASGRD
+>2_2116
+MWGIDDGDTVVVYDDDRGLSAARAWWLLRHAGLRDSMLLDGGLAAWRAGGLPLQPGEVIP
+MPGSARTSWGRMPVVDTAGAEAMASGGLLLDARAAERYRGETEPIDPVTGHIPGARSLPT
+AGSLAEDGRLRPAEELAARFDAVGVDDETPVAVYCGSGVTAAHAVLTLAVAGRPGVALYP
+GSWSAWIQDPSNAVAVGPDPHGEPGRD
+>3_2011
+MKDSTEGRPPSPASSPAADAPTDQTPLAELAEDATAPDPAAAEPPSLVDVGVLAGWLGLT
+PAEPVPAPPPGPVFDRRVDPGRVILLDVRYAVAGAGGSGHDAYLRGHLPGAVFVSLPNQL
+AGHAGPRQGRHPLPDPVQFAHSLRMWGIDDGDTVVVYDDDRSLAAARAWWLLRHAGLRDS
+VLLDGGLGAWRAAGLPLQPGEVIPQPGSVHPSWGRMPVVDTDGAEAIAAGGLLLDARSAE
+RYRGEEEPLDPVAGHIPGARSLPTSGNVAADGRLLDPAALAARFEDAGLSDEVPAAVYCG
+SGVTAAHQVLALAVAGRHGVALYPGSWSAWIQDPDRPVATGPRPEGD
+>4_701
+MHSETPDPSPVPDRDGAAPDRPDPLIVVDEGQGRVVPAPTAAPSSSHDAGGDPDADIDGV
+DPEAAEPPTLVTVDVLAGWLGLAPVEDLPPVPGGPAYAQPGRCRPNRVILLDVRFRATGG
+GPDHAAYLQGHLPGAVYVSLPSQLAGHAGPAAGRHPLPDARQFAETVRMWGIDEGDTIVV
+YDDDHGLSAARAWWLLRHAGLRDSVLLDGGLEAWRAAGLPLQPGEVIPVPGTARPSWGRM
+PVVDTAGAEAMASGGLLLDARAAERYRGEVEPFDPVAGHIPGARNAPTAESIAEDGRLRP
+AAELAERFDAVGVDDATPVAVYCGSGITAAHAVLTLAVAGRPGVALYPGSWSAWVQDPSN
+AVAVGPEPYGASGRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000678.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000678.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bfc5a8d9f15472ece90950a6cc9fc51df690f2d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000678.fa
@@ -0,0 +1,121 @@
+>0_739
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAEGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELASEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRSGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLRERQQELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLAQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPANVVSERHFDAWWKKARQEQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFSYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPEALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAQADARAGAEGRRRPEGPGRSGATPAFEERHRLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>1_478
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTAQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPVPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYAGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRAYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFAYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRGTGRGGRAPADARAGAEGHRRPEGPGRSGATPVFEERHGLTSWSIGT
+VPKTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSAEDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKDSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGMLTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
+>2_2114
+MTETPTPPAAASSAPAIVFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKTTQLPKMC
+LALGLGEAGVIGHTQPRRIAARSVAERIAEELGEDIGRTVGYQVRFTAQTSKATRVKVMT
+DGILLAEIPHDPQLRRYSVVIVDEAHERSLNIDFLLGYLRTLLPQRPDLKVIITSATIDP
+ERFARHFGRALAEGEEHEDAVPADDGGLVVPAPVIEVSGRTYPVEVRYRPLTGEPSPDDP
+EDDSDDAAETRDPLDAIGEAVLELAAEPPGDILVFLPGEREIRDAADHLSGVVASSKRLA
+GTEVLPLFGRLSMAEQHRVFGRAAAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISR
+YSHRTKVQRLPIERVSQASANQRAGRSGRTSPGIAIRLYSEEDYLSRPEFTDPEILRTSL
+ASVILQMLSLGVAATPADVQGFPFVQPPDGRQVSDGATTLTELGALHPPRPSGAKDGHDG
+GRGRGGRAPEPGTITPIGRRLARLPVDPRLGRMILESGERGCVREVMVLAAALTIQDPRE
+RPVEQREAADELHRRFADENSDFSAILNLWAYLQEQQKELSGSQFRKLCRREHINWLRVH
+EWQDLVRQLRQLAKDVGVAVHAGPVDPVGQHEAVHRSLLTGLLSQIGSYDERRREYAGAR
+GTRFAVFPGSALFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEAAGGLVKRTYNEPH
+WSRRAGAVVAREKVTLFGVTLIPDRSVKYGRIDPELSRELFIRHALVEGDWRTRHRFFAR
+NRAALEEVDALETRLRRRDLRIGDEDLFAFYDARVPANVVSERHFDAWWKKARQERPDLL
+DLDVAALLTADAEDLDTDAFPTVFPYPLSGGDVDLDLEYTFDPTGASGTDGVTVSVPVLL
+LNQVSPGPFAWLVPGLRVELVTALIKALPKAVRKQLVPAPDVARQLVADLDAHADPLADE
+LTEALSAAVRRVRGIVVEPGLWAPDAVPAHLRMDYRVVDARGAVMGAGQDLAALQARLAK
+ANRSAIAARLAGTDDPANARPGPGRQGGRRDGGGNDGGAGRRGSGRGVRGRGRDGTGRPE
+AGAQGAGGAAAAFAERHGLTSWSIGTVPRRITTDPGARGPAITGYPALVPETTAEGGPAA
+GLTVARSAEDQAAWHRAGVIRLLLATLPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVAD
+CSQAAVDRLVGDELPFDEAAFRALFDRVRADLIDTVFAVTRLVEQVLSRAAEVRRRLKGS
+VSLAMAPALSDVKAHLEQLVFPGFVAATGWERLQHLPRYLQGILVRLDRLDAGGHLQRDG
+QHMAVVQRLEDEFDAAVQAHRARFSGVPVPADLERVRWLIEELRVSFFAQELGTAVSVSE
+KRVRQALAQAARA
+>3_2009
+MTDFPQPPAAAPVITFPAHLPVAERREEIMDAVRENQVVIVAGETGSGKTTQLPKMLLAL
+GLGGAGVVGHTQPRRIAARSVAERIAEELGEDVGRTVGYQVRFTAQTSTRTRVKVMTDGI
+LLAEIPHDPDLRKYSAIIVDEAHERSLNIDFLLGYLKRLLPRRPDLKVIITSATIDPERF
+ARHFGTEDEPAPIIEVSGRTYPVEIRYRPLTEEPSPDDPDDDADDHAETRDPIDAVGDAV
+LELAGEAPGDILVFFPGEREIREAADHLAGVVASTPRLAGTEVLPLYGRLSMAEQHRVFG
+RAGAGVRRRIVLATNVAETSLTVPGIKYVIDTGTARISRYSHRTKVQRLPIERISQASAN
+QRSGRSGRTSDGIAIRLYSEEDFLSRPEFTDPEILRTSLASVILQMLSLGVADTPREVMD
+FPFVQPPDSRQVTDGAATLTELGALHADAPTRGGGRGRGKGAGNRSAAGTITDIGRRLAR
+LPVDPRLGRMILESGRRDCTREVMVLAAALTIQDPRERPVEQRQAADELHARFADDRSDF
+SAYLNLWEYLREQQRELSGSQFRKLCRREHINWLRVHEWQDLVRQLRQLSKDVGVSVHPG
+PVDPVGKHDDVHKSLLTGLLSQIGAYDERRREYQGARNTRFAVFPGSALFKKRHPFVMAA
+ELVETSRLWARAVARIEPEWIEEVAGDLVLRSYAEPHWSRKAGAAVAMEKVTLFGVTIVP
+ERSVRYGRIDPVLSRELFLRHALVEGDWRTRHRFFARNRRLLEEVDELETRLRRRDLRVG
+DEELFAFYDARVPANVVSERHFDAWWKKARQETPDLLDLDLDALLTQDADELDTDAFPTA
+FRYPLPGGDADLALDYTYDPTGASGTDGVTVAVPILLLNEVAPGPFAWLVPGLRGELVTA
+LIKALPKAVRKNLVPAPDVARLLVEDLDAHADPLRDELPAALSSAVRRVRGAVVEPELWR
+LDAVPDHLRMDYRVVDARGAVMGAGQDLPALQARLAKANRSAIAARLAGTDDPRNARPGQ
+GAGRGRGKTEPKGGDGGARGPAADTGRPGPSRTADGAPAFRERHGLTSWTVGEVPRQITT
+APGDRGPAITGYPSLIPETTADGSPAAGLVVARSAQDQAAWHRAGVIALLLATLPSTHRY
+VLDHLDNKEKLTFTQNPHGSVESLVRDATHVAVDRLVGTDLPFTEVGFRALFDRVRADLI
+DTVFAVTALVEQVLSRAAEVRRRLKGGVSLAMAPAKSDVQAHLEQLVFPGFLAATGWQQL
+QHLPRYVQGMLARLDKLDAGGHLQRDGQHMAVVQGLEDEFDAAVTAHRSRFPGTPVPAEL
+ERVRWLLEELRVSYFAQELGTAVSVSEKRVRQALAQARQG
+>4_703
+MTQTPPPSTPAAQPSATPHDAVAITFPEHLPVAERREEIMAAIRDHQVVIVAGETGSGKT
+TQLPKMCLALGLGEAGSIGHTQPRRIAARSVAERIAQELGEEIGQTVGYQVRFTTQTSKA
+TRVKVMTDGILLAEIPHDPQLRRYSVIIVDEAHERSLNIDFLLGYLRNLLPQRPDLKVII
+TSATIDPERFARHFGRPLAAGEDHADAVEADDGGRVVPAPIIEVSGRTYPVEIRYRPLTD
+EPSPDDPEDDADDAAETRDPLDAIGDAVLELAAEPPGDILVFLPGEREIREAADHLTGVV
+AGTTRLAGTEILPLFGRLSMAEQHRVFGRAGAGVRRRIVLATNVAETSLTVPGIKYVIDT
+GTARISRYSHRTKVQRLPIERVSQASANQRAGRSGRTSDGIAIRLYSEEDYLSRPEFTDP
+EILRTSLASVILQMLSLGVARTPGDVKEFPFVQPPDGRQVTDGATTLTELGALEAGGARA
+GTITRVGRRLARLPVDPRLGRMILEAGERGCVREVMVIAAALTIQDPRERPTEQREAADE
+LHRRFADENSDFSAILNLWAYLHERQKELSGSQFRKLCRREHINWLRVQEWQDLVRQLRQ
+LAKDVGLTVEAGPVDPVGRHEAVHKSLLTGLLSQIGAYDERRREYVGARGTRFAVFPGSA
+LFKKRHPFVMAAELVETSRLWARTVARIEPEWAEEVAGHLVKRTYNEPHWSRRAGSVVAR
+EKVTLFGVTLIPDRSVRYGRIDPELSRELFIRHALVEGDWRTRHRFFARNRAALEEVDAL
+ETRLRRRDLRIGDEDLFAFYDARIPGNVVSERHFDAWWKKARQDQPDLLDLDVAALLTAD
+AEDLDTDAFPTTFTYPMPGGDVELDLEYTFDPTGAAGTDGVTVAVPILLLNQVSPGPFAW
+LVPGLRVELVTALIKALPKAVRKNLVPAPDVAQQLVADLEAHADPLRDELPDALSAAVRR
+VRGVVVEPGLWAPDAVPLHLRMDYRVVDARGAVMGAGQDLPALQARLAQANRSAIAARLA
+GTDDPASARPGPRRTGRGGRAQADGRAGAEGRRRPEGPGRSGATPAFEERHGLTSWSIGT
+VPRTVSTAAGARGPAITGYPSLVPETTPDGGPAAGLTVARSADDQAAWHRAGVIRLLLAT
+LPSPQRYVLDHLDNREKLTFTQNPHGSVDSLVADCTQAAVDRLVGDELPFDEAAFRALFD
+RVRADLIDTVFAVTSLVEQVLSRAAQVRRRLKGSVSLALAPALSDVKAHLEQLVFPGFVA
+ATGWERLQHLPRYLQGILTRLDRLDAGGHLQRDGQHMAVVQGLEDEFDAAVAAHRARFAG
+TPVPAELERVRWLIEELRVSFFAQELGTAVSVSEKRVRQALARATRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..56198f331cccfc5ce9323c2ef49f1a1d05333118
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000682.fa
@@ -0,0 +1,40 @@
+>0_745
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLSITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMATVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGLVI
+IVMLVVTWIVERSTVRRRAARAARA
+>1_485
+MSHVTESSPAHPGRAEESTPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAALTVHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWAIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLIVTWIVERTTVRRRAARAARA
+>2_2109
+MSPVTESSPAHRGRAEESAPLRPTSRLGIAATFIGTTIGAGYASGNEILQYFVSFGFWGG
+TLALVIAGALFFLLSAIVLKMAQKLRTTDIHRLVNPTTSRVPTWFADLCITASLLGTLVI
+MLAGAGAAVNTSFGLPTMVGSLLMAAVCVLSVLAGISGLVRVQAVVVPLIIVVAVGVAWW
+GLANPGAPVEDVASLVTSSPLINQWWMSGILYVAFNFQLAYAVLAPIGRDSSSSGRTLVA
+GAGLGAVGLVVMAGAIMFAMAAHAHLIGRADLPMVELAAMIGGWAALVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRRVPGWAIAVATALAATLLSSVGFSDLVGTVYPVLGYAGIAI
+IVMLIITWIAERTLVRRRAARAARA
+>3_2003
+MSHVAQSTHENRPAQDGGNGLRPMSALGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGVLFFLLSAIVLKMAQQLRTTDIHRLVNPTSSRIPTWFADLCITASLLGTLVI
+MFAGAGAALDTWLGLPAWAGAALMAAVCVLTVLGGISGLVKVQGLVVPLIILVAVGVAWW
+GLTHPGAGADDVASLVTSSPLINTWWMSGILYVAFNFQLAYAVLAPIGKGSSSPGTSLVA
+GAGLGAIGLVVMAGAIMAAMGAHATLIGRAELPMVELAGMVAPWVAAVYTVILLLAQFTT
+AVSCLFGGVERIALLSPLRDVPGWLIAVVTAVVAVLLSSVGFSDLVGIVYPVLGYAGIAI
+VAMLIATWILDRTLVRRRAARADRA
+>4_712
+MSHVTESSPAHPGRAEESAPLRPTSPLGIAATFIGTTIGAGYASGNEILQYFVSFGLWGG
+TGALVIAGALFFLLAVIVLRLAQKLRTTDIHRIVNPTTSRVPTWFADLCITTSLLGTLVI
+MLAGAGAAVHTAFGLPSLVGSLVMAAVCVVSVLAGITGLVRVQAVVVPLIIVVAVGVAVW
+GLANPGAAVDDVAALVTSSPLINQWWLSGVLYVAFNIQLAYAVLAPIGEESSSSGRSLVA
+GAGLGALGLVVMAGAVMAAMTAHAQLIGRAELPMVELAAMIGGWAALLYTVVLLLAQFTT
+AVSCLYGGVERIALLSSMRRVPGWVIAVVTALAATLLSSVGFSDLVGTVYPVLGYAGIVI
+IVMLVVTWIVERSTVRRRAARAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11925cc716e3925840278061913b433c7f35a222
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000683.fa
@@ -0,0 +1,31 @@
+>0_746
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WDDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>1_486
+MTPAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
+>2_2108
+MLSIAGSDSGGGAGVQADLKTIAVWGGYGMTAITAITAQNTQGVQAVHPLPVDVVRAQLD
+SIAADIAVDAVKIGMLGTAELMGAVAGWLEETRPAVVVLDPVMVASSGDALTAVGDDDGR
+AAWSRLLRAAHLVTPNLPELARLTGRDSTDWEAALDAAGGLAAEHEVTVLLKGGHLDEAA
+AAEVPDAVVRVAGAVHEVRGPRVATRASHGTGCTLSSALATLAGAGLSWEDALERAKPWL
+ADAMRAGEALAVGDASRPTWHGPVDHGHARRG
+>3_2002
+MAPSPSTPPSSSPAAEGPAVPRVLSIAGSDSGGGAGIQADLKTIAEWGGYGMTAITAITA
+QNTQGVQAVHPLPAEVVRAQLDSVASDIAVDAVKVGMLGTAELMRVVADWLEEARPAVVV
+VDPVMAATSGHALTPVGDAEAHAAWGRLLRAAHLVTPNLPELARLAGRPLDSWAAALDAA
+RELAAAHAVTVLAKGGHLADLTRADPEGAEAGDDPDAEGGVPDALVRPDGSVHEVRGPRV
+ESGATHGTGCTLSAALATLAAGGLGWEDAIERAKPWLAQAMVAGEALAVGDRTRPTWHGP
+VDHGHARRG
+>4_713
+MTSAVPRVLSIAGSDSGGGAGVQADLKTIAAWGGYGMTAITAITAQNTQGVQAVHPLPVD
+VVRAQLDSVAADIAVDAVKIGMLGTVELMRAVAGWLEETRPAVVVLDPVMVASSGDALTA
+VGDDDGRAAWARLLRVAHLVTPNLPELARLTGRDATDWDAALDAARGLAAEHGVTVLLKG
+GHLDETEAPEAAAAEVPDAVVRVGGAVHEVRGPRVTTRASHGTGCTLSSALATLAGAGLS
+WEDALERAKPWLADAMRAGEALAVGDASRPTWHGPVDHGHAQRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000691.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000691.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1a53b3b614185dbe52541ceb70dd565b2d05c896
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000691.fa
@@ -0,0 +1,45 @@
+>0_754
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
+>1_494
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
+>2_2100
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRNTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGIEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLAGDRVTRVMGIANGTTNYILDKMDSEGAG
+FDEALAEAQRLGYAEADPTADVEGHDAAAKAAILATLAFGAPYTLDQVAVSGITAITAED
+NEAAADAGYVIKLLAIAERARAADSAEGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVAELPALDPAEAVTSCLV
+VLRVADEPGVLRRVAGVFEEQGVSIETLRQVQSDRDDAPGASLRLITHRARQRDLDATVE
+ALAALDAVHEVASVLRVEGN
+>3_1993
+MAEPTASAAQTAPAPARDALRVALLGGGTVGSQAARILTEDAAVLADRVGVRLELTGIAV
+RDTAAVRDWQADPSLYTTDAEALVDGADLVIELMGGIEPARSLIRRALQVGTSVVTGNKA
+LLAEHGEELYRLASETGAQLSFEAAVAGAIPILRPLRDSLSGDTVNRVMGIANGTTNFIL
+DRMDTEGASFADALAEAQRLGYAEADPTADVGGFDAAAKAAILATLAFGSSYTLDQVSVE
+GITEVTAEDNAAAADAGYVIKLLAIAERDTARDGTAGAILRVHPTLIPREHPLGSVRGAY
+NAVFVEAENAGQLMFYGPGAGGAPTASAVMGDAVAIGQRIVRGGPARLRTPVAALPALDV
+SEARTSCMVVLRVADQPGVLRRVAGVFEEHGVSIETLRQVQGADDAAGASLRLITHRARQ
+RDLDDVVAELTTLDAVHEVASVLRVEGN
+>4_721
+MPQHTDAPTALKVALLGGGTVGSQTARILTEDADILRDRVGADLELTGIAVRDTGATRDW
+QADPALYTTDAEALVDGADVVIELMGGVEPARTLILRALAAGTSVVTGNKALLAQHGEEL
+YAAAAATGAQLSFEAAVAGAIPILRPLRDSLGGDRVTRVMGIANGTTNFILDRMDSEGAD
+FDDALAEAQRLGYAEADPTADVEGHDAAAKAAILATIAFGAPYTLDQVAVAGITAITAED
+NAAAAEAGYVIKLLAIAERGRAADGAQGAVLRVHPTLLPREHPLASVRGAFNAVFVEAEN
+AGELMFYGPGAGGAPTASAVMGDVVSIAQRIVRGGPARLRTPVTALPALDPAEAHTSFMV
+VLRAADQPGVLRRVAGVFEEHGVSIETLRQVPSEREDAPGASLRLITHRARQRDLDATVE
+ALAALDVVHEVASVLRVEGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..180455583e41c3b3a9806fde37bbf7ecc8a4dfe2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000692.fa
@@ -0,0 +1,40 @@
+>0_755
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>1_495
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
+>2_2099
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVDQGAKAVVCASTGNTSASAAAYAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDALGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDEELPAVSTKTPVMWGFQAAGAAPI
+VLGHPVTEPDTIATAIRIGNPASWEQAEAARDGSGGMIDSVTDEEILAAHRWLSAKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKSWVITVTGHGLKDPQWALRDADGEDVTPRTVPFDV
+VTVAQALGLA
+>3_1992
+MAHVWRGVIREYAGRLPVTEDTRVVSLGEGGTPLIRAPHLSELVEGEVYVKFEGMNPTGS
+FKDRGMTMAITAAVENGAKAVVCASTGNTSASAAAFAAQAGLTCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDNCLDIARKLSENYPVFLVNSVNPARIEGQKTAAFEVVDLLGDAP
+DYHLLPVGNAGNITAYWKGYQEYSRPYVNPHPGTSDEELPAVATKTPVMWGFQAAGAAPL
+VLGHPVTEPETIATAIRIGNPASWDQATAARDASGGMIDSVTDEEILAAHRWLSSKEGVF
+VEPASAAGVAGLIKHHAAGNVPAGKTWVITVTGHGLKDPQWALKGADGDDVTPRSVPFDV
+VTVAEALGLT
+>4_722
+MAHQWRGVVREYADRLPVTEDTRVITLGEGGTPLIHAPHLSELVQGTVHVKFEGMNPTGS
+FKDRGMTMAITAAVADGAKAVVCASTGNTSASAAAYAAQAGITCAVLVPEGKISMGKMSQ
+AVAHGAEILQVQGNFDDCLEVARKLAENYPVFLVNSVNPARIEGQKTGAFEVVDTLGDAP
+DYHLLPVGNAGNITAYWKGYREYAAPYVNPHEGASDAELPAVATKTPVMWGFQAAGAAPI
+VQGHPVTDPDTIATAIRIGNPASWEQAEAARDESGGMIDSVTDEEILEAHRWLSAKEGVF
+VEPASAAGVAGLLKHHAAGNVPAGKSWVITVTGHGLKDPQWALRGADGADVTPRSVPFDV
+VTVAQALGLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000695.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000695.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cc1f1bef326c238165adaee9dad2dc758a7787e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000695.fa
@@ -0,0 +1,40 @@
+>0_758
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>1_498
+MFDSEQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYADSRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
+>2_2096
+MFDSEERREAVDRLLAEHRELTARLSDPAVHQDPVLARRLNRRFAELGAVVTAHAAWREA
+AAELADARELAAAGDDDAAAFAAEVPCLEEAETAAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAIRAGATDPAEGV
+FARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVRIDPNEVKTDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAAMRVLRSRLLERRRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVVASCLALDEER
+RLAALGGDA
+>3_1989
+MFESVERLLAEHRELAGQLSDPALHADAARARRVGRRYAELGAVVAAHREWEQAVADRDD
+ARELAAAPGEDAAAFAAEVPALEAAADEAAERLRRLLIPRDPDDGRDVILEIKGGEGGEE
+AALFAGDLLRMYLRYAESRGWRTEVLSATHSDLGGFKDVHVAVRGSAQDPAEGVYARLKH
+EGGVHRVQRVPVTESAGRIHTSAAGVLVLPEADAPDEVQIDPNDLKTDVFRSSGPGGQSV
+NTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAERDAEDSAARSAQ
+VRTMDRSERIRTYNFPENRIADHRTGFKAHNLDAVLDGALDPVIDSCVALDEQRRLARLG
+EEAR
+>4_725
+MFDSDQRREAVDRLLAEHRELTARLSDPAVHQDPALARRLNRRFAELGAVVTAHRAWSAA
+AEELADARELAAAGDDDAAAFAAEVPGLEAAEAEAAERLRRLLIPRDPDDARDVILEIKG
+GEGGEEAALFAGDLLRMYLRYAESRGWKTEVLSATHSDLGGYKDVHVAVRGSAADPADGV
+YARLKFEGGVHRVQRVPVTESQGRIHTSAAGVLVLPEVDAPDEVHLDPNDLKVDVFRSSG
+PGGQSVNTTDSAVRLTHLPTGIVVSMQNEKSQIQNREAALRVLRSRLLERQRAEQDAEDS
+AARAAQVRTMDRSERIRTYNFPENRIADHRTGYKAHNLDAVLDGDLEAVIASCLALDEER
+RLAALGGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000712.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000712.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf988814d42727fa741e6124d5d4a82d7628b5ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000712.fa
@@ -0,0 +1,30 @@
+>0_776
+MTPHASEPAPTHLAAATRRRAVDAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRTLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVELVGGRHGSEGLAWL
+>1_516
+MTPHAPEPAPAHLAAAARRRAADAPDPDLALVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+TQLVTYAGLLHGLDADTVAERTADLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AAGTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
+>2_2078
+MSEHPAEPHRTAPSSAEAPHAGPAPAEAPAVVPSAAARRRAVDAPDPDLALVTRGLTKRF
+GDKTALDGLDLDVPAGSFYGVVGPNGAGKTTALSMATGLLRPDLGQAWIHGVDVWAQPLE
+AKRRVGVLADGVRTFDRLTGAQLVTYAGLLHGVDADTVAARTEDLLRVMDLADAGRKLVV
+DYSAGMTKKISLAAAMVHAPDVLVLDEPFEAVDPVSAANIRDILHDYVGRGGTVIVSSHV
+MDLVQRMCSHVAVIAGGTLRAAGTLEEVRAGRDLEDRFVDLVGGRHEQEGLAWL
+>3_1970
+MRAQDAPDPNLALVTRGLAKRFGEKVALAGLDLEVPAGSFFGVVGPNGAGKTTALSMATG
+MLRPDAGRVWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTGAQLITYAGLLHGLDRDTV
+DVRTADLLRVMDLEEAGRKLVVDYSAGMTKKVNLAAAMVHAPDVLVLDEPFEAVDPVSAA
+NIRDILHDYVGRGGTVIVSSHVMDLVQRMCSHVAVIAGGVLRAAGTLEEVRAGRDLEERF
+VDLVGGRHTGEGLAWL
+>4_743
+MTPHAPEPAPAHLAAAARRRAVDAPDPDLAFVTRGLTQRFGDKLALDALDLDVPAGSFFG
+VVGPNGAGKTTALSMATGLLRPDHGRAWIHGVDVWEQPLEAKRRVGVLADGVRTFDRLTG
+AQLVTYAGLLHGLDADTVAERTTDLLRVMDLEDAGRKLVADYSAGMTKKVSLAAAMVHAP
+DLLVLDEPFEAVDPVSAANIRDILHSYVERGGTVIVSSHVMDLVQRMCTHVAVIAAGTLR
+AADTLEEVRDGRDLEDRFVDLVGGRHGSEGLAWL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000719.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000719.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d127b467a01da83e9a652b7b37040525979fc00
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000719.fa
@@ -0,0 +1,30 @@
+>0_784
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+ADESAPGAGDAEDEQ
+>1_525
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHNQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ
+>2_2070
+MAERFRWTRRGYTAQLEKPEVRLLRGLVKDVITLLEGRRRNVLSEADDLPADAPGAPEPS
+ADVAPVPQGPEAGAGPAAGLDEADAAFWELVSGLHLSQDRVPHRAAPADPAVARLLPEAM
+PQADAQERGAHRALTEDALSEGKLADARLALELLRSTRVEVPHHQAPAFGRALNDVRLVL
+AARLGVETEEDAERVHAVDDWRSAEDVESTMALLYNFTTWLLETLMTEMLSELPEGADED
+APGADEAGDDA
+>3_1960
+MAQRFRWTRRGYVAELEDAELRLLRGLVKDVVTLLENRQDEVAPPGSDAGTAEDAPEAGA
+EPVADARPGDAVGPGEETPHDAAFWALVGGLDLVADPVAERSAPEDPAVARLLPDAMPHA
+EPAERARQRALTEDALTAAKLADARRALEALRSVRVTVPHEHAVSFGRALNDVRLVLAAR
+LGIETEQDAARVHAVDDWRDAQDVEATMALLYNFTTWLQETLMAEMLSELPLEGAAGPDE
+EERA
+>4_753
+MAERFRWTRRGYTAQLELPEVRLLRGLVRDVVALLEGRRADVRPAEADPAEAPAAEDGVD
+TPEDPPAAPPSVSAAQDAGPVAGLDASDAAFWGLVSGLHLSQDPEPQRSAPTDPAVARLL
+PDAMPQAGAAEQGAHRALTEDALSEGKLADARLALELLRSTRVEVPHDQAPAFGRALNDV
+RLVLAARLGVETEEDAARVHAVDDWRSAEDVESTMALLYNFTSWLLETLMTEMLSELPEG
+SDESAPGAGDAEGEQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd2bf3e141d9975cd91b395dfa10599a3fc4831a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000721.fa
@@ -0,0 +1,30 @@
+>0_786
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWDRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRTERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>1_527
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEARAVYDGPLAVAVSGLSYGV
+>2_2068
+MKLTVIGASGSFPGPGSPASCYLVTAQGVAEDGVTPRTWRILLDLGNGSLGVLQRYIELE
+ELDGILLSHLHPDHCMDLCGMHVAIRWNPEGWHRDRMPVYGPTATADRIAEAYGMDPEPG
+MHEDFDFRVWRPGRTERFGPFRLTPVPVRHPIDEAYAIRVEADEPDGEGGTVTRVLTYSG
+DTDACEGLVEAARDADLFLCEAAFHEGRDDGIDGVHLTGLRAGQTAAQAGAKKLLLTHLP
+VWNDPQRAVLEAREAYEGPMAVAVSGLSYGV
+>3_1958
+MKLTVIGASGSFPGPGSPASCYLVTADGPDGNGGTRPWRILLDLGNGSLGVLQRHIELEQ
+IDGVLLSHLHPDHCIDLCGLHVAVRWNPEGWDAGRIPVYGPAATATRIAEAYGMDPEPGM
+QEDFDFRAWEAGRTEGLGPFRLTPFAVRHPIDEAYAIRVETTEPGPDGEPVTRVLAYSGD
+SDTCDGLVEAARDADLFLCEAAYHEGRDDHIDGVHLTGRRAGQMAAEAGARKLLLTHLPV
+WNDPQRCAQEAREAYVGPLAVAVSGLSYGL
+>4_755
+MKLTIIGASGSFPGPGSPASCYLLTAEGVAEDGVTPRTWRILLDLGNGALGVLQRYVELE
+DLDGILLSHLHPDHFMDLCGMHVAIRWNPAGWGRGRLPVYGPAGTADRIAEAYGMDPEPG
+MHQDFEFRCWAAGRPERLGPFRFTPVPVRHPIDEAYAIRVEVDRVDDDGDVTTRVLTYSG
+DTDACEGLVEAARDADVFLCEAAFHEGRDDGIDGVHLTGRRAGETAAQAGARKLLLTHLP
+VWNDPQRAVQEAREVYDGPLAVAVSGLSYGV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..09ba7030be1621f27afebe75edafb98e77321956
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000724.fa
@@ -0,0 +1,39 @@
+>0_789
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADADVLPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGAGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQRAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRG
+>1_530
+MSGGRAPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLGVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPPPNPTADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
+>2_2065
+MSGVLAPVPGLDFTAIDFETANGFRGSPCALGAVRVRDGVMVERAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAARFADVYDELAGFVGADVLAAHNAGFDVGVIESGLEVSGRDVPR
+LDFVCTLVLARRVYDLASYALPSAAREAGFAPGPHHDALADAEACAAILVDVARRVLGTE
+AGDGAAVAPAGARGLPEPFDVPRLMRAQGLTVNTLAQRAAGEGPESKATRQARRAQGVFD
+ARVPLKDERAMPDFLRWPDEGTNPVPNPDADPGHPLHGQTVVFTGGIGMSRQTAKVRAAR
+LGAQTANRVGAATTMLVVGDGFEAADLDRPAPAPGTREAVTTALAHRKTRDALRRRERGQ
+HISLVSEGEFLQMLDGNWPDAAR
+>3_1955
+MTAGIAPVRQPGLDFTAIDFETANGFRGSACQLGAVRVRDGLPASRAVWLMRPPAGFDRF
+DPRNVRIHGIHADRVVDAPRFAEVYDAFAAFAGDDVLVAHNAGFDLGVIESGLEVSGRDV
+PAHDYACTLTLARRIYDLPSYSLPSAAREAGFVPGRHHDALADAEACAAILVDLARRVCP
+PGEATVDALLASQGLRRSRLTARAAGTGRESRATRQARTMPGLFDATIPLADDRTLPDLM
+RWPDEGVNPEPAADADPGHPLYGQVVVFTGGIGMSRQEAKNRAAQRGAATANRVNGRTTM
+LVVGDGVDPAELVGAPEVHGVVVDPGATDPAGRGVDPGGAVTHRKTREALQRRAKGQAIA
+LVSEAEFLQMVDGAWPAGAR
+>4_758
+MSGGRVPVPGLDFTAIDFETANGFRGSPCAVGAVRVRDGVMVDRAEWLIRPPVGFDRFDP
+RNVRIHGITEDRVLDAPRFAQVYDELADFVGTDVLAAHNAGFDVGVIESGLEVSGRDVPG
+LEFVCTLVLARRVYDLPSYALPSAAREAGFTPGRHHDALADAEACAAILVDIGRRVLGAP
+PADAEILPGLTDAPAGRGVDRLMRAQGLSVSVLAPRAAGSGAESKATRQARRTEGVFDAR
+VPLRDERAMPDFMRWPDEGVNPLPNPAADPGHPLFGQTVVFTGGIGMSRQSAKTRAAAHG
+AQTANRVGAATTMLVVGDGFEAADLHRPRAEDGAPQAVTTALAHRKTRDALRRRDRGQAI
+ALVSEGEFLQMLDGNWPDAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000733.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000733.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1c0217d5c25dc7f271b84a58c8870280090488bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000733.fa
@@ -0,0 +1,55 @@
+>0_798
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG
+>1_539
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGKAVVNMLRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWEPVEPKFTTGVLGKYAKLVHSAAEGAYLG
+>2_2048
+MDTAASTPRTPSAAPDMKPRSRDVTDGMERAASRGMLRAVGLGDADFAKPQIGIASSWNE
+ITPCNLSLDRLAQAAKEGVHADGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADSVE
+TVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSTMPGHARLSDGTEKQVTI
+IDAFEAVGACARGLMSEEDLLRIEKAIVPTEGACGGMYTANTMASVGEALGMSLPGSATP
+PSPDRRRDDFARRSGAAVVNLLRQGITARDIMTKEAFENAIAVTMAFGGSTNAVLHLLAI
+AREAGVDLSLEDFNRVGDRTPHIADLKPFGRYVMTDVDRVGGVPVVMKALLDEGLLHGDA
+LTVTGRTVAENLAELAPDPVDGDVIRTMDRPMHPNGGIAILHGSLAPEGAVVKSAGFDAD
+VFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPRGGPGMREMLAITGAIKGAGLGK
+DVLLLTDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIAGRTLDVQVAEEELE
+ARRREWTPVPPKFTTGVLGKYAKLVHSAAEGAYLG
+>3_1946
+MDTSAADRTPQDVVTAPDMKPRSRDVTDGMERTAARGMLRAVGLGDEDFAKPQIGIASSW
+NEITPCNLSLDRLAQASKDGVHAAGGFPLEFGTVSVSDGISMGHEGMHFSLVSREVIADS
+VETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDGTEKQV
+TIIDAFEAVGACARGLMSEEDLLRIEKAIAPGEGACGGMYTANTMASIGEALGMSLPGSA
+AAPSADRRRDAFARRSGEAVVNMLRLGITARDVMTKPAFENAIAVTMAFGGSTNAVLHLL
+AIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRVGGVPVVMKALLDEGLLHG
+DTLTVTGKTLAENLAALDPDPVDGTVIRTMENALHPNGGIAILHGSLAPEGAVVKSAGFD
+ADVFEGTARVFDRERAAMDALEEGVIQAGDVVVIRYEGPKGGPGMREMLAITGAIKGAGL
+GKDVLLITDGRFSGGTTGLCIGHIAPEAADGGPIGLVRDGDRIRVDIASRTLDLLVEEAE
+LEARRTSWQPVPPKFTTGVLGKYAKLVHSAAEGAYLG
+>4_767
+MLTRLRGMDSAASTPSTPSAAPDIKPRSRDVTDGMERTAARGMLRAVGMGDEDFGKPQIG
+IASSWNEITPCNLSLDRLAQASKDGVHAAGGYPLEFGTVSVSDGISMGHEGMHFSLVSRE
+VIADSVETVMMAERLDGSVLLAGCDKSLPGMLMAAARLDLASVFVYAGSIMPGVARLTDG
+TERQVTIIDAFEAVGACARGLMSEEDLLRIEKSIAPGEGACGGMYTANTMASIGEALGMS
+LPGSAAAPSADRRRDAFARRSGEAVVKMIRQGITARDIMTKPAFENAIAVTMAFGGSTNA
+VLHLLAIAREAGVDLQLSDFNRIADRTPHIADLKPFGQYVMTDVDRIGGVPVVMKALLDE
+GLLHGDTLTVTGKTLAENLAALDPDPVDGKVIRTMDDAMHPNGGIAILHGSLAPEGAVVK
+SAGFDADVFEGTARVFDRERAAMDALEDGTIAAGDVVVIRYEGPKGGPGMREMLAITGAI
+KGAGLGKDVLLITDGRFSGGTTGLCIGHIAPEAAEGGPIGLVQDGDRIRVDIAGRTMDLL
+VDEAELAARRESWKPVEPKFTTGVLGKYAKLVHSAAEGAYLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000739.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000739.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e75fad2a0b32d1fa88b2fcebae455b4fdf728a8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000739.fa
@@ -0,0 +1,54 @@
+>0_817
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>1_548
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPADDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
+>2_2042
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIATDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQREGVTALELATRNAAVFKEMDDEVLDISYDRFIRTTDADHAEAVQEIWRRMEANGD
+VYLGSYAGWYSVRDERYFGEDETAVGEDGVRRAVETGTEVTWTEEESYFFRLSKYQEPLL
+EHYRRNPEFAAPRYRFNEVIRFVEDGLEDLSISRTSFDWGVPLPAPVDPDAEVADRRADH
+VTYVWVDALTNYLTGAGWPGRDPEAFGRYWPADLHVIGKDISRFHCIFWPAFLMSAGIEL
+PKRVMIHGFLNNNGAKMSKSLGNVVHPRDWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VGRKNADLANNLGNLAQRSLSMVAKNCEAAVPQPGPLTAEDEAVLAQVDALLERSRTAYA
+VQDFHDALEETWRVLGEVNAYFADQAPWVLRKTDEARMRTVLYVTLQAVRRVALLVQPVM
+PASASRLLDLLGVPAEGDAGRTGASGQGPRSFAAFHEDLVPGTALPKPEGVFPRHEEPAE
+A
+>3_1941
+MTDTRAPYYVTTAIHYPNGEPHIGHAYEVVGADALARFMRLDGRDVFFLTGTDEHGQKMA
+QTAERLGVTPMELATRNSAAFKAMDDEVLGVSYDRFIRTTDEDHHRASQEIWRRMEANGD
+VYLDRYAGWYSVRDERFFDEDETEVREDGQRYAAETGTEVTWTEEESWFFRLSKYQEPLL
+ALYRDDPEFAAPRSRFNEVIRFVEGGLEDLSISRTSFDWGIDVPAPADGAASDAHHVMYV
+WVDALTNYLTGVGFPDESSESFRRFWPADVHVIGKDISRFHCVFWPAFLMSAGIELPKRV
+MIHGFLNNNGEKMSKSLGNVVAPRDWVARYGLDAVRFFLLREFPFGADGSYSHEAVVGRK
+NADLANNLGNLAQRSLSMVAKNCGGGVPEPGSLTEADTAVLAQVDALLEHSRAAYTVQDF
+HGALEETWRVLGEVNAYFADQAPWVLKKTDEPRMRTVLYVTLQAVRRVALLVQPVMPASS
+SRLLDLLGVPAEGDAGATAASNAGPRSFAAFGEDLMPGTALPRPEGVFPRHEDPAEG
+>4_776
+MTDARAPYYLTTAISYPNGEPHIGHAYEYIASDAMARFQRLDGRDVRFLTGTDEHGQKME
+QTAQQQGVSALELATRNAAVFKEMDDDVLDISYDRFIRTTDTDHAEAVREIWRRMEANGD
+IYLGSYAGWYSVRDERYFGEDETEVGQDGVRRAVETGTEVTWTEEESYFFRLSKYQQPLL
+DHYREHPDFAAPRYRFNEVIRFVEAGLEDLSISRTSFQWGIDLPAPADPDAADADRRADH
+VTYVWVDALTNYLTGAGWPAEDPEAFARYWPADLHVIGKDISRFHCIFWPAFLMSAGLEL
+PRRVMIHGFLNNNGAKMSKSLGNVVHPREWVARYGLDAIRFFLLREFPFGADGSYSHEAV
+VSRKNADLANNLGNLAQRSLSMVAKNCGAAVPEPGEFTEADRAVLAQVDALLERSRSAYA
+VQDFHDALEETWRVLGEINAYFADQAPWVLRKTDEPRMRTVLYVTLQAVRRVALLAQPVM
+PGSASRLLDLLGVPAEGDAGRTGASGTGPRSFAAFHEDLVPGTPLPAPQPVFPRHEEPAE
+D
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6ea997f47db680ecd3ef9a6bb8a3100928b24c0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000747.fa
@@ -0,0 +1,40 @@
+>0_827
+MTVRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGSASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPPGPGWAAAGLAVLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAQAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARAPAGHRPLPGSGWDPFAG
+>1_558
+MTVRDPAAAAGATVGDLTESELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLPRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLCRTPAAA
+DRDRVLVEGADLVHAQAVPDGPRAAAPPGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
+>2_2032
+MTPAGGRPADGRTVGEVTEAQLLRVVLDGLAPAVRPGHWPPGTVAPGDDAALVPAPRGGT
+LVSTDAMGEGTDFLHRWPAGVRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PLAWVRSFAAGVVGAVDRLGAPGCRVAGGDLGTGERVHAAVTVLGDPHPAGVLRRAPAPA
+ARERVLAEGADLVHAQDAPGSSGAARSGALRPSAARPGPGWAAAGLALLLTDRDELARRA
+AALPPEDRPGARDLARAVRAQLRPRPPLALGPAAVEAGILTLMDVSDGLGRDAHRMAAAT
+GAAASAEAPPPVPWIDAAWLAEAAAPLRGVAALAGVSAESLVTGGGEDYGLLGLAWPETA
+LPAGFVRIGRLEPAGAPAPAGHRELPEAGWDPFGG
+>3_1925
+MSTPASTASAGGRPAPARTVGEASEAELLDLIQDALAPVARDVPWPAGTVPPGDDCAVVP
+APRGLVAVSTDAMGEGTDFLRRWPAGVRTRGHDVGWKAAAQNLSDVNAMGATPSALVTAL
+ALPAPTPLDWVASLAGGFTAAVRALGADRCRVAGGDLGAGESVQVAVTALGDPDPAGALR
+RAAGGERGARIARRGADLVLAAGSPRAAAAGEGQDSAWGPAGPGWAAAGLALLLTDRAVL
+TRRWADLAAHERPSARELARAVRGQLRPRPPLAAGPAAARAGLAALMDVSDGLGRDGHRL
+ARASSAPGAPLVPWVDRRWLAEAAEPLRRVASLAGTTPEALVLGGAEDYGLLGLAEPGLA
+LPSGFRRVGRLAPAGETPDGHVRLPEAGWDHFDAGRG
+>4_786
+MTMRDPAAAAGATVGDLTEAELLEVVLTGLAPAVRDGHWPAGTVAPGDDAALVPAPRGGT
+LISTDAMGEGTDFLHRWPAGPRTRGHDAGWKAVAQNLSDVNAMGGTASALVTALTLPPTT
+PVAWVRSFAAGIVGAVRHLGAPDCRVAGGDLGTGGRVHAAVTVLGDPHPGGVLRRTPAAA
+DRDRVLAEGADLVHAQAVPDGPRAAAPSGPGWAAAGLTLLLTDRAELERRADALPAADRP
+SPRELARAVRAQLRPRPPLALGPAAVTAGLLTLMDVSDGLGKDAHRMAAATGGAGPAPAP
+WLDEAWLAEAAAPLRRVAALAGTSPEALVTGGGEDYGLLGLAWPETELPRGFTRIGRLVP
+AGARPPAGHRPLSESGWDPFAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54d5f6c4200c2e18cd47dcfa38ce61f318fdb7bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000748.fa
@@ -0,0 +1,50 @@
+>0_828
+MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV
+PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV
+ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR
+DTLTPDRLVIGMHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF
+INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL
+DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI
+AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA
+VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD
+PERLLRAA
+>1_559
+MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV
+PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV
+ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR
+DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF
+INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL
+DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRIRRAEASGPAPTPASVQVLNGTRI
+AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA
+VDGAELTLLLTEWRQFREMDPDTVGARVASRLLIDGRNVLDVAAWREHGWDVIGLGHRFD
+PERLLRAA
+>2_2031
+MTHPSAPAEQDRAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPEKIARLSRGEVPFH
+EPGLPELLRTHVESGRLRFTTDVAEAARWADVHFVGVGTPQKVGESGADLRYVDAAVASL
+AAAIDRDALIVGKSTVPVGTARRLAAMVRRVRAEAGLPGEVELAWNPEFLREGFAVKDTL
+TPDRLVIGTDGPRAEQVLRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISFINA
+FSEITEAVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGLDRT
+MRFLAEVDDINLRRRDRVVDLAVQVLSAARDAGRGEAAAYGGKTTASGVEVLRGARIAVL
+GVTFKPDSDDVRDSPALDVANRLYTAGADVRVHDPEGNANAAARFPRLDYVDSLEEAVEG
+AELTLLLTEWQAFREMDPAAVGALVDARLLIDGRNVLDLAAWAEHGWTVVGLGHRFDPAA
+LGA
+>3_1924
+MTETAVVPAAAESEEAPARPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLAR
+GEVPFHEPGLPELLRAHVASGRLRFTTDVAEAASWADVHFIGVGTPQKVGEAAADLTYVD
+AAVESLARAIDRDALIVGKSTVPVGTARRLAARVAEIRAAEGLPGEVELAWNPEFLREGY
+AVKDTLTPDRLVIGTHGPRAELLLRTVYATPLAAGTPWISTDLETAELVKVAANAFLATK
+ISFINAFSEITETVGGDIGTLADAIGHDGRIGRRFLNAGVGFGGGCLPKDIRALQARVSE
+LGLDRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARQGVVRSAPGGARTAPTPAGVQVLN
+GTRIAVLGVTFKPYSDDVRDSPALDVANRLFTAGAEVAVYDPEGNANAAARFPRLGYVDS
+LDAALQGAELVLLLTEWDEFRQMDPAAAGELVAQRILIDGRNVLDVDAWGEHGWTVLGLG
+HRFDPAALNGGRPGDDAQA
+>4_787
+MTETTAPAAPAEQEAAPRLSVIGTGYLGATHAACMAELGFEVLGVDVDPAKIERLARGEV
+PFHEPGLPELLRTHVASGRLRFTTDVAEAARWADVHFIGVGTPQKVGETAADLSYVDAAV
+ASLAAAIDRDALIVGKSTVPVGTARRLAELVRTVRAEAGLPGEVELAWNPEFLREGFAVR
+DTLTPDRLVIGTHGPRAEGILRRVYARQLAADTPWISTDLETAELVKVAANAFLATKISF
+INAFSEITENVGGDIGTLADAIGHDARIGRRFLNAGVGFGGGCLPKDIRALQARVSELGL
+DRTMRFLAEVDDINLRRRDRVVDLAVQVLSAARDGRVRRADASGTAPTPASVQVLNGTRI
+AVLGVTFKPDSDDVRDSPALDVANRLYTAGADVRVYDPEGNANAAARFPRLDYVDSLEAA
+VDGAELTLLLTEWRQFREMDPDAVGARVASRLLIDGRNVLDAAAWREHGWDVIGLGHRFD
+PERLLRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..927c4edc3465edd22c01f9c64999112c94181d08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000758.fa
@@ -0,0 +1,35 @@
+>0_838
+MGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACPAQDDAGAVLAHAGAAALDSA
+RGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRAARQALSDPREGTILTVLSAA
+ARSLARSSTQAPDTPAVAGDADPAVRLGPAVTLMLADCVQAVEETESLLAPLTRAHVVDA
+GAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGAHAAEAEPAAAAEAPAEGAVEVMGT
+LALTPLAAAELRRRLTEVGDAVILAPLGTARDGQGRVPWRVHVHVPRAEDAIGPLRAAGD
+VEGLTVTDLAGPSHGDDAAPDGCHGR
+>1_569
+MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDAGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ
+AVEETESLLAPLTGAQVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE
+GEPAAAAEAPAEGAVEVMGTLTLTPLAAAELRRRLADVGDAVILAPLGTARDGQGRVPWR
+VHVHVPRAEDAIGPLRAAGDVEGLTVTDLAGPSHGDDAAPDGCHGR
+>2_2021
+MSTPPRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDAGAVLARAGAAALDLARGNSGTLLAVALAGMAEPLRGRARADAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAASRSLARSATQAPDSPAVAADVDPAVRLGPAVTAMMADCLR
+AVEQTESQLAPLAQARVVDAGAVGLLWVLEALRAAVTDTAPDEELATALHGYVEGVRPGP
+EPAGEDAVEVMGTLALTPLAAADLRRRLAETGDSVILAPVGTERDEHGRVPWRVHVHVPR
+AADAVELMRAAGEVQGLAVTELSGDAAGPDADGCHGR
+>3_1914
+MIRARLRGALAWLRGAEAALAQAAPRLDALNLFPVPDADTGSNMLATVRAARQAAERSAG
+TDMSAVLRDAGAAALDSARGNSGTLLAVALVGLAAPLTPDAPLTTAELAAGARAADRAAR
+AALSDPREGTILTVLREAATVLEAAAAGGREPAEALGSVVEAARRAVEDTEGQLAPLTRA
+RVVDAGAVGLLLVLEALRAEVTRTPFDEGVVAALHGWADGPGAAGEDPQADGREAPGVEV
+MCSIDLTPVDAAGLRRGLEEAGDSVILAPLSRAVDGAGRLRWRVHVHVARAEDAVALLEA
+AGAPEEVAVTDLWDPAHRHPDDPAEGDAASPAPDGHGR
+>4_797
+MSTPSRPSLVRHWLALAEELVGRAAPRLDALNLFPVPDADTGTNMLATLTAARTAADACP
+AQDDVGAVLAHAGAAALDSARGNSGMLLAVSLAGMAEPLRGRERVDAFALAAAFGAADRA
+ARQALSDPREGTILTVLSAAARSLARSSTQAPDTPAVAGDADPAVRLGPAVTVMLADCVQ
+AVEETESLLAPLTRAHVVDAGAVGLLWVFEALRAVVTGTPVDEELATALPGYGEGVHAAE
+GEPAAAAETPAEGAVEVMGTLALTPLAAAELRRRLADVGDAVILAPVGTARDGQGRVPWR
+VHVHVPRAEDAIGPLRAAGDVEGLAVTDLAGPSHGDAAPDGCHGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000763.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000763.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7cd645d76a5530ae75ca6a5547abbc82dcf5526e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000763.fa
@@ -0,0 +1,35 @@
+>0_843
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDTKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL
+>1_574
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDAKRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVEAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGARHEDLGADLRAWLREF
+TAGL
+>2_2016
+MTVPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEARRAGLQDVLM
+ITGRNKRALEDHFDRHPALEATLERKGDATRLAQIRESDLVGDIHYVRQGEALGLGHAVN
+CARRHVGDEPFAVLLGDDIIGDGEALLARMIDVQQRLGGSVVALMEVPEEAVSAYGVAAV
+EAVPGEGEDVVRVTGLVEKPAREDAPSTLAVIGRYVLASQVFDVLDRTPPGRGGEIQLTD
+ALQTLADDDGEGGGVHAVVFDGRRYDTGDKLGYLQAVVEFGTRHEELGGDLRAWLKAFAA
+GL
+>3_1909
+MTEQSTAASPTRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVAEAVSAG
+LGDVLMITGRNKRALEDHFDRHPALEQVLEAKGDTKRIDLIRASDLVGDIHYVRQGEALG
+LGHAVGCARRHVGDEPFAVLLGDDLIGEDEGLLARMIDVQHRLGGSVIALMEVPEDAVSA
+YGVAAVAPVDGEDDDVVAVTSLVEKPARGDAPSNLAIIGRYVLAPQVFEVLERTAPGRGG
+EIQLTDALQTLAAGEGEGFGVHAVVFRGRRYDTGDKLGYLQAVVELGVRHPELGGDLREW
+LKGFAAGL
+>4_802
+MTVPPPSRPRTRKAVIPAAGLGTRFLPATKAMPKEMLPVVDRPAIEYVVTEARRAGLADV
+LMITGRNKRALEDHFDRHPALEAALEHKGDATRLAQIHESDLVGDIHYVRQGEALGLGHA
+VNCARRHVGEEPFAVLLGDDIIGDGEALLERMIDVQQRLGGSVIALMEVPEEAVSAYGVA
+AVQAVPGEGDDVVRVTDLVEKPAREDAPSTLAIIGRYVLAPQVFDVLDETPPGRGGEIQL
+TDALQRLATEDGEGRGVHAVVFDGRRYDTGDKLGYLQAVIEFGTRHEDLGADLRAWLREF
+TAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4309b279f12a0eb818e8c080ac9973edb218d77b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000766.fa
@@ -0,0 +1,26 @@
+>0_846
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>1_577
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
+>2_2013
+MHVTAETLERALTHRSYAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVHPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGEGRTGGADKDSILADTLEALIGAVHVDHGLV
+AASALVHRHVVPLLDEPDLVRESTDWKTVVAEAANRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEADLPAAGR
+>3_1906
+MASPQTRTGSVPVPESSALLERLGVHITAGTLERALTHRSYAYEHGGLPTNERLEFLGDS
+VLGFVVTDHLFTAFPDLPEGDLARRRAAIVSTRALAKVARRIGVGPHVRLGTGETRTGGA
+DKDSILADTFEALIGAVYRDHGAVAAAALVHRHVVPLLDEPGLLRESTDWKTVVAEAASR
+HGLGEVRYDIEGQGPAHDPRFRATLTVGGRAFGSAVASSKKQAERDAAAEGWPELSATLP
+AAGS
+>4_805
+MHITAGTLERALTHRSFAYEQGGLPTNERLEFLGDSVLGYVVTDHIFTVYPDLAEGDLAR
+RRAAVVSTRALAKVARRIGIGPFVRLGTGERRTGGADKDSILADTLEALIGAVYVDHGAV
+AAAALVHRHVVPLLDEPDLLRESTDWKTVVAEAASRHGLGAVRYAIEGQGPAHDPRYRAT
+LVVGEREYGSAVASSKKQAERDAAAASWPALEAGLPAAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000776.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000776.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b55122d5c1452bee63bc267b2d00f972eb3159a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000776.fa
@@ -0,0 +1,43 @@
+>0_870
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>1_598
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSEDGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGGVDELGLIWVDTLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTSGILGTVLIGFFALPGEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
+>2_1996
+MNEMTLDAGTVWMVVSAGLVLLMTPGLALFYGGMTRSKSALNMMMMSFVSMGLVGVVWIL
+WVSGMTGGEGWLGLVGSPLADPGLTTAMEEGGLIAAGFGATFAIITVALISGAVADRARF
+LTWCVFVPVWVTLVYAPLAYMVWGGGLLAEEGAIGSRLGEALDFAGGLVVHISAGVAALV
+LALMMGKRKGFGVDPGHKPHNVPFTMLGAALLWFGWFGFNGGAAGDTGQLGLIWINTLAA
+AAAGMLGWVVVEWVRRGRPTSIGTASGIVAGLVGITPACAFVSPLGALVIGVASGAASAL
+AVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPSEGPAGLFYGGDGRLLLAQTVAV
+VVAVVFTAVLTFLIALVLKATLGLRVSEEDEERGVDLTLHDESAYHYDVGFGGVPVPADA
+QAHRGGAAG
+>3_1893
+MTETTPLDAGAVWTVTAAALVLLMTPGLALFYGGMTRAKSALNMMMMSFVSMGLIGVAWI
+LWAYGMTSGDGLAGIVGSPLNDLGAVQSMADGDLISVGFSATFAIIAVALISGAVADRAK
+FSTWCVFVPVWVTLVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLAMMMGKRQGFGVDAAHRPHNVPFTMLGAALLWFGWFGFNSGAASDVEQLGLTWVTTLV
+AAAAGMLGWVLVEWLRRGRPTSIGTASGIVSGLVAITPACAFVSPLGAVVIGLVAGAACA
+LAVNLKYRWGFDDSLDVVGVHLTAGILGTLLIGLFALPETGHAGLFHGGDGSLLLAQTVA
+VVVAVVFTAVVTAVIAFVLRATLGLRVSVEEEERGVDLTLHDETAYDVGFGGVPVPTDAQ
+ARSTAAAE
+>4_818
+MEESNVLDAGTVWMVTSAAMVLLMTPGLAIFYGGMTRAKSSLNMIMMSFVSMGLVGVVWV
+LWVHGMTGGDGWAGVVGNPAGDLGLTGTMAEGGLVAAAYGATFAIIAVALISGAVADRFK
+FVTWCVFVPVWTTVVYAPLAYMVWGGGLLSADGAIGARLGEALDFAGGLVVHISAGVAAL
+VLALLLGKRHGFGVDPGHRPHNVPFTMLGAALLWFGWFGFNGGAAGSVDELGLIWVATLA
+AGAAGMLGWVFVEWLRRGRPTSIGTASGIVSGLVAITPACAYVSPLGAVVIGLVSGAASA
+LAVNLKYRLGFDDSLDVVGVHLTAGILGTVLIGFFALPDEGRAGLFYGGDAGLLVAQTVA
+VLVAVVFTAVVTTAIALVLRGTMGLRVSKEDEERGVDLTLHDESAYDVGFGGVPVPAEAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000778.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000778.fa
new file mode 100644
index 0000000000000000000000000000000000000000..661b39831ce988548e2045f3ab1d6fe431da50e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000778.fa
@@ -0,0 +1,20 @@
+>0_872
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAAEAPAEDAEKSE
+>1_600
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
+>2_1994
+MAVKIRLKRFGKIRAPYYRIVVADSRTRRDGRAIEEIGKYHPTEEPSYIEVDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKAEE
+PKAKESAEAETPAEEAPEAPAEDAEKSE
+>3_1891
+MAVKIRLKRFGKIRAPYYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKITGDWQKFKGEAGAEGTLKTKGEKEAFVAPAKESVILPEEPKQEE
+APAESAEAEAPVEEAADAEAPAEDAEKAE
+>4_820
+MAVKIRLKRFGKIRAPFYRVVVMDSRTRRDGRAIEEIGKYHPTEEPSFIEIDSERAQYWL
+SVGAQPTEQVAALLKVTGDWQKFKGESGAEGTLKSKSEKEAFVAPEKGSVILPEEPKQEE
+APAESEQAAEAPAEEAAEAPAEDAEKSE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000783.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000783.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a066417ab4da70a490d40365107f22b7e8a3004
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000783.fa
@@ -0,0 +1,29 @@
+>0_877
+MRTSEPRDPRRSRGSVASGAGSSPGTTAAPASGASRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP
+>1_605
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLHHGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLRNGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTMD
+APSGDTP
+>2_1989
+MSHPEPRDPRRSRGSAVSRSVAPGSGRGTTPARGSGGTAWWAWIGLTVAAAVGAAAVLRA
+LTGPVYLIPSGSMEPTLHPGDRVRVDASAAGGEGVRRGDVVVFDGAGSLAPYRSVGSLER
+GLEDVARSWGLGASGDAFVKRVLALPGDRLECCAPDGRLLRDGAPVDEPYLGRPVTAQDP
+AADGSWTFEVPEGRMVVLGDNRSASRDSRALLGGAGGGLIPLKRVEGRAAEVVWPLDRRG
+PVDASAPEAAPGAAP
+>3_1886
+MRAQEPRDRNRSRGSRASGEAGRPWWALVLLTLAGAVVAAALLRAFTGPVYLVPSGSMEP
+TLLPGDRVHVDTAAADGAGLEHGDVVVFDGAGSLAPYRSRTALDRGLEDVAAFWGVGAAQ
+DVYVKRVLALPGDTLSCCTADGRLERNGAPLDESYLGRTVDAAAPASRSTWAFEVPEGRM
+VVLGDNRDVSRDSRALLGAPGGGLIPVEKVIGRVDSVAWPLDRRGDVPAGAQDGSRG
+>4_825
+MRTSEPRDPRRSRGSVASGAGSSSGPTAAPASGTSRWWAWLGLTVVAAVVVAAVLRALTG
+PVYLIPSGSMEPTLQPGDRVRVDAAAAGGQGLQRGDVVVFDGAGSLAPYRSAGSLERGLE
+DVARWWGVGAAEDVFVKRVLALPGDRLECCAPDGRLLREGEPLDEPYLGRPVTADEPAAA
+GTWSFEVPDGRMVVLGDHRAASRDSRALLGAPGGGLIPLERVEGRAAEIVWPLSRRGTVD
+APSGDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12a5b449778d04efc4d694320ea7b140f6d0805b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000790.fa
@@ -0,0 +1,35 @@
+>0_884
+MAPSSSVRPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDYVAGTA
+ATAGTPPVDDDAPARHGPSAPDVLPELDIEDLRGWLAAMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WERLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>1_612
+MAPSSSARPAPAPRAPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLRALIDHVAGTA
+GTSGSPAADDDAPARHVPSAPDVLAELDIEDLRGWLAAMSGAGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQDRVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
+>2_1981
+MASSSSSARPAAARAFAPSPRDAAWLEAFEEHLRHERNRSPQTVRAYATDLRDLVAHVAS
+GTWGGHPGTATSEAAVEADAVAPDVFAEVDVEDLRGWLAAMTDAGLARTTLARRVAAVRT
+FTGWLRREGLREDDPALRLRSPRPAATLPHVLQEQQAERLLAGAQARVAEAAVGDDPAAH
+ALALRDAALLELLYATGARVAELSALDVDDLEPGRAVARLTGKGDRQRTVPYGAPAARAL
+DAWLRLGRPRLARDGSGPAVFLGVRGGRLGVRQVRAVVDRALEGLGDTAARGPHALRHTA
+ATHLLDGGADLRSVQEVLGHSSLRTTQVYTHVSIDRLREGYRQAHPRA
+>3_1879
+MHPPHAHHAPGAPLPPASARDEAWLEAFAEHLLHERGRRPRTVRAYLADLRHLAAHVTDD
+GADAFAEVDLEDLRRWLARMRDQGLSRATVARRVAAARTFLGWLHRSGLRPDDPTLRLRA
+PAPDSRLPQVLQAEQAQRLLQAAEERVHEARRADDLHGAALAARDVALFELLYATGARVA
+EVAALDVDDLDLDRRTARLTGKGDRQRTVPFGAPAAAAVERWLRVARPVLATEHSGVALL
+LGARGGRADVRVLRGAVDRALERLGDTAARGPHALRHTAATHLLDGGADLRSVQELLGHS
+SLQTTQRYTHVSVDRLRDGYRRAHPRA
+>4_832
+MTPSSSARPAPVPRDPSPRDTAWLEAFEEHLRHERNRSPQTVRAYLADLHSLIDHVAGTA
+GTSDTPAVDDDAPARHASSAPDVLAELDIEDLRGWLADMSGSGLARATLARRVAAVRTFT
+AWLRREGLRSDDPALRLRSPRPEGTLPHVLQEQQATRLLAAAQERVDAAAAGDDPAAHAL
+ALRDAALLELLYATGARVAELSALDVDDLEAGRGVVRLTGKGDRQRTVPYGAPAGRALQA
+WQRLGRPRLARPDSGPALFLGARGGRLGVRQARTVVDRALEGLGDTAARGPHALRHTAAT
+HLLDGGADLRSVQELLGHASLRTTQVYTHVSIDRLREGYRQAHPRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c389e2f4029a56847953326148ed388d0ea7930a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000795.fa
@@ -0,0 +1,35 @@
+>0_889
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLATHVAGLSPSDPRLPLLSNRDGETVESGTDVLARIV
+DQVTRPVRWDLCMATMAARQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>1_617
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLTPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
+>2_1976
+MLAIVCPGQGSQTPGFLSPWLELDGTRALLESLSDAAGVDLVRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPASTLVAGHSVGEITAAAVTGVLSPADALALVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIEAADLAPANVNGAGQIVAAGTAEALAALGESAPAR
+ARVIPLKVAGAFHTEHMRPAVEELAAHVAGLSPADPRLTLLSNRDGQAVDAGAEVLSRIV
+DQVTRPVRWDLCMEAMAEREVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHTA
+>3_1874
+MLAIVCPGQGSQTPGFLAPWRELEGVPSLLDRLSAAAGVDLTAHGTVSDEETIKDTAVAQ
+PLIVAAGLVAADVLGLDALAPDRVLAAGHSVGEITAAAVAGVLSPEDALALVRVRATGMA
+EAAAATPTGMAAVVGGDQDEVLAAVEAAGLTPANVNGGGQIVAAGTQDALDALAAQPPAR
+ARVIPLKVAGAFHTEHMRPAVDALAAHVTGLSPADPRLTLLSNREGAAVASGTEVLERIV
+NQVTRPVRWDLCMEAMAERGVTGIMEVLPGGTLAGLAKRGLKGVPSLAVKAPDDLDAARA
+FIAEHTA
+>4_837
+MLAIVCPGQGSQTPGFLAPWLELDGTRDLLASLSDAAGVDLIRHGTESDEETIKDTAVAQ
+PLIVAAGLVAAAALEADAAAPKSTVVAGHSVGEVTAAAVTGVLSPAEALSLVRVRATGMA
+RAAAATPTGMAAVVGGDQDEVLAAIDAAGLAPANVNGAGQIVAAGTAEALGALAESAPAR
+ARVIPLKVAGAFHTEHMRPAVDDLAAHVAGLSPSDPRLPLLSNRDGEAVESGTDVLARIV
+DQVTRPVRWDLCMATMATRQVTGVLELLPGGTLTGLAKRGLKGTAQLAVKTPEDLDAARA
+FLAEHSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e966cfdb3a45e568750f9600f79ef923394dfec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000802.fa
@@ -0,0 +1,25 @@
+>0_896
+MGLLRDLLTRRSARDRSSDPPATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAASRAWA
+ERLGEPAPPPVRPG
+>1_624
+MGLLRDLLTRRSARDRSSDPTATLGRHLDNAAAIVAAARRADVPLAVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVLVTRERYEELVARVAQGEKSNGVGPAQITWPPYFAQAAERGL
+HLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLSDGVTAYGRRLAAATRAWA
+ERLGESAPPPVRPG
+>2_1968
+MATTPSVGRMSWFPRRRAASAPRALAARLENADAIAAAARRADVPLPVAAALAQLESGGR
+NVFGHDAGGVHAAPRGTDVPVTRELFEELEARVAAGETSNGVGPAQITWPPYFAQARRRG
+LRLWEPEDNMAFGLEILRGHLGGDLTEEGIARAGTLYNAGTLQGGVTDYGRRLARASRDW
+ARRLGEPAPPSSSPGRGAGRDGDRGRARSGAPGRTHVIEPGDTLWAIARANGTDVATLRR
+LNPDLVPEALAVGAPVRLP
+>3_1865
+MDPVTVLSASLAHPEAIVAAAGRARVPVSVAAALAELESGGRNVFGNDVGGVFSSPGAPD
+VEVTPERVAELRRRVADGERSNGVGPAQITWPPLFDRADAEGLDLADPEDNMTLGLSLLR
+DSARGDFSVAGLERAGTLYNAGTLAGGVTDYGRRLAAAAAAWERRLTARG
+>4_844
+MGLLRDLLTRRSARDRPSDPTATLGRHLDNAATIVAAARRADVPLPVAAALAELESGGRN
+VFGHDAGGVHSAPRGTDVPVTRERYEELVARVAQGETSNGVGPAQITWPPYFAQAAERGF
+RLWEPEDNLAFGLEILRGHLRGDLSAEGIARAGTLYNAGTLTHGVTAYGRRLAAATRVWA
+ERLGELAPPPVRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b891e306cebdee9379346aa493be6e6ce293f6f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000803.fa
@@ -0,0 +1,20 @@
+>0_897
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>1_625
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
+>2_1967
+MLFLQDGQWSILGLFQDELAGKATARTLDALLQSVTCLRMGGRDVLDGADTPRPGVEWAG
+YDREFEEADVAESRDVEPHGRIWILPATDGATVGLKLPGHRRYHDAVAQFADVDAARAAV
+AAIDELLGVGPRG
+>3_1864
+MPATPHGFWKLPAPSDAGPRHLAVITGGEAEQTMLFLQDAAGWHVLALFQDELAGRTTAR
+TLDRLLQSVTYLRMGGADLMDGADTERPGVEWAGYDREFEEQDAADETAADPAARLWILP
+ATDGASVGLKLPGHPRYADAVAQFVDAGTARAAVDAVDALIGARRPGAARPAAD
+>4_846
+MSATPLGFWKLPARPDGAARHLAVITGGEAQQTMLFLQDGQWSILALFQDELAGKAAART
+LDALLQSVTCLRMGGRDVLDGADTPRPGIEWAGYDREFEEADVAEQRDVEPRGRIWILPA
+TDGASVGLKLPGHRRYDDAVAQFADVDAARAAVAAIDELLGVGPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000817.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000817.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b9e61620b71e84b681f4a6cb571e52e45b056ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000817.fa
@@ -0,0 +1,25 @@
+>0_921
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>1_643
+MSETSTPAPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNTLDEGIDLVIRPSAAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAEVVSGAQA
+>2_1890
+MSETSTPAPENAPLVWIDCEMTGLHPHVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LAQMDPFVRDMHTTSGLLPELEHGLTLENATARVMEYLTARVPAGKALLAGNTVGQDKLF
+LSAYMPAVVEHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+RAAVMAPSPGPTSEEAQAIARVVAEAQA
+>3_1841
+MSETSTPAPESAPLVWIDCEMTGLDPDVDVLVEVAVLITDSELNVLDEGLDLVIRPTPEA
+LAQMDPFVRDMHTSSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNSVGQDKLF
+LARYMPAVIDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIRDSITELRYY
+REAVMVPAPGPTSEEARAIAEVVSGAQA
+>4_867
+MSETSTPTPESAPLVWIDCEMTGLHPQVDELVEVAVLITDAELNILDEGIDLVIRPSEAA
+LEQMDPFVRDMHTTSGLLPELAEGLELDDAAARVLEYIAARVPAGKGLLAGNTVGQDKLF
+LARYMPAVVDHLHYRIVDVSTVKELARRWYPRAYYQAPAKTGGHRALGDIKDSITELRYY
+RAAVMAPAPGPTTEEARAIAQVVSGAQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000840.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000840.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d3b70dcbc9a94cca25b2357731c612719266bfa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000840.fa
@@ -0,0 +1,45 @@
+>0_949
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>1_672
+MSTALLDRRAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPVRTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
+>2_1863
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARSGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYSEEVFTAIADDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVLRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>3_1809
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPQVIVAVNKIDLVDYSEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPQDGATLAAGMVRGGDEA
+>4_892
+MSTALLDRHAPAGTLFRLATAGSVDDGKSTLVGRLLHDSKAVLADQLEAVARTSAERGFG
+GAEGGLDLALLTDGLRAEREQGITIDVAYRYFATDRRTFVLADCPGHVQYTRNTVTGAST
+ADAVVLLVDARKGVVEQTRRHLSVVALLRVPHVIVAVNKIDLVDYAEEVFTAIAEDVRRV
+ARELGLSDAVSVPVSALQGDNVVTRSERTDWYTGPTLMELLESLPGADAEDDAAASFRFP
+VQLVVRPQGALAPGLDPEVFRDYRGYAGQVVAGTVRPGDAVAVLTPGQPARTTTVVGVDA
+AGESLEEASSPQSVVLRLADEVDVARGDTIAAADTAPRPTAEVAAALCWLSAAPLRVGQQ
+VLVKHGTAVVRALVQEVAGRLDLDTLRLDPAETLGLNDIGQVRLHLAAPLPVEPYAVHRR
+TGAFLVIDPHDGATLAAGMVRGGDEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..813b7895128db66f020164ac3b5df6056204c681
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000847.fa
@@ -0,0 +1,25 @@
+>0_959
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>1_682
+MPATPLTDDIRLSPADDIPAEEARLTWYARPAGTAALLLITSLVALTATIIIIVERTLLT
+ADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFARW
+YWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTLPA
+PAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
+>2_1854
+MPSTPTADRVRPAQPAETPASDGTLSWYARPAGMAWTLLVTSLVALTATIVIIVERSILA
+ADPGHRTSCDLNPWVSCGRVMQSWQAMTFGFPNTYIGIVAFSVLITVAVSLFAGARFARW
+YWLLMNVGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNIQTGTLPA
+SPGAARLARELAWPVILILYVLVFATILLELGFGVIGLD
+>3_1799
+MDVTETAENPPAPRAHHAAHALPEDRSLSWYARPLGTAWMLLITSIVAVTATIIIIVERS
+ILAENPNYRTSCDINPWLSCGTVMQSWQAHTFGFPNTFVGIVAFPVLITVAVSLFAGARF
+ARWYWVLMNVGILAGFAFAAWLWYSAVYSIGTLCLYCMIVWAMVILQLVLVTSRNLQTGA
+LPSSPGLARLAQDFAWPVIVLLYALVFASILLQLGLGVIGIR
+>4_902
+MSMPTTPPTDDVRLSPADDVPAEEARLTWYARPAGTAALLLITSLVALTATIVIIVERAL
+LTADPTHRTSCDLNPWVSCGQVMQSWQAHTFGFPNTYIGVVAFSVLITVGMSLLAGARFA
+RWYWLLMNAGILAGFAFCVWLWYSAVYSIGTLCLYCMIVWAMVIAQLVLVTSRNLQTGTL
+PAPAGLVRLARELAWPVIVLLYVLVFASILLELGLGVVGID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000848.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000848.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21e124af52ea5c27c0d11dc68180f8b6f7311f49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000848.fa
@@ -0,0 +1,96 @@
+>0_960
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
+>1_683
+MAANNEDTTRADERVEETAEQAVTQTAADTADGAEPERTAASDDAADPAEEPSAPTLQVD
+PTDPFAVPANLIEVLRTETTSRQRSEDEDAGESEDRAEGAVVSRRRRRRRRGEVDMELDG
+GEAGDPEHTVTRVRAPRQAVGTASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAE
+FLARREAVDRKMLVRQRDQRIQIAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSM
+EAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARL
+TSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQ
+ELQNDINRLRAQWEGIQEKASGTKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEAT
+WDNIEAYVTYVAPHLLGRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVI
+DRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVL
+EANRDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGI
+LIQDTPVERGRSGGEQRGEAEGRRRRRRRGDGEGEHAHAAAATTTGAEHADSEDERQRRE
+RAEAARVALHSIAKASGKVAEDEAPAQESAPAEQAADAAEDSAAEAVEAASAGPAEAGQP
+AGTDEEETPRRRRRRGRRRSRGRAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEE
+EAAEPAAAAAPEHQDPVVQAEEAVAAVAEAEADAEAESPEDAAEQDDRPRRSRRRRGGRG
+RSRRGGEAASTEADADAEDHGAERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVP
+AEDAPAPRRRRSRRASSDGVVRPAAGADASAERTADRTDAAPVEATEPSPEESTDATEVH
+EQPAAPAAVEEAVMVEPAATEPTAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRR
+AVSSDGVHVQVQAAPGGAQGGRFTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
+>2_1853
+MAANEDTTGAEERAEQTEQTTAETSAAVAGQAAAESPVEDGGTVTQAQADAAEGADAPER
+TAEAADIEDEAETDTAAEPEPDEAPGAPALQFDPTDPFAVPANVMEILRTEKSERRPARD
+ERPARGAEDEEEAPGRSRRRRRPSRDRDQAETEAGAEDEAVETAEGEQDAETAERGEGAV
+VSRRRRRRRRGDVDMELDGGEDGDPENTVTRVRAPRQALSTGSDAVQGVKGSTRLEAKRQ
+RRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQ
+DSLIGNVYVGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNWDAAQLDGKPKKIENALKSG
+DTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGISRKLPDVERSRLKKILKDH
+LPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASSTKVLAPELLYAEPDLTIKT
+VRDVFNEDFSAVLVQGEATWDNIEAYVTYVAPHLLDRLHHWVPQDHDGEDLYATHRVDEQ
+LHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQ
+LRLRDIGGIIVIDFIDMVLEANQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMG
+TGLVEVFSETCEHCAGRGILIHDTPVERGRSGGEPRGEGEGRRRRRRKGAGEGEQAQPAE
+STTTAGGEEVDAEDERQRRERAEAARAALHSIAKASGKVSEDEDPAEQAAPAEQAADAAE
+DQAAEAVEAARQDAAEETGEAGAQDGEGAEDEDEAPRRRRRRGRRRGRGRSEEAAEAAEA
+ASEDGSRDADAAPAGQAPAADEEEAPAADPVAQAEAAVTAVAEAEADAESGGEEREAEPA
+GDEEGARPRRARRRRGGRGRSRRGADREASTADADDEAAQPAQEPAQADAGAAGDRARAS
+RAGRVGAARAARVRPGRGRGGRRAASRPAPPPFAPRFERRCRAPGRGPGRRPGVVRPGDP
+VPRGGGRRRGDRAHRGAVHGRHRGARAPGRPRPGGGGRDGRAGGGRPRPGRAGRARPAAR
+PELRARRPPSPGAVGPVARCPRTACACRSRTPPGRHGADASRRPPPSPRPPPSRAPRRP
+>3_1780
+MAADESTTQDTHETAEGSTTPVEATEEETAAEVAESPAGEAAEATAAPDVRFDPTNPFAV
+PEGLLPLIEAETVERRRRRPAADPVPEGAADDAHADDEDDEDRPAVSRRRRRRRRGTVDM
+ELAGGEDGDPEDTVTRVRAPRRALSTGPEAVQGVKGSTRLEAKRQRRRESRSGGRRRTVI
+TEAEFLARRESVDRKMLVRQREHRIQIAVLEDGVLAEHFVSNTTQDSMIGNVYLGKVQNV
+LPSMEAAFVDIGRGRNAVLYAGEVDWDAAQLDGKAKKIENALKSGDTVLVQVTKDPVGHK
+GARLTSQISLPGRYLVYVPGGTMTGISRKLPDVERARLKKILKDHLPQDAGVIVRTAAEG
+TSEQELQNDINRLRVQWEGIQEKASSTKTLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQ
+GEATWDSIEAYVTYVAPHLLDRLHHWVPEDHDGEDLYATHRVDEQLHKALERKVYLPSGG
+SLVIDRTEAMTVVDVNTGKFTGSGGNLEETVTKNNLEAAEEVVRQLRLRDIGGIIVIDFI
+DMVLESNQDLVLRRLVECLGRDRTKHQVAEVTSLGLVQMTRKRMGTGLVEVFSEVCEHCG
+GRGILIQDTPVERNRWGHEHRAEPEARRRNKRRRGTESGEGGPAEPTAAELTEEERLRAE
+RAAAARTALMSIAKASGKAADEEPSEEAAPRAEDAPEEAADEVRPSPAGDAEEQGESESG
+GRRRKRRGRRRGRGRGGDDAARSAEEQDAPAEHPAEAAGEPAPAEAGAPDPAETATEDAD
+ADSASDAPAAQAEADEDGRSGGRRRSRRRGGRRAESPQGSGAPASAPEASVEAEQDPEEP
+AGAAEAEEALAAEEAPASPEPAAVVTFDGEPVAVPRRRRSRRATSDGVSAPRPSGMDALE
+AAVDRRAEDAAAAAQRSPATPAATPTAAPEPAPAPVAGEGPAAAAPRRRSRRAVSADGAT
+VQVQEGAAAGGGRFTAQAAQAAPAGETAAPVMLGVGVKAADIVRGE
+>4_903
+MAANNEDTTRADERVEETAEQAVTQTAADTAAGAVQPERTPASDDAADAPEEPSAPTLQV
+DPTDPFAVPANLIEVLRTETTSRQRSEDEDDPDTSGRSRRRRRPSREDDRAEEGAADASA
+DAEDREDASESEDRAEGAVVSRRRRRRRRGEVDMELDGGEAGDPEHTVTRVRAPRQAVST
+ASDTVQSVKGSTRLEAKRQRRRDSRSGGRRRTVITEAEFLARREAVDRKMLVRQRDQRIQ
+IAVLEDGVLAEHFVSHTTQDSMIGNVYLGKVQNVLPSMEAAFVDIGRGRNAVLYAGEVNW
+DAAQLDGKPRKIENALKSGDTVLVQVTKDPVGHKGARLTSQVSLPGRYLVYVPGGSMTGI
+SRKLPDVERSRLKKILKDHLPQDAGVIVRTAAEGTSEQELQNDINRLRAQWEGIQEKASG
+TKVLAPELLYAEPDLTIKTVRDVFNEDFSAMLVQGEATWDNIEAYVTYVAPHLLDRLHHW
+VPEDHDGEDLYATHRVDEQLHKALERKVYLPSGGSLVIDRTEAMTVVDVNTGKFTGSGGN
+LEETVTKNNLEAAEEIVRQLRLRDIGGIIVIDFIDMVLEANRDLVLRRLVECLGRDRTKH
+QVAEVTSLGLVQMTRKRMGTGLVEVFSETCEHCAGRGIIIKDTPVERGRSGGEQRGEAEG
+RRRRRRRGNGEGEHAHAAAATTTGAEHADSEDERQRRERAEAARVALHSIAKASGKVAED
+ETPAQEPAPAEQAADAAEDSVAEAVEAASTGPAEAGQPAAADEEETPRRRRRRGRRRSRG
+RAEESGDTGAEDAGSEDAARSHDDGPAESAGQTRQTEEEAAEPAAAAAPEHQDPVVQAEE
+AVAAVAEAEADAEAESPEDAAEQGDRPRRSRRRRGGRGRSRRGGEAASTEADADAEDHGA
+ERATPSRHEAADADSSVAVSSEVASEPVPAEDAPAPVPAEDAPAPRRRRSRRASSDGVVR
+PAAGADASAERTADRTDAAPVEATEPSPEESTDATEVHEQPAAPAAVEEAVMVEPAATEP
+TAEPTADADQASAADAPTEAQAAPTAPVPGSPRRRSRRAVSSDGVHVQVQAAPGGAQGGR
+FTAAVAEASTPAEPQGAAPVMLGVGVKAADLARRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000859.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000859.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1f53093c02254064e40c7975cd8b5b81a70ee6d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000859.fa
@@ -0,0 +1,16 @@
+>0_976
+MYPTPMTFDVARAGRALAQVSARTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGAGVRRIFSAEKSRRIKAMENEGGPAYEDDI
+>1_699
+MYPTPITFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALLK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRIEAMENEGGPAYEDDI
+>2_1834
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGTGVRRIFTAEKSRRLEAMENEGGPAYEDDI
+>3_688
+MESQHISNGDMTRAARILVKVSAQYIAREANVTKEELRDFEKGRHDLSEKKQERVRAALE
+ELGAEFLPDGPNGGYGIRLKFGRSRIYSLERCEGEGGPRLTTESDRRTQAHVPFSEPDSN
+LPFHLEDRTTASLRILVPLRLGRLWPSHLASVPGMEARAR
+>4_920
+MYPTPMTFDVARAGRALAQVSVRTLATAAGLEKEQLRRFEKGLADLRVDERLRLEKALRK
+YGVGLVPEDEFGGAGVRRIFTAEKSRRLEVLENEGGPAYEDDI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cc114b9239ffae1fc20293949801fa10efe2c214
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000860.fa
@@ -0,0 +1,45 @@
+>0_977
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQDQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>1_700
+MTATPDLEQTRHLATELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTSPIPGE
+TRTALFNSGAEAVENAVKVARAYTGKQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIREHFAQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRAAGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTNALQSA
+>2_1833
+MSSTPDLEQSRHLATALPGPRSQALAERQKAAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTAPISGQ
+TRTALFNSGAEAVENAVKVARSYTGKQAVAAFDHAYHGRTTLTMALTAKNMPYKHHFGPF
+APEVYRVPGSYPLRDGLSGAEAARRAIGALETQIGAENLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCRANDVLFIADEVQSGVARTGSWFACEAEGVEPDLMTTAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVAAAAALAVFEAIEDEDLLAKATRIEEVIREHFAAHADD
+RIAEVRGRGAMMAIELVEPGTGEPDAALTAAVAAAVRATGVILLTCGTYGNVIRFLPPLT
+IGEDLLKEGLSEVTKALQSA
+>3_1724
+MTSPVTAPEQSRHIATELPGPKSRELAARQAGAVPAGVATTMPVFASRAGGGIIEDVDGN
+RLIDLGSGIAVTSVGASHPKVVEAVQEQVADFTHTCFMITPYEGYVAVAEKLGEKAPISG
+ETRTALFNSGSEAVENAVKVARAYTRKQAVVAFDHAYHGRTTLTMSLTAKSMPYKHSFGP
+FAPEVYRVAGSYPLRDGLNGAAAAKKAISAMEKQIGADNLAAVIMEPLQGEGGFIVPAEG
+FLQAIVEWCTANDVLFIADEVQSGFARTGAWSASELEGIEPDLMCTAKGIAGGMPLSAVT
+GRAEVMDAVHPGGLGGTYGGNPVATAASLAVFEAIEEDGLLQEAQMIERVIREHFEQNAD
+ERIAEVRGRGGMMAIEFVDPASGEPDAALTGKLAAAVRAAGVVLLTCGTYGNVVRFLPPL
+TIGEELLREGLAEVTTALQSA
+>4_921
+MTATPDLEQTRHLVTELPGPRSRELAERQKRAVPAGVATTMPVYAARAAGGILEDVDGNR
+LIDLASGIAVTSVGASHPRVVAAVQEQVAQFTHTSFMITPYEGYVAVAEQLDRTCPIPGE
+TRTALFNSGAEAVENAVKVARAYTGRQAVAAFDHAYHGRTTLTMALTAKSMPYKHSFGPF
+APEIYRVPGSYPLRDGLSGAEAAQRAISALEKQIGADNLAAVIMEPIQGEGGFIVPAEGF
+LPAVVEWCKANDVLFIADEVQSGIARTGAWFASETEGIEPDLMATAKGIAGGMPLSGVTG
+RAEVMDSVHPGGLGGTYGGNPVATAAALAVFEAVEEDGLLEKARRIEQVIRDHFEQNADD
+RIAEVRGRGAMMAIEFVDPATGEPDATLTATVAAAVRATGVILLTCGTYGNVVRFLPPLT
+IGEDLLKEGLSEVTKALQSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..79fe0a470f0ae2d66205eb28e0ecc71c62f2175e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000864.fa
@@ -0,0 +1,31 @@
+>0_981
+MRTARPTRLAVALGAGVLLTGVGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPAMEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPRGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA
+>1_704
+MRTARPTRLAAALGAGVLLTGLGATPVLASPAHPAGWTAEHDLPGGSFLVASAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYR
+>1_705
+MLPTAWDTTLLAAPGERHVFISSYTGDEAAPLTLVAGPAEGRVVEVAEEETGGPRGYVYQ
+APEGFTGSDTVTLRATRDGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGLFDDA
+PAPGQPADPDTPTSPAEPETPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVR
+RHRVAA
+>2_764
+MSARRTTRPLSTALAAAVLAGGLAASTAAPALAAPAETTDGWQNGHFVGGTFGSTELSPR
+TGSFYTQHAVKDVRVTVAPFYPAFTDLEEISYKVPGEMGPETDVEFTYDAELEAGYVDVL
+EQRRVLDEEGTAGAVFTLYVDGKATATLVFGEDRNLGDDVPGMFLDATGPQAYDFSARPT
+VDHQTRLAAPGSRLVHLQGNSTGDAPVEDSTRTVVEQPEHGTLVELPRIGDPTNWTSDGA
+NGSFASTVYVADEGFTGTDQAVFTLTDGSTGEQKTLVVTFSIGDPRAADPHLGVQGTGLP
+FDEARVWEALEAQGEDDASEAPAPESPATPAPDSTDAPEASEPSEPADEHTVPETVETGS
+GQAWWLAAVAAAGTGALVAGRRRFGLAR
+>4_925
+MRTARPTRLAAALGAGVLLTGLGATPALASPAHPAGWTAEHGLPGGSFLVAGAEGETGAS
+FGTEFEVDESDVRLTVAPVLEGEARGAETEVPFTYDDELERGDFDVAAARRSLGESGTGP
+VVYTLYVLGGEVAALTYGPDADLTDADPGEPLRADQRHELGFHMLPTAWDTTLLAAPGER
+HVFISSYTGDEAAPLTLVAGPAEGRVVEVTEEETGGPGGYVYQAPEGFTGSDTVTLRATR
+DGVTTTRTVTVRFGDPRVDLYDWENGRIPGFVTFPVAGPFDDAPGQPADPDTPTSPAEPE
+TPADPADGEHTVPDTVETGRGPAAWPVAVAVLAAGVLAVVRRHRVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eac54f0a80190310cd19ad2aaa6f969b707bc026
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000865.fa
@@ -0,0 +1,15 @@
+>0_982
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>1_706
+MSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRGHAAALTAG
+AVEDIETNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPR
+>2_1829
+MTARDAAGGPAVTRNDAESRYELHDGGTLLAVLDYRDNGTAVALTRAFTIPVHRGHGHAA
+TLTAGAVEDIEARGGAAGGRQIVPLCWYVAQWLEEHPEKAHLVAPR
+>3_1721
+MDASDSPTTFTRNDAASRYELHDASGELLAALDYRDNGTAVSLTRAFTVPVHRRQGHAAT
+LTAGAVADIEARGGAAGGTTVVPMCWYVARWFEEHPEKAGLLDAR
+>4_926
+MTTGGCPGMSTSPTVTRNDAESRYELHDGGTLLAVLDFRDNGAAVSLNRAFTIPVHRGRG
+HAAALTAGAVEDIATNGGPAGGRRIVPMCWYVAQWFDEHPEKSALLAPH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..be1318338da246950db45310039b7e8f44b09a6c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000867.fa
@@ -0,0 +1,20 @@
+>0_984
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGMWT
+>1_708
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
+>2_1824
+MTVAADPGHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVQKLELPEDRVARLPLITREPT
+LGATAPYVLLTPTYGGGDGPGAVPKQVIKFLNVPGNRTWIRGVIASGNTNFHEAYCLAGY
+IIARKCQVPLMYKFELMGTPEDVDSVRGGLEGLWT
+>3_1713
+MTTATAGPNHMRDAEAQGLVPTDARLIYFSSASGYTHRFVEKLGLPLGQAARLPLLTREP
+TLGATAPYVLLTPTYGGGGDTGGEVPKQVIKFLNVPGNRALIRGVIASGNTNFSGAYAAA
+GYIISRKCQVPLMYKFELMGTPEDVVAVREGLERLEEGQHA
+>4_928
+MTVAADPSHIRSAEAQGLVPTDAGLIYFSSASNYTHRFVEKLELPEDRVARLPLITREPT
+LGATAPYVLMTPTYGGGSGPGAVPKQVIKFLNVPENRHWIRGVIASGNTNFHEGYCLAGY
+IISRKCQVPLMYKFELMGTPDDVERVRGGLEGLWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000869.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000869.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f4daf81c8b0e41e630b9b0caa90e67bcc557ba2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000869.fa
@@ -0,0 +1,35 @@
+>0_986
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SGHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>1_710
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENRNLQAKAGLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
+>2_1822
+MTEVTDTVKTNHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTKEIDEAFRWSRENENLQRKASLIVERYDGEDPYKRKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLSEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDADWDF
+>3_1708
+MTEPHHGPSVHDHLVEAINWNRIQDEKDNEVWQRLVNNFWLPEKVPLSNDVQSWNQLTDD
+ERLLSMRVFTGLTLLDTIQGTVGAVSLIPDAITPHEEAVYTNIAFMESVHAKSYSSIFST
+LASTKEIDEAFRWSRENPNLQRKAQLILERYDGEDPYKKKIASTLLESFLFYSGFYWPMY
+LSSHARLTNTADLIRLIIRDEAVHGYYIGYKYQRNIETLPEERREELKAFTFELMFELYE
+NEVEYTHSLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTDVNPAILSALSPNSD
+ENHDFFSGSGSSYVIGKAEATEDEDWDF
+>4_930
+MCPAVTETQQSHLVEAINWNRIQDEKDVEVWNRLVNNFWLPEKVPLSNDVQSWSHLTDEE
+RLLSMRVFTGLTLLDTIQGTVGAVSLIPDAMTPHEEAVLTNIAFMESVHAKSYSSIFSTL
+ASTPEIDEAFRWSRENPNLQAKARLIVERYDGQDPYKKKIASTLLESFLFYSGFYWPMYL
+SAHARLTNTADLIRLIIRDEAVHGYYIGYKYQRSIETLPEEKREELKAFTFELLFELYEN
+EVEYTHDLYDAVGLAEDVKKFLHYNANKALMNLGYEPMFPAETTNVNPAILSALSPNSDE
+NHDFFSGSGSSYVIGKAENTEDEDWDF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33d520d7e3206a3226e6aba99e8841bbb90e0781
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000884.fa
@@ -0,0 +1,30 @@
+>0_1010
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>1_732
+MTDTAAKFSEYAHPEKLVSTQWVADHVDDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEVAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTERAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRTDAGLREGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
+>2_1799
+MTETATEFSQYAHPEKLVSTQWVADHVGEEGVVVLESNEDALLYATGHIPGAQRIDWHTE
+LNDPVTRDFIGPEAFAEMAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDVRLMN
+GGRDKWIAEGRETTREVPTVARGEYPVVPRDDTTERAAREDVLQAVGTTPLIDVRSRPEY
+TGETTHMDGYPQEGTLRGGHIPTAASVPWAQAANEDGTFKSREELEAVYRDGAGLKDGDD
+VIAYCRIGERSSHTWFVLKHLLGHENVRNYDGSWTEWGNSVRLPIVVGEEPGAAPAR
+>3_1688
+MTETPAEFAEYAHPEKLVSTQWVADHIDDEGVVVLESNEDTLLYSTGHIPGAVKIDWHTE
+LNDPVSRDFVGPEAFAELVASKGIGPDTTVVFYGDKSNWWAAYALWVFTLYGHRDVRLMN
+GGRDKWIAEGRPTTREVPEVTPAPSYPVSQRDDATDRAAREDVLAAIGSTPLVDVRSPKE
+YTGETTHMDGYPQEGTLRGGHIPTAASVPWAKAANEDGTFKSRAELEEIYKEGAGLGESD
+SVIAYCRIGERSSHTWFVLKQLLGYENVRNYDGSWTEWGNGVRLPIALGDEPGEAPAR
+>4_951
+MTDTAAKFSEYAHPEKLVSTQWVADHVGDEDVVVLESNEDALLYSTGHIPGAQRVDWHTE
+LNDPVTRDFVGPEAFAEFAASKGISRDTTVVFYGDKSNWWAAYALWVFTLYGHEDLRLMD
+GGRDKWIAEGRETTREVPTVARAEYPVIERDDHTDRAAREDVLQAIGTTPLIDVRSRPEY
+TGETTHMAGYPQEGTLRGGHIPTAASVPWASAANEDGTFKSRAELEQVYRAGAGLQEGDD
+VIAYCRIGERSSHTWFVLKYLLGHEDVRNYDGSWTEWGNAVRLPIAVGEEPGEAPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..45dfe19400da8c8b1f1e2b7e4d6e99efab063715
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000886.fa
@@ -0,0 +1,34 @@
+>0_1012
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGLS
+SRPASAEGGDRVTA
+>1_740
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPVSAATGLQAVRAAAFGGGSHAAPAVAPDGSS
+SRPASAEGGDRVTA
+>2_1797
+MTQPRLAHQTPLGRMYARSLTGLPEVPSITTVIGMERTDLDGWIGWMAAQSVTQDPRLAE
+SVGSAARLKQVARQSADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTLAETRAKLIE
+HGEGAYADRFDEWWDLYDVRPLAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTG
+RDGRVKALDPKVVMQLTAGLKAEESLVDAEAGTWEEWRHGQAEMLLGVALGETEVAVHQA
+NPGVLPRHWHKFWALRQVWKHAQAADDAGPALRVIGPPPPSVPLHRG
+>3_1686
+MYARSLSGLPEVPSITTVIGMERTDLDGWVGWMAANAVAQDPRLGESLGSPARLRQVAKQ
+SADAAARYRDAAAERGDRVHDYAEQVALRALGRPHTMAASREELQRHGEGAYADRFDEWW
+DLYDVQPVAAEITVWNHSVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDAEAGTWEPWAHGGAEMLLGVALGETEVAVHQANNAALPRHWHKFWA
+LRQVWKHALAVDDAGPALRVIGPPPVSVPGAAGGLSAARAAAFGAPPAVAHDPGTSAPAD
+RLQP
+>4_959
+MYARSLSGLPEVPSITTVIGMEKTDLDGWVGWMAAQSVTQDPRLAESVGSAARLKQVARQ
+SADAAARYRDAAAERGDRVHDYAEQVAQRALGRPHTMAEARARLIEHGEGAYADRFDEWW
+DLYDVRPIAAEITVWNHTVGYAGTLDLVARIGGRLCLIDYKTKGTGRDGRVKALDPKVVM
+QLTAGLKAEESLVDPEAGTWEEWRHGQAEMLLGVALGETEVAVHQANPGVLPRHWHKFWA
+LRQVWKHAQAVDDAGPALRVIGPPPPSVPASAATGLQAVRAAAFGGGSHAAPDVAPDGSS
+SRPASAAEGGDRVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000887.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000887.fa
new file mode 100644
index 0000000000000000000000000000000000000000..070ca3a490318d3744f9ee887f7ccf2b8b5966ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000887.fa
@@ -0,0 +1,25 @@
+>0_1013
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPGAPAAGTGAAR
+>1_741
+MTVLPVRTIPDPVLRTAASPVPAGADVRALVADMIETMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPARAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
+>2_1796
+MSVLPVRTVPDPVLRTPARPVPAGMDVRALVADMVETMHAVGGVGLAAPQVGVGLRVFVF
+DVQGVAGHVVNPVLETGEETVREPGEGCLSVPGLRYHPARAAEAVVRGVNVDGHPVEHRG
+TGLVARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRTARRVGAERAAAVGSVF
+AAPAAPPTPARAPRGGTR
+>3_1685
+MTVLTLRTVPDPVLRTPAAPVAAGQDVRALVEDMVETMHAVGGVGLAAPQVGVGLRVFVF
+DCAGASGHVLNPVLETFGSPVREPGEGCLSVPGLRYHPARAERAVVRGVDVDGNPVEHRG
+EGLLARCLQHETDHLDGILYVDRLDGDDRREARRRLRADAPDPEAERIRARRDALAGSVF
+GARPSVSPSAARTTPRRGAQ
+>4_960
+MTVLPVRTVPDPVLRTAASPVPAGADVRALVADMIATMHAVGGVGLAAPQVGVGLRVFVF
+DVAGVAGHVVNPVLETAGQALREPGEGCLSVPGLRYHPTRAAEAVVRGTDVDGNPVEHRG
+TGLLARCLQHETDHLDGILYVDRLDGEERREARRRMRAGEVDRAARRIGAARAAAVSSVF
+GAPAVPAAGTGAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000892.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000892.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4c3e4151d91f329938ecd611f377a3acba946d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000892.fa
@@ -0,0 +1,43 @@
+>0_1018
+MNAAETPSADPMDLAVGAALRGVRGANPLVGAVLTDAAGRILAVGHHRGRGTAHAEVDAL
+TRWRAARAADPALATLDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRTHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>1_746
+MSAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCNHTGSTGPCSQAVLDAGVGALRYAVADPTG
+HDGGGAARLAAHGVRVTGPTGEVAALALTARWREARDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAAGAELAHQPVPVVQGHR
+PVPDGAALRAHPVLLHVPDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGPRWHPDPAEGGPARALGDDVWTHLSPV
+PAPRLPTAPAPTRFQED
+>2_1791
+MSGAPDPMALAVGAALRGVRGANPLVGAVLTDDAGRVLAAGHHRGRGTAHAEVDALARWE
+AARAADPALAALDPAGLTLHVTLEPCDHTGSTGPCSGAILASGVGAVRYAVADPTGVDGG
+GAARLAAHGVRVSGPTGEPAALALTERWRRARDAGRPWITGHLAQSLDGHAAAADGTSRW
+ITGAASRAHAHRVRARVDAIVVGTGTVLADDPRLTVRDAAGAETGPQPVPVVQGRTPIPA
+GAALRARPETLHVPAHEPEAVLAALAARPGPWPHGGARPGHVLIEGGPRVLGAWIRAGLV
+DELMVYTAPLLLGAGRPAVAGLDVGTLADGLRWHPDPAEDGPVRALGEDVWTHLAPVPAP
+APEGPDPQEDCMFTGIVTHLGTVLALEPDPAADTARLVLDAGGALEGLPAGGSLAVDGVC
+LTALDGPGAEPGVFRADLMGQTLRMTSLGGRTPGDRVNLERCLRPTDHLDGHVVQGHVDG
+VGEVLSVTPQGAWTTVRIGLPAALARYVPAQGAIALQGVSLTVSAVSEPGADAHWFEVGL
+IPATLEATTLGALRPGDRVNLETDVLARYAERLALLPAAPAASPSAAPAEEVRP
+>3_1680
+MSAPAARHDDAGRPAEPLDLAAAAALAGVRGANPLVGAVITGPDGAVLAVGHHRGRGTAH
+AEVDALNRWAAARAADPSLHVDPAACTIHVTLEPCDHTGSTGPCAGAILDAGLGAVRYAV
+ADATGTAGGGAARLTRAGLRVEGPTGHAASAALTARWRRVRDAGRPWITVHLAQSLDGRA
+AAADGTSRWITGPASRAHAHAVRARVDAVVCGTGTVAADDPRLTARDAAGEQLPVQPVPV
+VMGERDLPAGAALAARADLIHVRSHDPRAVLAALASRPGPWPHGGSRPGHVLIEGGPHVL
+GAWLAAGLVDEVFAYTAPVLLGDGLPGVAGLDVPTLAAGHRWAPDPAEDGPVRALGDDVL
+THLAPVTDPAD
+>4_965
+MNAAETPSADPMDLAVRAALRGVRGANPLVGAVLTDEAGRVLAVGHHRGRGTAHAEVDAL
+TRWRAARATDPALAALDPAGLTLHVTLEPCDHTGSTGPCSQAVLDAGIGALRYAVADPTG
+HDGGGAARLAAHGVHVTGPTGEAAALTLTARWREVRDAGRPWVTGHLAQSLDGHAAAADG
+TSQWITGPDSRVHAHEVRSRVDAIVVGTGTVLADDPRLTARDAVGAELAHQPVPVVQGHR
+PVPDGAVLRTHPVVLEVLDHDPHAVLAALAAHPGPWPHGRRAEHVLIEGGPRVLGAWLRA
+GLVDELMVYTAPLLLGPGRAAVAGLDVATLSEGLRWHPDPAEGGPVRALGVDVWTHLSPV
+PAPRLPTAPAPTRFQED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e9b3ae0a9f3ac371e386bc98048afeb958f0a3a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000893.fa
@@ -0,0 +1,20 @@
+>0_1021
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TEQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>1_749
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
+>2_1789
+MAVVAAQWHTEIMDGLIAGARAAAADLGLEPVLVRVPGTVELSVAAARLAEDFDAVVVLG
+VVVRGDTPHFDYVCQAVTQGVTEVSVRTGTPVGFGVLTVDTEQQARDRAGLPGSREDKGR
+ESLEAAVLTELALRDVQA
+>3_1677
+MSGAGAPTLALTTLTDADRAAAGSLRVAVVAAQWHTEIMDGLIAGSRAAAADLGIDVDLV
+RVPGTVELSVAAARLAATHDVVVVLGVVVRGGTPHFDYVCQSVTQGVTEVSVRTGVPVGF
+GVLTVDTVEQARDRAGLPGSQEDKGREALEAAVLTELALRAALG
+>4_968
+MSGAGAPTFTPDPAAASGLNVAIVAAQWHTEIMDGLIAGAQAAAADLGLEPVLVRVPGTV
+ELTVAAARLAERFDVVVVLGVVVRGDTPHFDYVCQSVTQGVTEVSVRTGVPVGFGVLTVD
+TDQQARDRAGLPGSREDKGREALEAAVLTELALRSVTPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000894.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000894.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b99a6b002dc61a4ef7acfb7b53b814fdbdbfc9a6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000894.fa
@@ -0,0 +1,15 @@
+>0_1033
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>1_761
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
+>2_1788
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGIALEDVYRHL
+>3_1674
+MKTFEELFAELTRKVAERPEGSGTVAQIDAGVHAIGKKIVEEAAEVWMAAEYESHDAAAE
+EISQLLYHVQTMMIAKGIGLKDVYRHL
+>4_982
+MKTFDELYAELTRKVQERPEGSGTVAQIDAGVHAIGKKVVEEAAEVWMAAEYESDEAAAE
+EISQLLYHVQTMMIARGISLEDVYRHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000899.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000899.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bab3222b210ed70a65d416938bbb53745ee072d8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000899.fa
@@ -0,0 +1,25 @@
+>0_1038
+MRRRTVVLAALAAGALVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>1_766
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
+>2_1782
+MRRRTVVLAALAAGSLVLLAAGQTWVVGSGLTGGLSEEATTSGGAAAPGATAMALVVLAG
+ALALTTARRVGVVVVGALLVLAGIVIVTGAAGAALDPAGTAASAVAEATGTTAAAGSYAV
+TAWPWVAVTGGVLAALCGAVAALAGRGWVSVRRYEKAEATDAAEPAAPGRAAAPGRTEAE
+RRRTEQMDAWDELSRGNDPT
+>3_1669
+MRRRWIVLAALLAGVLVLAATGQTWVTASGLEGSPVPQATAGGGRVAPVATALALVVMAG
+ALALTTARRVGVVLVGVLMTLAGVVIASTAVTAALDPVAAAAGAVSELTGTTAPAAAYAV
+SAWPWVSAAGGVMAAVLGVATLVVGPRWAASRRFESPATADEPAAAAPPSRHVDRMDAWD
+ELSRGEDPT
+>4_987
+MRRRTVVLAALAAGGLVLLTAGRTWVTATGLSGGIASEATTSGGAAAPVATAMALVVMAG
+ALALTTARRLGAVIVGVLMALAGVVIASTSVTAALDPATTAAAAVADATGTTALAQDYAV
+TAWPWVAAAGGVLAALCGVVAALAGRGWRSSRRYEKAPAASEPGPAAAGEQPAQSAREAA
+QRRRVDQMDAWDELSRGNDPT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000906.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000906.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f06205ea495434a1004f5a55cf5fdff80654462
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000906.fa
@@ -0,0 +1,50 @@
+>0_1045
+MADPRGFLKNRERVDRPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>1_773
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRRRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
+>2_1774
+MADPRGFLKHRERVARPSRPVPVRIMDFKDVHVRQDEAIVRTEASRCMDCGVPFCHAGCP
+LGNLIPEFNDLVYRDDWDEAGARLEATNNFPEFTGRICPAPCEASCVLGINQPAVSIKQV
+EQSIADHLFDAPSLTPHPPQRQNGLTVAVVGSGPAGLAAAQQLTRSGYTVVVYEKDEALG
+GLLRFGIPDFKLEKHLIDRRIAQMTEEGTRFRTGVRIGTDMSWEALQRRYDAVVLATGAP
+VGRELPLPGRGLDGIHLAMDYLVPVNRRVAGGEPEPISAQGRHVVILGGGDTGADCIGTA
+HRQGAASVTTLAIGRRPPEQRPEHQPWPTVPTLFEVASAHAEGGERTYLASTVEFLGDAE
+GRVRALKVAETEIRADGTRGPRAGTEHEIPADLVLLALGFTGADLDELVDRSAVSLERGL
+VVRDETYATQAPGVFACGDVSRGASLVVWAIAEGRAVAAEVDRFLTGDTMLPAPVRPSDH
+GFVLR
+>3_1662
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAVVRTQASRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWEDAAARLHSTNNFPEVTGRICPAPCEDACTLGINQPAVTIKQT
+EVAIAEQIFDHDWLEPVVPTRINGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDDRPG
+GLLRYGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGRDLAWDALKARFDAVIVATGAP
+VGRELPVPGRGLDGIHLAMDYLVQSNHATAGDDVPGQITAEGRHVVVLGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVDRPVHQPWPTVPKVHQMTTADAEGGQREHLASTVEFLGDE
+NGRVRALRVAETEYRADGTRGPKAGTEREVKADLVLLALGFTGVEEEALTAQLAVRTERG
+LVARAGTYETDEPGVFVCGDAGRGASLVVWAIAEGRACAQAVDESLESWSRLPHPVDPTD
+RGLVLG
+>4_994
+MADPRGFLKNRERVERPTRPVPVRIMDFKDVYVRQDEAIVRTQAGRCMDCGIPFCHSGCP
+LGNLIPEWNDLVRRGRWDEAAARLHSTNNFPEVTGRICPAPCEDSCTLGINQPAVTIKQT
+EVAIAEQIFDNDWLEPVVPARLNGHTVAVVGSGPAGLAAAQQLTRAGFTVVVYERDERLG
+GLLRLGIPDFKLEKDVLDRRLAQMEAEGTRFRTGVEIGVDLPWDQLKARFDAVIVATGAP
+VARELPVPGRGLDGIHLAMDYLVQSNRAVAGDEVPDQISAEGRHVVILGGGDTGADCIGT
+AHRQGAASVTTLAIGQQLPVERPVHQPWPTIPKVHQQTTADAEGGARAHLASTVEFLGDE
+HGRVRALRVAETEYREDGTRGPKAGTEREVQADLVLLALGFTGIEEGLLTQQLGVHVTRG
+LVARKDGYETDEPGVFACGDAGRGASLVVWAIAEGRACAQEVDESLERWSRLPHPVDPDD
+RGLVLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000908.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000908.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e879f3f6d495fb2eb2b9a8948cccf8d5398334db
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000908.fa
@@ -0,0 +1,25 @@
+>0_1047
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>1_775
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
+>2_1772
+MPMTTPAEGTGLRAVVAEDETLIRLDLVEVLTGAGYEVVAEAGDGAAAVAAVREQRPDIV
+VMDVQMPVMDGIAAASEIAQDRLAPVVMLTAFSQRDLVERARTAGAMAYVVKPFTEHDLV
+PAVELAVARFEELRSLESEVRDLGDRLETRKLVDRAKSVLQDRLRLSEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVR
+>3_1660
+MTIPAESADPTAGLRVVVAEDEALIRLDVVETLTHAGHTVVAEVGDGQAAVAAVREHRPD
+IVVMDVMMPVMDGIAAAGEIAAERLAPVVMLTAFSQRDLVERASQVGAMAYVVKPFTEKD
+LLPAMELAVARFDQLRGLEEEVRGLEDRLATRKLVDRAKSLLQAHMGLSEAESFRWIQKT
+SMDRRLTMREVAQTVVDQIGA
+>4_996
+MSTLTPPEETGLRAVVAEDETLIRLDLVEVLTGAGYRVVAEAGDGRAAVEAVREHRPDIV
+VMDVKMPVMDGIAAAGEIAGERLAPVVMLTAFSQRELVERARTAGAMAYVVKPFTEADLV
+PAIELAVARFDELRSLEAEVRDLGDRLETRKIVDRAKALLQERMRLTEAESFRWIQKTSM
+DRRLTMREVAQAVIDQVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000911.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000911.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8a547c9da6bbbb9796112b32eb547183a69d0193
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000911.fa
@@ -0,0 +1,55 @@
+>0_1050
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWVLLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
+>1_778
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
+>2_1768
+MSPEALGQLLPLFVAVPLITAGLLTLAGDRPRVHRLVVALVLCLTAGAGALIVARSLDGD
+VLATSVGGWPGGIGIGFAADMLTGLMLLLTSLLTLVGVNLAHGTRVVNSLYFGPLMLVLM
+AGVNGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+VVAVGFLYALTGTVNLAVMAGAAARDERVAIAGGLVLFALSIKASVVPLHGWLARAYPST
+SPAVTAIFAALHTKVAVYALYRVFSVLFDNDARFLPLLLALAGLTLAVGALASVGVHGVR
+LVLSWQMVSGIGGILVGLGLSTQLGLSAGLFYLVHHMVAMGCLLAATAAVEVRYGTGRLA
+DLRGLARREPLIAVVFFVGLLSIVGIPPFSGFVGKLMLVTAGVEAGRLVTVAVVLVGSLV
+SLWALLRVWDAWFWGEPGTPHGLRERLATAALPVVGRGAERTGPSGRGSSTDHERTESWT
+STQTIDPPTGVLPVTFAADEDVTRSRIPVRLAMPGVVLAAATLVLGLAGQALWTLTDVAA
+QGLLDPARYIEAVLAP
+>3_1657
+MSDHAVGLLLPLFVAVPLLSAGLLVVAGSRPRLHRAVLAAVLAGGTVGGGLLMARAADGS
+VAAAGVGGWPDGIAIAFAADMLTGLMVALTAGLTLVGAWFAYGSRVANSAHFAPFMLVLM
+AGVHGALLTADLFNLFVFIEVMLLPSYGLYVLSANRREPLRRVDGARMYVTLNLLTSTIL
+VTGVGFVYALTGSVNMAVLAGAARGDVRVALAAGLVLFALSIKASMLPMHGWLARAYPST
+SPAVTAIFAALHTKVAVYAMYRIYMVVYDGDPRLLGLILTLCLATLMVGAVASVGEHGAR
+AVLSWQMVSGIGGIMVGLGLATQAGLSAGLFYLVHHMVVMACLLTATGAIEVRYGSGRLA
+DLQGLAVREPLIAAAFFVGMLSLVGIPPFSGFAGKLALVLAGVAAGRTVTVVLVLVASLI
+SLWALLRIWDAWFWGRPRAPHGHRERLDTAALPLVHGDGVMPAAGAPVHPAGRGSSTDSE
+RAEAWASTETLDTPTGVLPVVVDPDEDHTASRIPLRLAGPAALMAAATLALGLGAEGLWS
+VTDQAARGLADPTAYIEAVLGR
+>4_999
+MSAVPLGQLLPLFAAVPLLSAGLLVLAGERPRLHRAVLFAVLGLVTTGGLALGVHALDGS
+VLATSLGGWPGGIGIGFAADMLSALMLVLTSALTIVGAAFAYGSRVANSQFFAPLLLILI
+GGVNGALLTADLFNLFVFIEVMLVPSYGLYVLSANRREPLRRVDGARLYVTLNLLTSTIL
+LVGVGFVYGLTGSVNLAMLAGSAAADPRIAIAAGMVLFALSIKASVAPLHGWLAWAYSST
+SPAVTALFAALHTKVAVYGLYRIYSVMYDGDARLLPLILVLSLATLVVGALASVGEHGVR
+AVLSWQMVSGIGGILVGLGLSTRLGLAAGLFYLVHHMVAMGCLLMAAGAIEVRYGTGRLA
+DLQGLARREPLIAVAFFVGLLSLVGIPPFSGFVGKLMLVSAGLDAGRGVTAALVLGASLV
+SLWALLRVWDAWFWGAPTAPHGHRERLATAAMPIVGRAGSVPSPSGRGSSTDHERTESWA
+SQETLDPPTGVLPVTVDPDEDVTRSRIPGRLAAPAVVLAMATLALGLGGQALWTVTDLAA
+QGLMDPSRYIEAVLNP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0939f9269d94efd907523ea5c660681d3632e78
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000914.fa
@@ -0,0 +1,20 @@
+>0_1053
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>1_781
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+APDEV
+>2_1765
+MDLVLTVIGSVLVVAGALVFVTAGLGLIRFPDPYTRISATGTAGGVGMILIVVGGLVLAP
+SVANVVKVALIVVLQLGSAAVATMALGRSAYLTGVPMNPGHYDELAEDTPGREHGEPAPR
+TPDAS
+>3_1654
+MDLVMTVAGSVLAVAGAVVFLGAAVGLIRFPDPYTRISATGTAGGVGMILIVTGGLLLMP
+SVANLVKVVLIVVLQLGTAAIATMALGRSAYLTGVPMNLAHYDELAEDTPGREHGEPAPR
+HPED
+>4_1002
+MDVVLTAAGSVLVVIGALAFVTAGLGLIRFPDPYTRVSAVGTAGGVGMILIVVGALLLAP
+GVAAFVKVALIVVLQLGSASVATMALGRSAYLTGVPMNPGHYDELAEDTPGREGGRAAPR
+LPDMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cc69db2aa923d4109d29ddbb550a4e25c039096
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000916.fa
@@ -0,0 +1,85 @@
+>0_1055
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLETMRLEMPEREPVEELFDALQFHRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGPDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPRESAQQRAQGS
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEKATALLKERMGRAAELSVPLDVHVGQGRSWHDAAH
+>1_783
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEAEAAPEFTEATTAEDVRSFLAAEAGNLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVTLDGDAPDPALVAAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTDAADAAKESAWASVAEETGGMQVNLGSPKQLQEVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
+>2_1763
+MAADPTPEDPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTITLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVMAKYG
+VSPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLTQYGDLDGVLAHADEIKGKKGEALR
+AHLDDVRRNRRLNALVRDLDLPIGLEAMALEMPEREPVEELFDALQFNRIRERVFEVFSE
+RIGETAPAAQVEEAPEFTEAATAQDVADFLAAEAGNLLGVHVDVEGPALLPKRKVPVPGT
+FGTAVGVALVGEHAGLHVSLDADAPDPALLAALREALGEGGLSKAVHDLKRVLKAIAEPA
+EATALEAGTPLDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLAAPREPAEADAQGA
+FDLDGGAAAAERAARAADAVRAAWVVRRLSVLFTPQVLERGAQRLLQELEIPLARLLARI
+ELTGIAVDAQALETLRADFSEAAAAAQESAWASVAEETGGMKVNLGSPKQLQEVLFEHLD
+MPRTRKTKTGWSTDVDSLQDLLEQTRHPFLENLMRHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIREVFVADRVAGEDAVLLSADYSQIEMR
+IMAHLSEDAGLIQAFREGEDLHSFVGSQVFGVAPDEVSSEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLAEHGMASRLLLQVHDELILEVPAAE
+LEQATALLQERMGRAAELAVPLDVHVGQGRSWHDAAH
+>3_1652
+MGENSTEARPRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTSMLLTMIRQQAP
+THVAVAFDLSGPTFRSAEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTKEDFEAD
+DIVATLSAQAEAQGWDVCVVSGDRDAFQLISERTQVLYPKKGVSDIPPMTAADVEAKYGV
+RPEQYPELAALVGESADNLPGVPGVGPGFAAKWLQKYGDLDGVLAHADEITGKKGEALRA
+HLDDVRRNRRLNALVRDLDLDVSLDAMELTMPEREVVEELFDALQFQRIRERVFEVFAER
+LGSAAPAAPVAEAPAAVLAATADDVHAFVSAHAGTLLGLHVEIDGPDLLPKRKVPVPGTF
+GTPVGLALAAEDAALYVDLTDADADPGLVAALGDLLAEDGAAKAVHDLKRTLKAIAVPTG
+PTALPADTSLHGVVDDVALSAYLIQPDRRDTDLATLSQAHLQEPLEAPESAAAGAQGAFD
+LDGAQEEAERTARAARAARSAWVVRRLSQAFTPQVLERGAQRLLQEMEIPLARLLARMEL
+AGIAVDGDALSALLADFTDRAEAAKESAWASVAEETGGMKVNLGSPKQLQEVLFEHLDMP
+KTRKTKTGWSTDVDSLQDLLEQTQHPFLENLMAHRDATKLRQTVEGLRETVAPDGRIHTT
+YSQTVAATGRLSSLHPNLQNIPVRTEAGRRIREAFVAAPVDGEPAELLSADYSQIEMRIM
+AHLSEDAGLIEAFNSGEDLHSFVGSQVFGVDPDDVTSEQRSKVKAMSYGLAYGLSSFGLS
+KQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARRDGFTSTIEGRRRYLPDLTSDNRQ
+LRDMAERAALNAPIQGSAADIIKRAMLDVQAGLVEQGLRSRLLLQVHDELILEVPASELD
+AATALLQERMGRAADLSVPLDVHVGHGGTWHAAAH
+>4_1004
+MAADPTPEAPQRLLVLDGHSMAFRAFYALPAENFATDTGQHTNAVYGFTAMLLTMIRQQR
+PTHVAVAFDLSGPTFRSEEYGEYKAGRSETPAEFAGQIELTVKVMEALGIPTLTLEGYEA
+DDIVATLSARAEEAGWEAVVVSGDRDAFQLISERTTVLYPKKGVSDIPPMDADAVKAKYG
+VAPAQYPELAALVGEAADNLPGVPGVGPGFAAKWLKQYGDLDGVLAHAHEITGKKGEALR
+EHLEDVRRNRRLNALVRDLDLPIGLEAMRLEMPEREPVEELFDALQFNRIRERVFEVFGE
+RVGEDAPPPEVEAAPEFTEATTAEDVRAFLAAEAGTLLGVHVDVEGPALLPRRKVPVPGT
+FGTPVGVALVGEHAGLHVSLDGDAPDPALVGAVREALGEGGLAKAVHDLKRTLKALAAPT
+EGDGLGRDAALDGVVDDVLLSAYLIQPDRRDTSLEALAEAHLHTPLTAPREPAQQRAQGT
+FDLDGGQAAAERADRAADAVRAAWVVRRLSTQFTPQVLDRGAQRLLQELEIPLSRLLARM
+ELTGIAVDVDALTGLREDFTVAADAAKESAWASVAEETGGMQVNLGSPKQLQDVLFERLN
+MPRTRKTKTGYSTDVDSLQDLLEQTRHPFLENLMAHRDATKLRQTVEGLLETVAPDGRIH
+TTYSQTAAATGRLSSLHPNLQNIPVRTEAGRRIRGVFVADEVAGEQAVLLSADYSQIEMR
+IMAHLSEDEGLIQAFREGEDLHSFVGSQVFGVDPDDVTAEQRAKVKAMSYGLAYGLSSFG
+LSKQLKISVDEARGLMKGYFDRFGGVRDYLRDVVAQARQDGYTSTIEGRRRYLPDLSSDN
+RQLRDMAERAALNAPIQGSAADIIKRAMLDVQAGLEEHGLASRLLLQVHDELILEVPAAE
+LEQATALLKERMGRAAELSVPLDVHVGRGRSWHDAAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df5a85ede6e227ec1996b9517296d9bfadfda3ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000918.fa
@@ -0,0 +1,37 @@
+>0_1058
+MSEPLPRGVTPDVAHGGLPDDLTAGVDFAALDRWPLPPEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGEA
+GELERTATPEDAARGARTVLLPLPRSLDELDRLSRIVAAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTPRPPEEADRDVPGVGSLHLVAHAGAFG
+GAAADPGSRLLLASLADDPRPPGRLVDLGCGNGLLSVGAARLWPHVTVLATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGTEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRPVLEDLVGPTRQTARDRTFTVTVSERR
+>1_786
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDTADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
+>2_1759
+MDLGCGNGLLGVGAARLWPHVRVLATDQSAVAVASTLATARANGVADRLEAVRDDALAGR
+PDASEECILLNPPFHDGNAVDPAVAHRLVAEAARVLAPGGRLWCVWNSHLRHRPVLEAEV
+GPTRQVARDRTFTVTVSTRR
+>3_1649
+MDAIAQTPPRDPGPARLTATELVTPDAAGRGLPRDWTAEFPFERLGRWPLPESRERQAHD
+AADLLLVDTLAGWTADGRVPGPVAVLHDQHGAVSLPLLARGLNVRLGLDEASAARSVERN
+LDLFRDADGALPAGWGRLTVGGVDAATLADARTVLLLLPRALDALHLTAARIAVHAAPDV
+LVLGAGRDKHMTPSMNDVLARSFAAVVPGRGRSKSRVITAARPVDDATEPAPRRAQHRLG
+RLGAVTLVGGWATFGGAAADPGSLLLAGTLADRAPALPVPAPHRMRTDSGLGVDIPWATR
+AGAPDVVDAGSGNGMLSVVAARVWPEAAVLASDQSADAVASSAATAEANGLAERITAVQD
+DALGALPDASVRAVLLNPPFHDGTAVDPTVAHRMIEAAGRILAPGGELWCVWNSHLRHRP
+VLETAVGPTRQVARNRTFTVTVSTRR
+>4_1007
+MSEPLPRGVTPDVARGGLPDDLTAGVDFAALDRWPLPTEPDRQAHDAADLLLLDTLAGWI
+ASGHVPGPVAVLEDRHGALTLPLLTAGHDVRIHQDDASAERSLDANLAAWRAAGRLGGET
+GELERTATPEEAARGARTVLLPLPRSLDELDRLSRIVSAAADPGVVLLAGGRDKHMSPRM
+NAVLGAAFEDVVAGRGRRKARVLTARGPRPGVTARPPEEADRDVPGVGRLHLVAHAGTFG
+GAAADPGSRLLLASLADDPRPPGRVVDLGCGNGLLSVGAARLWPHVTVVATDQSAVAVAS
+TLATARANRVADRVRAVRDDALATWPDGEEECVLLNPPFHDGNAVDPSVAHRLVAAAARV
+LEPGGRLWCVWNSHLRYRSVLEDLVGPTRQTARDRTFTVTVSERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000921.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000921.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6b0ae0c227ef12afe84890cfff4c7ddba2510fc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000921.fa
@@ -0,0 +1,65 @@
+>0_1062
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRAPATGEGAEAPAVDPASL
+PAKDLADLIEQMSQQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>1_790
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
+>2_1754
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSVNEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGEEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREETEMYIFPASHYVAGDERMGRAVTAIEDELRERLQELESQDRLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPDGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLDAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIEETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDYGMGHRGLSSLDREEGQERAGGGPAVDAASL
+PAKDLADLIEQMSLQMHQAAADLQFELAARLRDEVGELKKELRQMRREQ
+>3_1645
+MSLAKQINRVVAPFEVVSPYQPSGDQPTAIAEIAERVQAGEKDVVLMGATGTGKSATTAW
+VIEQLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVVVVATVSCIYGLGTPEEYIAQMVTLRRGQEMDRDA
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEVESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAIATIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGQYELSQADGVVEQII
+RPTGLVDPTVVVKPTQGQIDDLLEQIRTRTEKDERVLVTTLTKRMAEDLTEYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADRVTDSMRRAIEETERRREVQIRYNAEHGIDPQPLRKKI
+ADITDALAREDADSADFLKGMGGVKAGFDYGMGHRGLGSLDHEPPAGEVPSGSPAVDPAA
+LPAKDLAQLIEQMSAQMHQAAADLQFELAARLRDEIGDLKKELRQMKREQ
+>4_1011
+MSLAQKINRVVAPFEVISPYQPSGDQPKAIAELAERVEAGEKDVVLMGATGTGKSATTAW
+LVERLQRPTLVMVQNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEK
+DSSINEEVERLRHSATNALLTRRDVIVVATVSCIYGLGTPEEYIEQMVTLRRGAEMDRDV
+LLRRFVQMQYVRNDVDFHRGTFRVRGDTVEIIPMYEELAVRIEFFGDEIESIQTLHPLTG
+QVVREEEEMYIFPASHYVAGDERMGRAITTIEDELRERLQELESQDKLLEAQRLRMRTTY
+DLEMMQQMGYCNGIENYSRHIDGRPAGSAPHCLLDYFPDDFLLVVDESHVTIPQIGAMYE
+GDMSRKRTLVEHGFRLPSAMDNRPLKWDEFLERIGQTVYLSATPGAYELGQADGYVEQII
+RPTGLVDPQVVVKPTEGQIDDLLEQIRVRTAKDERVLVTTLTKRMAEDLTDYLLEAGVKV
+EYLHSDVDTLRRVELLRELRKGTFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSTT
+SLIQTIGRAARNVSGEVHMYADNVTDSMRRAIDETERRRAVQIAYNEEHGIDPQPLRKRI
+ADITDQLAREDADTADFLKGMGGVKSGFDFGMGHRGLSSLDRDATTGEGTEAPAVDPASL
+PAKDLADLIEQMSKQMHQAAADLQFELAARLRDEVGELKKELRQMKREQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25aff95c69f214e1b02eb4ef7b5d2c68eb376b82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000922.fa
@@ -0,0 +1,25 @@
+>0_1063
+MSAAPPVAAVIADIVGSRALPDRDRAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGPAWYRAREAVERAHER
+AVGAATAFRAADPSLTAAVDGLVLLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQAVARSGIDRLLELDAELAAAATEVAP
+>1_791
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
+>2_1752
+MTRAPQAAAVIADIVGSRRLPDREAAQEQILAAFAVAEKDVPPLRAAWATVGDEFQALHG
+VWPQAVRAVVRVSLALPPGLELRFGIGVGERRSLDDGAGDRIEDGTAWYRARAAVERAHA
+RADGAATAFVAADPSLTAAVDGVLLLRDHVLGRLKARERRLAAALLGGATQTQAARAERI
+TQSAVSQAVTRSGIDRLLELDAALAEAAAGRPGHAGAAGEGAGDEGDAG
+>3_1644
+MSLTDEGPVRGTAVIADIVGSRGLRDRAAAQEAILAAFAAAEEAVPARIPAWATVGDEFQ
+ALHADWAAAVRATLRVAVALPEGVELRFGLGDGVHREVTGAADDDGRPILDGSAWHRARE
+ALEAAEHRTRGLAGAYRGPDADLTAAVDGQLLVRDHVLRRLKARERRIAAALLAGRTQAE
+TATAERITQGAVSQAVARSGVRELLALDAALGALPGAGRGAKATAEEDRP
+>4_1012
+MSAAPPVAAVIADIVGSRALPDRERAQEQILAAFAAAEQDVPPLRPAWASVGDEFQALHR
+TWPDALRLTVRVTLALPPGLDLRFGIGLGQRRALDAGGDGIEDGTAWYRAREAVEHAHER
+AAGAATAFRAADPSLTAAVDGLALLRDHVLGRLKARERRIAAALLGGATQAEAARAERIT
+QSAVSQTVARSGIGRLLELDAELAAAATEVAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4499a91cef219318ab0464e42c7bceef4267f93e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000924.fa
@@ -0,0 +1,50 @@
+>0_1067
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
+>1_795
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRATGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTASDPVN
+>2_1749
+MSAPAPRVPGDPRGFAPLEPARHRVGERTELYDGTVAVDHWFTVPVDHALTLAEAEAQDA
+AGTGVGPHGRGTLTVFAREIRAAGDADGARPWALYLQGGPGGAGPRPARGGGWIGALASE
+HRVLLLDQRGTGRSTAASVAALTAPGAFASDEALAEHLVHLRAPSIVRDAEMVRLALGAA
+PWTTLGQSFGGFCTLTYLSFHPEGLRRCLVTGGLAPLTGHADRVYQATYARMRDRAHEFF
+ARHTGDRAAWAEAVALIRAAEQAGEPVRLPDGGLLTVARAQALGMLLGGNTRVDRLHWIL
+AEAVDRSGPAPRLSETFLAAVAEQNDRHVNPLYTVLHESIYAQPAELAGGRAATDWSAAR
+VLAEHPDFDPDAADAPLPTGEHVMPASLELDPHLRPLRGAARLLAERTDWGPLYDVEALA
+RNIVPVAAAVYTDDVYVDRDLSLETAGRVRGLRVWETDAFHHDGLADDGPAIVRRLLEMT
+GEGAAPAAAEGAERSDSAPAASETTTAPGPVD
+>3_1641
+MTRTGTGDAAFVPGDPRGFAPVGPAAHREGERTVLFDGTVAVDHWFTVPVDHALTLAEAL
+AQDAAGTGLGPGGRGTLEVFAREVRHPEDPEGERPWLLYLQGGPGSGGPRPARLGGWQCE
+LAQHHRLLLLDQRGTARSTPVTAATLAGLPDDAARAAYLTHLRAPQIVQDAEMIRVALGA
+PPWTTLGQSFGGFCTLSYLSWRAEGLERCLVTGGLAPLTGHADRVYRATTARMHARWQEF
+LERHPQDAGHWAEAVALIRAAQDDGDPYVLPDGTALTVGRAQQLGMLLGGNTRVDGLHWV
+LAEAVDRSGGEPRLSPGFLAAVAAQTTRAVNPLYAVLHEAIYAQPAALTDGRGATAWSAQ
+RVLAEHPDSSPAADPAPVPTGEHVLPWSFETEPELRALAGVAALLAAKDDWGALYDLDAL
+AANEVPVAAAVYTDDVYVDRDLSLETAARVRGLQVWETDAFHHDGLADDGPGIVRRLRGM
+LGA
+>4_1017
+MAGDPRGFAPLEPARHRVGERTELYDGTVTVDHWFSVPIDHALGLAEAEAQDAAGTGVGP
+HGRGTLTVFAREIRAKDDPEGERPWALYLQGGPGSAGPRPARLSGWLGALAESHRVLLLD
+QRGTGRSTPATVATLTAPGAFATDEARAEHLVHLRAPSIVRDAEMLRLALGAGPWTTLGQ
+SFGGFCTLSYLSFHPEGLQRSLVTGGLAPLTGHADRVYRATYARMRARTEEFFDRHPADR
+DAWSEAVGLIRAAEAAGAPIPLPGGGPLTVGRAQGLGMLLGGNTRVDRLHWVLAEAVDRT
+GPAPRLSETFLAAVADQDDRLVNPLYTVLHEAIYAQPADLAGGRADTGWSASRMLAEHPD
+FDPEATTVPLPTGEHVMPWSVEVDPRLRPLAGTARLLAERTQWGPLYDVAALAQNTVPVA
+AAVYADDVYVDRDLSLETARRVRGLQVWETDAFHHDGIADDGPAILERLLAMTAPDGAGT
+TTAPDPVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000925.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000925.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e7769f184ef310e48183dc9a804d27102dabac5c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000925.fa
@@ -0,0 +1,80 @@
+>0_1068
+MTSAATNPPSLTDRIDALPPAPDADDVFGAFAAWTEDRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEEFVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>1_796
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSREEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVAAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>2_1748
+MTSPATNPPSLTDRIDALPPTPDADDVFGAFAAWTEVRGISLYPAQEEAALELVQGRHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLIERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKSPPAGFVSWGPATFERLVAAEPEPLVSRMQITHSMLLNILDRPGDPVVAVRRLL
+RGTHETPARQAILMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALELLDPAEPDHALDVVSVIEATLDPPRQVLSAQVKKAKGEAVAAMKAEGMDYND
+RMRALDEVTHPQPLADLLEQQFEVYRASAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRQTVPEASRTEELQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIEELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEELARLSGDLSA
+DDWADALDAYFGDHEDIDDGPAARGTELFRVAESPDVAPPVELAGSRWWAVRQVLKDPDG
+VHDHGVNAVVDLDASDEAGHPVIRVVSVGAPESGWGL
+>3_1640
+MTPSATNPPSLTDRLDALPASPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGRHVI
+LATPTGSGKSLVALGAHADALAHGKVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+SVNADAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQLPLLELPQAR
+FLLMSATLGDTSMLERDLAERTGREVAVVAHAERPIPLSFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAVGLASISVTTKEEKEAIAERIAGFRFSAGFGKTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQEGRLKVISGTDTLGVGINVPIRTVLLTALSKFDGEKTRILQS
+REFHQIAGRAGRAGFDTQGYVVVQAPEHVIENKAAERKAAAKFAGIKDEAERAKRMKQSV
+KGSKRKTPPQGFVSWGPATFDKLVASEPEPLVSRMRITHSMLLNILDRPGDPVLAVRRLL
+RATHETPARQAQLMRRALGIFRELLATGVVEVLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPAAPDHHLDVVSVIEATLDAPRQVLSAQVKKAKGEAVAAMKAEGMDYSD
+RMRALDEVTHPQPLAELLEQAFERYRQDAPWLAEFELSPKSVVRDMFERAMGFGDYVRFY
+GLARSEGVLLRYLTDAVKALRQTVPQEDRTEDLQVLLDWLDEMVKQTDSSLLEEWEDLMS
+GDIAELRRDLESLEPTPPPRLTDNAAVFRVMVRNAMFHRVRLFGDEQDARLAELSGDLSA
+NDWADALDAYFDEHEDIDDGPDARGQEFFRVATAPGARCPVELEGSRWWAVRQVLKDHDG
+DHDHGINAVVDLEASDEAGHPAIRVVSVGAPVPGWDL
+>4_1018
+MTSAATNPPSLTDRIDALPPTPDADDVFGAFAAWTEDRGISLYPAQEEAVLELVQGKHVI
+LATPTGSGKSLVALAAHADALAHDAVSYYTAPIKALVSEKFFALVDVFGAENVGMVTGDS
+TVNGDAPIICCTAEILANRALREGSGMEIGTVVMDEFHYYADPSRGWAWQVPLLELPQAR
+FLLMSATLGDTTRLEADLTERTGREVAVVAHAERPIPLTFEWSEVPLQEKVEELVSTHQA
+PVYIVHFSQLDAVETAQGLSSISVTSKEEKEAIAARIAGFRFSAGFGHTLNRLVRAGIGV
+HHAGMLPKYRRLVEKLAQDGLLKVICGTDTLGVGINVPIRTVLLTALSKFDGEKTRLLQA
+REFHQIAGRAGRAGFDTSGTVVVQAPEHVIENKAAERKAAAKFANVKDEAERAKRMKQSV
+KSGKRKTPPAGFVSWGPATFERLVSAEPEPLVSRMRITHSMLLNILDRPGDPVIAVRRLL
+RGTHETPARQAVLMRRALGIFRELLATGVVERLPEPDAEGRTVDLTVDLQPDFALNQPLS
+PFALAALDLLDPADPDHALDVVSVIEATLDPPRQVLSAQVKHAKGEAVAAMKAEGMDYND
+RMRALDEITHPRPLAELLEQQFELYRQDAPWLAEFELTPKSVVRDMFERAMGFGDYVRFY
+GIARSEGVLLRYLTDAVKALRHTVPEAARTEDLQVLLDWLDEMVKQTDSSLLEEWEDLVA
+GDIDELRRDMEALEPPAPPRLTDNEPVFRVMVRNAMFQRVRLFGDERDEALARLSGELSA
+DDWADALDAYFDDHEDIDDGPAARGPELFRVTAAPDVAAPLELAGPRWWAVRQVLKDPDG
+DLDHGINAVVDLDASDEAGHPVIRVVSVGAPESGWGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d5db9097551bdc1f67adaa0ce875f45c6694a021
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000926.fa
@@ -0,0 +1,34 @@
+>0_1069
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGAPANLRFEAVDASQW
+RPSGATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGAAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MAGQKPA
+>1_797
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>2_1747
+MSQIAPESPHPDTDAVAGDVTGRQGGGFTWDPAQYESFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLKRAREQAARTGAPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEECSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
+>3_1639
+MSTVPAVTGRETAGFTWDPAQYEGFAEHRARPFHDLVARVEAEAPRVVVDLGCGPGTLTR
+TLAERWPAAEVIGLDDSPAMLERAREGAADADLPNLRFDRVDASQWRPGPEVDVIVSNAM
+LQWIPTHRRLIRRWLGDLHPGAWFGAQLPRPYQQASHATIVALADEPVFSEALHGVETTR
+TVAPPEEYTRLFLEAGWTPSVWETEYQQVLTGPDPVLRWTSGAALRPSLQALAAWDAEEG
+AAEGAGLLELFVARYRQAMREAYPPVPGVSDADGGPLTVFPVRRMFLVGRKPGE
+>4_1019
+MSQIAPESPHPDTDAVVGDVTGRQGGGFTWDPAQYEGFAEHRARPFHDLVGRVRAEAPRV
+VVDLGCGPGTLTRTLAERWPDAEVIGLDDSPAMLERAREQAARTGTPANLRFEAVDASQW
+RPSRATDVVVSNAMLQWIPTHRRLIRRWLGDLTPGAWFAAQIPRPYEQPSHAAIVALAED
+PAFSEPLHGVATTRTVAPPEEYTRLFLEAGWSPVVWETEYQQVLTGEDPVFRWTSGAALR
+PSLQALARWDAEEGSAEGAGLLEAFVDRYRAAMREAYPPVPGVTADDGGPVTIFPARRLF
+MVGQKPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a10558e69d4708b355f8eea000f28def7bb15559
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000928.fa
@@ -0,0 +1,60 @@
+>0_1073
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+ADDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>1_801
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTRAM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEPEM
+VAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEVTEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVEGD
+DQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLAELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHFGS
+VAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
+>2_1743
+MADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLGSYFQDPARLTTKTRTM
+VFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQVM
+RGDRRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGKCS
+APCVGRISPAEHRELAQDFCDFMAGDAQRFIRELERAMQGAVEELRYEDAARLRDDIAAL
+RRVFERNAVVLPESTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVSEPEM
+VTHLLQQVYGDLAGEDRIPHEILVPAEPDDAAQLVEWLSGLRGARVNVRVPRRGTKADLM
+ETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEIAEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASMKDVLSRRFARLAEERAEGAPLSGQLEGE
+EEGRDRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEFPV
+VLPRTSEALYLLQRIRDESHRFAIAGHRGRRAKAMTASALDGISGLGPAKRTALLNHFGS
+VAQIRAAGVERLTEVAGIGPTLAQTVHAALAPAEPTDTVEP
+>3_1635
+MADPRTYRPAPGEISTSPGVYRFRDPDGRVIYVGKAKNLRARLSSYFQDPARLATKTRTM
+VFTASAVEWTVVASELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNERFPRVQVM
+RGDKRPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRAQAQDRPCLLGYIGKCS
+APCVGRISPDEHRALAQDFCDFMAGDADRFVRELEKAMAGAVEELRFEDAARLRDDIAAL
+RRVFERNAVVLAESTEADVFALHSDELETAVQVFHVRQGRIRGQRGWIMERVEDVGEDEA
+VAELLTQVYGDVPDTERIPHEVLVPVLPAGAEQVTEWLSGLRGARVQVRVPQRGPKADLM
+GTVRENAEMALKLHKTRRSGDLTTRSAALRELQDALEIDEPLLRIECYDISHSQGTNVVG
+SMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARMAEDRREGGVLTGQIDAE
+EAEGERRRFAYPPSLVVVDGGPPQVAAAAEVLAELGLDDLPVVGLAKRLEEVWLPGDEFP
+VVLPRTSEGLFLLQRIRDESHRFAIAGHRSRRTKAMTASALDDVPGLGPTRRRALLTHFG
+SVERMRQAGPAGLTEVAGIGPALAEAVHAALTASDGGDTVAP
+>4_1023
+MPVADPASYRPAPGEISTSPGVYRFRDADGRVVYVGKAKNLRARLSSYFQDPARLATKTR
+TMVFTAAAVEWTVVGSELEALQLEYTWIKEYRPRFNIMYRDDKSYPYLAVTMNEQFPRVQ
+VMRGDRKPGVKYFGPFHPAKAIRETVDLMLRVFPVRTCSAGVFKRARAQDRPCLLGYIGK
+CSAPCVGRISPADHRALAQDFCDFMAGDANRFIRELEKAMARAVEELRYEDAARLRDDIA
+ALRRVFERNAVVLPENTEADIFALHADELEVAVQVFHVRQGRIRGQRGWVMERVEDVAEP
+EMVAHLLQQVYGDLEGPERIPHEILVPVEPDDAAQLTEWLSGLRGSRVAVRVPRRGSKAD
+LMETVRENAEMALKLHKSRRSGDLTTRSAALRELQEALEITEPLLRIECYDISHSQGTNV
+VGSMVVMEDGLPKKKDYRRFNVTGEAARDDTASLRDVLRRRFARLAKERAEGAPLSGQVE
+GDDQEAGRRFAYPPSLVVVDGGPPQVAAAAAVLEELGLDDLPVVGLAKRLEEVWLPGDEF
+PVVLPRTSEGLYLLQRIRDESHRFAIAGHRSRRSKAMTVSALDGIPGLGPAKRTALLNHF
+GSVAEIRAAGVDRLTEVAGIGPRLAEAVHTALTADTPADTVES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000936.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000936.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a95f17d01fbe11fc566c86ce72d175fd0ff58b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000936.fa
@@ -0,0 +1,15 @@
+>0_1081
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>1_809
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTMES
+>2_1734
+MDMLTLILQILVVVLSVVIVLLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRLTV
+GTVAAWALLIVTLGVLPRLAMES
+>3_1627
+MDILTLLLQIAVVALSVVIIMLVLLHKGRGGGVSDMFGGGVTTSMSSSGSAQRLLTRVTV
+SATVLWGLAIVALALIARFSVES
+>4_1031
+MDVLTLALQILVVVLSVVIVLLILLHKGRGGGVSDMFGGGVTSSMSSSGSAQRLLTRLTV
+GSVVAWGVVIALLGVLPRLTLES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000941.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000941.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b89c7d3a8b943eeba61357c47288fdfb5548f904
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000941.fa
@@ -0,0 +1,69 @@
+>0_1086
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>1_814
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEVAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYVGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
+>2_1729
+MTDAQHPSTAPALDRTAPARDFVYSEQDRRMVDTLKVLSADAVEQAGHGHPGTAISLAPV
+AWQMYQNVMHLDPQDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIRALRTEGSK
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVSARYEAYGWHVQ
+EVDWTNGALGHAVTEYTEDVEALYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGVH
+GSKLGAEELAGLKEGLGFDPAESFDVDPEVLANSRSIAERSAAYRRTWEGAFQAWREAHP
+ENARLYDRLAGRELPEGFAEAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+RSNNTTMKGEPSFIPARRSTATWQGDEHGRTLHFGIREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSVYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLENRDRPAGMVLSRQNLPVLPRDTDGFASAEGVARGAYVLVDAVGGS
+GAPAPARVLLIATGSEVSVAVHARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTAVSRGARVSLEHYGESADGARLMEKYGFTGEAVAQAA
+RGLL
+>3_1622
+MTDTASTALDRTLPARDFVYDEQDRRMVDTLKVLAADAVEKAGHGHPGTAISLSPVAWQL
+YQNVMHLDPSDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLELEDIAALRTEGSLTPGH
+PEYGHTHGVEVTTGPLGQGLAMAVGFAYEQRRLRGLMDPDAAPGTSPFDHHVFVLASDGD
+IQEGVSSEASSLAGHQELGNLVVVYDANRISIEDDTDISFTEDVAKRYKAYGWHVQEVDW
+SNGAQGHEVTEYTEGVQDLYEALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIHGSKL
+GGDEVVGLKEALGFDPQKSFDVDPEVLAHARSISERSAAYRETWEAAFAAWREAHPENAR
+LYDRLASRELPAGFEDAFPSWDADEKGVATRAASGKVLTALAPVMPELWGGSADLAGSNN
+TTMEGEPSFIPAHRSTAAWQGDPFGRTLHFGIREFAAGAIVNGITIGGLTRAYMGTFLTF
+SDYMRGAVRLAALMGTPAVYVWTHDSVGLGEDGPTHQPVEHLAALRAIPGLDVVRPADAN
+ETAWAWRTILQHRDRPAGLVLTRQNVPVLPRGTEGFAPADGVARGAYVLVDGADASGAAA
+PARVVLIATGSEVSVAVGARELLQAEGVPTRVVSAPCLEWFAEQDEAYRAEVLPDGPGAP
+VRVSVEAGIAMPWHELTVTQSSRGARVSLEHYGESADGPHLLKKYGFSPENVADTARGLL
+>4_1036
+MTDAAQPSTPPTLDRVAPARGFVYSEQDRRMVDTLKALSADAVEKAGHGHPGTAISLAPV
+AWQLYQNVMHLDPTDDRWEGRDRFILSAGHASLIQYLQLFAAGAGLEIEDIQGLRTEGSR
+TPGHPEYGHTHGVEVTTGPLGQGLAMGVGFAYEQRRVRGLMDPDAAPGTSPFDHHVFVLA
+SDGDIQEGVAAEASSLAGHQELGNLVVVYDANRISIEDDTDIAFTEDVVRRYEAYGWHVQ
+EVDWTNGAQGHAVTEYTEDVEALYDALVAAKAETGRPSLIKLRTVIGWPSPTKQNTGGIH
+GSKLGTDEVAGLKESLGLDPTKTFDVDPELLARARSIAERSAEYRRGWEAAFQAWREANP
+ENARLYDRLAGRELPAGFADAFPSWDADEKGLATRAASGEVLTALAPVMPELWGGSADLA
+GSNNTTMKGEPSFIPARRSTATWQGHEYGRTLHFGVREFAAGAIVNGITIGGLTRAYMGT
+FLTFSDYMRPAVRLAALMGTPSTYVWTHDSIGLGEDGPTHQPVEHLAALRAIPGLDVVRP
+ADANETAWAWRTVLEHRDRPAGLVLSRQSLPVLPRDTDGFAPASGVARGAYVLIDATDAD
+GAPTPARALLIATGSEVSVAVRARALLQADGVPTRVVSAPCLEWFAEQDEAYRAEVLPDG
+PDAPVRVSVEAGIAMPWFEHTVTASSPGARVSLEHYGESADGARLMEKYGFTGEHVAEVT
+RGLL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bcf4f7a03bb23b3df52bf632d6f04f3d1af1285
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000945.fa
@@ -0,0 +1,35 @@
+>0_1090
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>1_818
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGSLAELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLDESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
+>2_1725
+MVPRPVLTPDPAPRDEPVLRLRDVHRSLGRGRARTPVLRGVDLTARAGAVTVLLGPNGAG
+KSTTLGLCHGMDRPDAGAVRVFGADPWRAPADLRARIGVMWQEGGLPPSVPARRFVGHVA
+SLYRDPMPVEPLLERLLIADVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLD
+PETRPVVHEVVREQTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGSLADLTRVAE
+GDVVDVDFGDAAPEAVRAWADALPEPLRAAGLAEPARLRVAGVHGPAELAALAASWHRHA
+LMPTRFERAGLRLEQILRETAA
+>3_1618
+MPETSPHPDAPALRLHEVRRTLGRGAARTEVLRGVDLEARRGAVTVLLGPNGAGKSTTLA
+LCHGSDRPDSGTVRVFGRDPWRADADLRARLGVMWQEGGLPPSVTARRFVRHVASLHGDP
+LDPDALLGRLRIDRVADRPIRRLSGGQRQRVALAAAVVGRPDLLFLDEPTAGLDPETRPV
+VHDVVREHTARGAAVLLTTHLLDDAERLADDVAILRAGRVVRAGTLAELTRVQDGDVVDV
+RFDEARAADVRAWVAAAPASFRAVASAGAPAARVAGVRSPADLEALAASWTRAGLFPTRL
+ERAVLRLEELLQSPDADTPSPERSR
+>4_1040
+MPRDEPVLRLSDVHRSLGRGRSRTPVLRGVDLTARAGAVTVLLGPNGAGKSTTLGLCHGM
+DRPDAGTVRVFGADPWRASADLRARIGVMWQEGGLPPAIPARRFVGHVASLYRDPLPVEP
+LLERLLIAEVAGRPLRRLSGGQRQRVALAAALVGRPDMLFLDEPTAGLDPETRPVVHDVV
+REQTDRGAAVLLTTHLLDDAERLADDVAILRAGRVVRSGPLSELTRVAEGDVVDVDFGDA
+SPDAVRAWADTLPAPLRAAGLGESARLRVAGVRGPDDLAVLAASWREHALMPTRFERAGL
+RLEQILRETAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000950.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000950.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ab61991675a79918a40c40ca3faef227341d16ae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000950.fa
@@ -0,0 +1,15 @@
+>0_1095
+MTETANQVPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>1_823
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>2_1720
+MTETANQVPTEDVREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
+>3_1613
+MTDTAAQTPVEDIREALKDVIDPELGVNVVDLGLLYGLHYAEDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGKDQMRALGFNI
+>4_1045
+MTETTNQAPTEDIREALKDVIDPELGVNVVDLGLLYGLHYADDGALLVDMTLTTAACPLT
+DEIEDQVSRAIGTMVDEWRLNWVWMPPWGPERITEDGRDQMRALGFNI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4997051f28b64cf212fa4fecc30f85fac6b6a9c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000966.fa
@@ -0,0 +1,45 @@
+>0_1116
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDAVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>1_844
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+AATDPALRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVSTADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGETLAKVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGHGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
+>2_1697
+MTDRYGAFAASALGRRLTGALGLPQPVELRRHAPGEPVLHGSVLVLGAGPAAADARTLLA
+SWGLEVADAPREGARLAGVVACFDDAAAPGDLGETVLQIGGALRSLGASSRVVTVSVDPE
+AAAEPAVRAARQGVQGLTRSLAQEMRRGGTANGIVLGEGVPLTAPGAAGALAFLLSGRSA
+YVSGQFLPVTTRDGATPADAARPLADKVAVVTGAARGIGAAIVRTLARDGATVVGVDVPV
+AGESLAAVVNEVGGTALALDITAPEAGARILEHCRARHGRMDVVVHNAGITRDRMLANMD
+AARWDSVIAVNTASQLAMNEAFLADDAREVTGEGLRIIGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPALAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNSLQQGGLPQDVA
+EAVAWFASDAAGGTNGATLRVCGQSKLGA
+>3_1593
+MPANDPYGDLVRTRLGRRLTGALGLPQPAELRRHTAGDPAVRGTVLVLGATSAADAARAL
+VTAEGARAVAHPAEGERLAAVIACFDGVAAPGDLSDTALALGGALRSLEPSAHVVTVVED
+PEEAEVPAVRAARAGVMGLTRSLAHEMRRGGVANGLLLRGGARLGDAGPAGALRFLLSGR
+AAFVSGQFLPAAAGAGSAPASADARPLEGRVAVVTGAARGIGAAILRTLARDGATVVGVD
+LPAAGEDLVRIVNELGGTALPLDITAPDAGARIVEHARARHGRLDVVVHNAGITKDKLLA
+NMDAARWDAVLAVNTASQLAINEVLLSAEAADVVSPDIRIVGLASISGIAGNRGQTNYAA
+SKAGVIGLTAATAPDLAARGGGITAVAPGFIETEMTAKIPLVTRELGRRVNSLQQGGRPE
+DVAEAVAFLSSPAASGINGTTLRVCGQSMLGA
+>4_1066
+MTDRYGTFVASPLGRRLTGALGLPQPVELRRHTPGDPVLPGSVLVLGATPAAADARTLLA
+SWGLEVADAPREGARHAAIVACFDGVATPADLGAVALEIGGALRSLGSSSRVVTVFEDPE
+SATDPTLRAARQGVTGLTRSIAHEMRRGGTANGLVLGEGVPLTAPGAAGALAFLLSGRAA
+YVSGQFVPVATADGAVPADAARPLAGKVAVVTGAARGIGAAIVRTLARDGAVVVGVDVPA
+AGEALAEVVNEVGGTALALDITAPDAGARILEHCRTRHGRMDVVVHNAGITRDRMLANMD
+AARWDSVLAVNTTAQLAMNEAFLAEDARDVAGQGLRIVGLASISGIAGNRGQTNYAASKA
+GVIGLTAASAPVLAARGGTINAVAPGFIETEMTAKIPLATREVGRRLNALQQGGLPQDVA
+ETVAWLASDAAGGTNGATLRVCGQSKLGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92568cc3bae2e11d183bc2d08f5c8e0ed9a1585f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000977.fa
@@ -0,0 +1,36 @@
+>0_1127
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFRAEDVEAWQPA
+DEARWTPEALGERPITDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>1_855
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDTVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
+>2_1685
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERREEFADVARANVEAFFGAEHPAWSIHLGDAQEQMTRVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLATGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAERGVDAYGGSIQEQDQD
+>3_1582
+MSDATAPETPAAPTTPDTAAPAGRPAGVTARRGPLRAGQRVQIKDAKGRLNTITLLPGGE
+FHSYQGVLRHDDLIGGPEGIVVQNSSGHAYQVLRPLLNDFVLSMPRGATVVYPKDAGQIV
+QQADIFPGAVVVEAGVGSGALSMSLLRAVGDAGRLHSYERRAEFAEIARGNVESFFGGVH
+PAWSIHLGDAQEEMPKVHEPHSVDRVVLDMLAPWECLDAVATVLAPGGVWLNYVATATQL
+SRVAEAIRASGKFTQIEATETLVRGWHLDGLAVRPDHRMVAHTGFLLTARRLAAGEDALV
+MKKRLKVSEFTTEDVEAWTPSDGARWTPQALGERTVTDKKARKAAKEARLTARRARAALE
+GRDPRTVGQDKD
+>4_1077
+MTEPTGVSARRGPLRAGQRVQIKDAKGRLNTITLLPGGEFHSYQGVLRHDDLIGGFEGVV
+VENSAGQPYQVLRPLLNDFVLSMPRGATVVYPKDAAQIVQQADIFPGAVVVEAGVGSGAL
+SMSLLRAVGDHGRLHSYERRPEFADVARANVEAFFGAEHPAWSVHLGDAQEEMPKVHEPG
+SVDRVVLDMLAPWECLDAVAEVLAPGGVWLNYVATATQLSRVAEAIRDSGRFTQVEANET
+LVRGWHLDGLAVRPDHRMVAHTGFLLTARRLASGEEALRLKKRSKVSEFKAEDVEAWQPA
+DEARWTPEALGERPVTDKKARKAAKEARLMAARSRAAEQGVDAYGGRTPTGEQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000982.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000982.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32ee768f7a6dfc10bd13e771c52f1a552ce4a9aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0000982.fa
@@ -0,0 +1,15 @@
+>0_1132
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>1_860
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQRLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>2_1680
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLESNAEEFVKGFVQK
+GGQ
+>3_1577
+MAQEQIRPRPAGGPEDEGAAAQAQAKAAPQDTGLDGLLDEIDSVLESNAEEFVKGFVQKG
+GQ
+>4_1082
+MSQEQIRPRPSGGDDETGAAAGQAHVKPAAQDQGLDSLLDEIDSVLVSNAEEFVKGFVQK
+GGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..038013e2edc950481dfa02d711eb7ee866f418cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001007.fa
@@ -0,0 +1,20 @@
+>0_1159
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>1_887
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
+>2_1651
+MALSADETGVEIGATQDSEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVQVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>3_1548
+MALSAEETGVEIGATEDATGLPPHEVELTDVAAAKVRALLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYLMGATIDFEDTISKQGFTIDNPNAV
+GSCACGDSFH
+>4_1116
+MALSAEETGVEIGATQDAEGLPPHEVELTDVAAGKVRSLLEQEGRTDLRLRVAVQPGGCS
+GLIYQLYFDERVLDGDTVRDYDGVEVIVDKMSVPYIMGATIDFEDTISKQGFTIDNPNAG
+GSCACGDSFH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001022.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001022.fa
new file mode 100644
index 0000000000000000000000000000000000000000..86adcd04345b377034670dda5ce38a5c0c963bef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001022.fa
@@ -0,0 +1,20 @@
+>0_1175
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA
+SHVSKGRPFRYPFNLRILR
+>1_903
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAVYGVMGA
+SHVSKGRPFRYPFNLRILR
+>2_1636
+MNPSAQPDAGRPGHEPPAWLASAGGRATPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESKEALNFSGPPTLITTLFFFLALLPVIGAIFAILGALSWAVMAVYGVMGA
+SNVSKGRPFRYPFNLRILR
+>3_1532
+MATTPSTTPAGETATPRRAAGGSAAHEAPAWLRDAAGGRAPLTAKQDRDRAALSHLSLAC
+GLPGPLVMWLLYRDRGPFTAQESREALNFSLAPTLLIVLLFLLGGVPLLGGLLAILGALL
+WIALALYGVMGASQVAKGRPFRYPFSPRLLR
+>4_1133
+MNTRAQPDAGRTGHGPPAWLVSAGGRGAPLTAKQDRDRAALAHLSLAFGVLGPLVVWLLY
+RDRGPFTSQESREALNFSGPPTLITLLFFFLSLLPVVGPIFAILGALTWAAMAAYGVMGA
+SHVSKGRPFRYPFNLRILR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001025.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001025.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a2bd18767424d37833fc9de70c4d07727d13bb2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001025.fa
@@ -0,0 +1,15 @@
+>0_1179
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEPEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>1_907
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>2_1632
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>3_1529
+MANIKSQKKRILTNEKARQRNIAVKSELKTAIRAVDKAVAAGEQDAAVEALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
+>4_1137
+MANIKSQKKRILTNEKARQRNVAVKSELKTAIRAVDKAVAAGEAEAAAAALRTASRKLDK
+AASKGVIHKNQAANRKSGIAARVKALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001029.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001029.fa
new file mode 100644
index 0000000000000000000000000000000000000000..274a2bcf320999a4483a3b9cf6d7e957fce1eaae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001029.fa
@@ -0,0 +1,35 @@
+>0_1183
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTVYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAADAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELAVERAGEDPVRIAVHEYGDPETAMQLAERLQPISTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>1_911
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
+>2_1628
+MATIEQWRDDALVRLRSRRSQLVGRARYGLKPPRRDRTAVVTDSAAALPAAALGHSLAAG
+IRQVPLPVMVGDQIHAEGTDDLALELPLALAAGTAVRTSRPSPGAFRSVYAQLAREGYAR
+ILSVHLSGELSGTAEAARLAAVDAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMTVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLIGTLLHVRPVLAVDDGAISLVDRPR
+SAARAVDRLVELATERAGDVPVRIAVHEYGDPETAAALAERLTPVSTTPVPVVELPAVLA
+AHLGLGALGVVVCPLESPTGGSGD
+>3_1525
+MASTSQWLEDAVERLRARRGQLVGRARYGLKPARRDRTGIVTDSAAALPVEVFAHPFAAG
+IRQVALPVMVGEQIHVEGDADLDLELQLALAAGTPVRTSRPAPGAFRAAYADLAQAGCAR
+ILSVHLSGELSGTVEAARLAAADAPVPVVVLDSRTAGLALGHAVLDAAVEAGFGRPLDQV
+AAIAQACADQSSVLFTVPHLEQLRRGGRIGAVPSLLGALLQVRPVLGLQDGSVHLVDRAR
+TSPRALERMVDLARERAAGGPARIAVHEYGDPAGATALAERLQSASATPVPVVPLPAVLA
+AHLGLGTLAVVLSPLEPVPSTSSSPAQAN
+>4_1141
+MASIEQWRDDALVRLRSRRSQLAGRARYGLRPPRRDRTAVVTDSAAALPGAVLGHGLAAG
+IRQVALPVMVGEQIHTEGTDELALELPLALAAGTPVRTSRPSPGAFRTAYAELARAGYAR
+ILSVHLSGELSGTVEAARLAAAEAERPVTVVDSRTVGFALGMAVVDAAVDAGVGMPVARI
+RERLEATVDSSHVLFTVPSLEQLRRGGRISGLASLLGTLLQVRPVMAVDDGAIGLVDRPR
+SAARAVDRLVELATERAGEDPVRIAVHEYGDPETAVQLAERLQPVSTTPVPVVELPAVLA
+AHLGLGALGVVICPLESPTGGSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001039.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001039.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16e9440e9146a2bc8a171969f0d33cdff1bc33ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001039.fa
@@ -0,0 +1,31 @@
+>0_1193
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEVGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>1_921
+MTTTATGGAGPRAPFGRRLAQAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
+>2_1618
+MAQAGPLCLGVDPHPSLLRQWGLPDTPAGLEAFSLTGLEAAVGPDGPRVAAIKPQVALYE
+RHGSAGLAALERLLAEARDAGVLTIADAKRGDIGSTMDGYAAAWTSDASPLAADAVTLSP
+YLGFGTLVPTIEAAHAAGRGVFVLALTSNPEGREVQHVGRDAGEGAVARRIAAAAADLNA
+ALRAEDEWGPVGLVLGATVAEDAERLGLDLPGLAGPLLAPGFGAQGATAAGMREGFGRAW
+PQVLATSSRGILAGGPTVAALVERIERDRADLG
+>3_1515
+MSVPAASMTREPFGRRLAAAMAAAGPLCLGIDPHPSLLQAWGLPDTAAGLESFGLTALEA
+AAGDGAARVAAVKPQVALFERHGSAGLAVLERLLAEARDAGVLTIADAKRGDIGSTMDGY
+AAAWLDDASPLAADAVTLSPYLGYGTLTASIERAAAAGRGVFVLALTSNPEGASVQHVGA
+SEGQGAVAARIVTSAAADDARLAGLDGWGPVGLVVGATVAGHARELGIDLAALRGPLLAP
+GFGAQGATGAGMREAFGAAWPQVLATSSRGILAAGPTVTSLTRAIDAARADLGVEGPDPR
+HAAGRDA
+>4_1151
+MTTTATGGAGPRAPFGRRLAHAMETAGPLCLGVDPHPGLLRQWGLSDTPAGLEAFSLTAL
+EAAVGPEGPRVAAIKPQVALYERHGSAGLAALERLLAAARDAGVLTIADAKRGDIGSTMD
+GYAAAWIADASPLAADAVTLSPYLGFGTLVPTIRAAHEAGRGVFVLALTSNPEGREVQHV
+GEGSAEGSVARRIAAAAAAENAALRGDDAWGPVGLVLGATVAAEADRLGLDLPALGGPLL
+APGFGAQGATARGMRADFGTAWPQVLATSSRGILSAGPSVASLVDTIEENRAALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001040.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001040.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49c6723b5438a0139b4af231b485eae37bf265ab
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001040.fa
@@ -0,0 +1,100 @@
+>0_1194
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>1_922
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVAHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
+>2_1617
+MPKRPDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLHRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPADGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPRELL
+RRARTATTDRLAQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADQIRDAEVLDES
+LLRHAKRHGFSDAQIGSLRHMGADVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGRSVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVLGVYVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDRAGLVAPKNGTAVSFEDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGERMYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATEQIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGVGKSIADLQAEGVLPTAYDGATLPLGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHYDTAFAKSQAAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQIVSTGGTAEVLRRNGIPAETVAKIAEAGGEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRAYEWSV
+TSLQEHDARLQQAVEASA
+>3_1514
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVILVNSNPATIMTDPEL
+ADATYVEPITPEVVAKIIEKERPDAVLPTLGGQTALNTAIALDKDGVLEKFGVELIGANI
+AAIELGENRELFKGVVERAGGESARSHIVHTMEEAFAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLRRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPEDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADATLTTTMKSVGEAMAIGRSFSEALQKALRSLEQKGSELSFDRDADPASLL
+ASARTATTQRLAQTQRALYAGATLEEAFEATAIDPWFLDQLMLINEVADEVREAPQLDEA
+VLRRAKRHGFSDAQIGSLRHMDPAVVRGLRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLESEVDEHAAPSVVILGSGPNRIGQGIEFDYSCVHATLALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEATGGVAGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPEAIDLAEHRGEFARVLDEAGLIAPKNGTAVSFEDARRVADEIGYPVLVRPSYVLGGRG
+MEIVYTEEALAHYVTNATEITPTQPMLVDRFLEDAIEIDVDALYDGHELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVRTATEKIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAAMIGMGRTIAELRAAGTLPTAFDGASLPMGASVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDRHFDTAFAKSQAGAGGPLPTEGRVFVSV
+ANRDKRAVVGQAKRLVDLGFEIVSTGGTAEVLRRNGVPAEVVAKIADASDADGAGTVLEQ
+LHEGRVDLVLNTPSGGEARTDGYEIRAAATSLGVPVITTTAEFAACLQAIEAMRTYEWSV
+TSLQEHEERLAQAVAAEASA
+>4_1152
+MPKRTDLKSVLVIGSGPIVIGQAAEFDYSGTQAIRVLKEEGVRVVLVNSNPATIMTDPEL
+ADATYVEPITPAVVAKIIEKERPDALLPTLGGQTALNTAIALDKDGVLERFGVELIGANI
+EAIELGENRELFKGVVERAGGESARSHIVHTMEEALAAVEDLKYPVVVRPSFTMGGLGSG
+MAYDEADLYRICGAGLQYSPTSEVLLEESILGWKEYELEMMRDKNDNVVVVCSIENVDPV
+GVHTGDSITVAPAMTLTDREYQKLRDISINVIREVGVDTGGCNIQFAVNPVDGRVVVIEM
+NPRVSRSSALASKATGFAIAKIATKLALGYTMDEIPNDITQKTPASFEPVLDYVVVKVPR
+FAFEKFPAADPTLTTTMKSVGEAMAIGRNFTEALQKALRSLEQKGSELAFPQDADPQALL
+AAASTATTDRLSQTQQALYAGATIEEAFEATAIDPWFLDQFVLINEVADEIRDAEVLDEA
+LLRRAKRHGFSDAQIGSLRHMDAAVVRGVRHALGVRPVYKTVDTCAAEFEAFTPYRYSSY
+DLETEVAPHEGESVIILGSGPNRIGQGIEFDYSCVHATMALREAGYETVMVNCNPETVST
+DYDISDRLYFEPLTLEDVLEVIAAEEASGGVRGVFVQLGGQTPLKLAQQLADAGVPILGT
+SPAAIDLAEHRGEFALVLERAGLVAPKNGTAVSFDDAKRVADEIGYPVLVRPSYVLGGRG
+MEIVYSEEALAHYVEHATEITPDQPMLVDRFLEDAIEIDVDALYDGTELYLGGVMEHIEE
+AGIHSGDSACVLPPVTLGPDVLERVHRATERIAAGVGVRGLINIQFALASDVLYVIEANP
+RASRTVPFVSKATGVQLAKAAARIGVGESIADLRAAGMLPTAYDGGTLPIGAPVAVKEAV
+LPFTRFRTAEGRVVDSLLGPEMRSTGEVMGIDKHFDTAFAKSQSAAGGPLPTSGRVFVSV
+ANRDKRTLVGQAKRLVDLGFQVVSTGGTAEVLRRNGIPAEVVAKIADAGHEDGAGTVLEQ
+LHAGTVDLVLNTPSGGDARTDGYEIRAAATSLGVPVITTTAEFGACLQAIEAMRSYEWSV
+TSLQEHDARLQQAVAGPEAAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93f58966fcf0866063e614d28faa96eebbd49f8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001047.fa
@@ -0,0 +1,40 @@
+>0_1201
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDL
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSPRLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>1_929
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
+>2_1609
+MTDRHPDPAEPEIPGEPPAAEPAAAGQEDVTVIPVSGGQEAAAHGGYDVVVGRGLLARLP
+EMLGPGVQRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVL
+GQNDFTRSDAVVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTS
+EGKNLVGAFHPPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEQDPAQSQ
+NPHSARLRELIERSIRVKADIVSRDLRESGEREALNYGHTMGHAIELAERYQWRHGAAVS
+VGLVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQL
+RFVLLDGLAQPSTVDIPDPSLLFAAYQEIAE
+>3_1506
+MTEHQPDQSDPIAEHSAAAPEQDVTVIPVAGGPENRAGGGYDVVVGRGLLGRLPAVLGPQ
+VRRVLVIHPRALRATGDVVKNDLEAAGLVSLTAEIPDAEEGKHLQVAGFCWQVLGQNDFT
+RSDAIVSVGGGAVSDLAGFVAATWLRGIRVVHMPTTLLGMVDAAVGGKTGINTAEGKNLV
+GAFHPPAGVLADLDTLLTLPSNELVSGLAEVVKCGFIADPRILELIEEAPEQAQNPHSAV
+LRELIERAVRVKAEVVSGDLREAGPREALNYGHTLGHAIEHAERYQWRHGAAVSVGLVFA
+AELARSLGRLDDATADRHWSVLQSLGLPVSYRGDRWQTLLEGIKRDKKNRGDQLRFVLLD
+GLARPTTVDIPDASLLFAAYQEIAE
+>4_1159
+MTDREPDITEQETPGAAPAAAPAAPEDVTVIPVAGGHEAAVHGGYDVVVGRGLLARLPDM
+LGPTVRRVLVIHPRALRATGDVVKNDLEAVGLTALTAEIPDAEEGKHLQVAGFCWQVLGQ
+NDFTRSDAIVSVGGGAVSDLAGFVAATWLRGVRVVHMPTTLLGMVDAAVGGKTGINTAEG
+KNLVGAFHNPAGVLADLDTLLTLPANELISGLAEVVKCGFIADPAILDLIEEDPAQAQNP
+HSARLRELIERSIRVKADVVSRDPRESGAREALNYGHTMGHAIELAERYQWRHGAAVSVG
+LVFAAELARSLGRLDDATADRHWSVLTALGLPVSYRGDRWQTLLEGIRRDKKNRGDQLRF
+VLLDGLAQPTTVDIPDASLLFAAYQEIAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dfdb95004c63179b6693ea0fa41f9179777755b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001058.fa
@@ -0,0 +1,55 @@
+>0_1213
+MPRLARLATAVTAAALSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>1_941
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
+>2_1597
+MRTLSRLAAATSMVALSAAVVAPLTVAAPAANPSGRSIELTAAGTHATGVFDASAAEIPA
+FDKTTGRLFVVNAQKGAIDVLTVGEDAEPAAESVLSVAGLPAADGSVTGAGAVVNSVAVA
+GAVMAATVEAEDKTGHGWLVFFDTRTLGFLGGVRVGALPDSVALAPNGAYAVVANEGEPA
+DDFSSDPEGTISVVSVPKNARQFARLGQDAVRTVDFRAYDEGAALPEGVRVFGPDVAVPS
+GHEEAGRIARNLEPEYASIDPTGRTAYVSVQEANAVVAVDLASASLADFWALHLTDWSTE
+GVLDVSDKDGAISPAYQPVLGVPMPDGLATYKHRGQTLVVTANQGDSREWGDFVDAERVK
+DLELCGDVFPHAKALQKNEALGRLNVLTDLGYDAERGCHTELHALGGRGFSIYTADGQRL
+FDSSGMLEEQIARLIAAGELPAHAFNANNDETPSFDSRSDDKGVEPESVVVGEVQGRQYA
+FVGLERIGGVMVFDITDPTDARYVDYINERAWDAVGEDGDAGLGDMGAEGLAFVPASDSP
+SGTALLIVATEVSGSTTVYEVDPVKGGKRT
+>3_1494
+MSRIVRLTRLGAAAGALALSAAVVAPSAVSAPVTATAAAANPSGKTVELSLAGTHETGVF
+GESAAEIPAFDAATGRLFVVNAEKGAVDVLRVGADGAPAAETVLSAEGLRTADGSVTDGG
+ATVNSVAVSGGVLAVAVEAADKTGLGWVAFFDTTTLSYLGGVRVGALPDSIAFSPDGAYA
+VVANEGEPADDFSADPEGTISVISVPKNVRQFARLTQAAVRTVDFRAYDAGTALPEGVRV
+FGPDVQVPEGQEPAGRIARNLEPEYVTIDDTGRTAYVSVQEANAVVAVDLKSATLKDFWA
+LQLTDWSKEGVLDASNEDKAITLRNQPVLGVPMPDGVDTYRYRGQDLVVTANEGDSREWG
+DFVDAARVKDLELCTAEYPDAKALQKKPALGRLNVVTDLGYDADRDCFSQLHAFGGRSFS
+IYTADGTRLFDSAGMIEEQIAQLIADGELPESAFNANNDETPSFDSRSDDKGPEPEAVVV
+GRVQGRTYAFVGLERIGGVMVFDITDPTKATYVDYVNERNWDAEGDDAAAGLGDMGAEGL
+TFVPANESPSGTALLVVANEVSGSTTVYEVNPVRR
+>4_1170
+MPRLARLATAVTAATLSTAFLAPASLSAPAPHSATAQRAAIAANPSGKSIELTRAGTHET
+GVFGESAAEIPAFDAVSGRLFVVNAQRGAVDVMRLGADAAPVAERTLSAEGLRTADGSVT
+DKGATVNSVAVSGGVMAVAVEAAEKTDHGWVVFFDTTTLRYLGGVRVGALPDSLAFSPNG
+AYVVVANEGEPADDFSVDPEGTISVVSVPKNARQFSRLTQDAVRTVDFRAYDAGTALPAG
+VRVSGPDMAVPAGHEPAGRVARNLEPEYVTVDPTGRTAYVSVQEANAVAVVDLKSATLED
+LWALTPTDWSTEGVLDASDKDGGIELGHWPVDGLPMPDGIDTYRWRGQNLVVTANEGDGR
+EWGDFNDSERVSDLDLCAAEFPGAKALQKKDALGRLKVLTDLGYDSERECHSSLTTLGGR
+SFSIYTADGTRLFDSAGMIEEQIARLVAAGELPEHAFNANNDETPSGDSRSDDKGPEPES
+VVVGTIQGRTYAFVGLERIGGVVVFDITDPRNATYVDYVNDRDWDAAGDDATAGLGDMGA
+EGLTFVPADESPSGTALLIVANEVSGSTTVYEVNPTRRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001060.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001060.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9c02dd3b5330e41959a5be50d9f391503c4ab411
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001060.fa
@@ -0,0 +1,60 @@
+>0_1215
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>1_943
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVREEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKHT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGAALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPEA
+>2_1594
+MNPTISSGRSPDGEDAFVLRTHQLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDAS
+GFAQVVVRDEADFDPLRNEWVLQVSGVVERRPEGNENPNLPSGEIELIAETVTVLNTAAA
+LPFQVDEHVEVGEEARLRHRYLDLRRPEPSRIMRLRSEVNRTAREMLHGEGFTEVETPTL
+TRSTPEGARDFLVPARLAPGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADR
+QPEFTQLDIEASFVEQDDVIALGEKIVKAVWALVGVDVPTPIRRMTYAEAMEKYGSDKPD
+LRFGLELTDLTAYFKDTPFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAY
+VLIQEDGSLTGPVSKNISDEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGR
+RCELFTDAGNGVEAKDADWAFVWVVDAPMFEPAADAVASGDVAVGSGAWTAVHHAFTSPK
+PEFADTFDTDPGSALAYAYDIVCNGNEIGGGSIRIHRQDMQERVFSVMGLSQEDAQEKFG
+FLLEGFKYGAPPHGGIAFGWDRVVALLAGTESIREVIAFPKTGGGFDPLTAAPAPITAQQ
+RKEAGVDAKPEPKKAEGEKAEAAGQPQA
+>3_1491
+MLRTHHLGELNASLIGQTVTVTGWVAKRRDHGGVAFVDLRDASGRAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPTGEVELIADDVVVLNTAAALPFQIDEHVEVGEEARL
+RHRYLDLRRPQPARIMRLRSEANRVARELLNEQGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGLEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEQIVKALWGLVGVEVQTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQPRRTLDAWQEWAKQRGAKGLAHVLIQEDGTLTGPVSKNI
+TDEEKAGLAAAVGANPGDCVFFAAGKAKESRALLGAARVEIGRRCELFTDAGDGVEAKDA
+DWAFVWVVDAPLFEPAADAVASGDVAVGAGQWTAVHHAFTSPKPEFMDTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQKRVFSVMGLSEEDANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTESIREVIAFPKTGGGYDPLTAAPAPITPQQRKEAGVDAKPEAKKAEG
+AASEGAEAQAKANDEKTAADEAQLR
+>4_1172
+MLRTHSLGELNASLIGQTVTVTGWVARRRDHGGVAFVDLRDASGFAQVVVRDEADFDPLR
+NEWVLQVTGTVERRPEGNENPNLPSGEIELIAETVTVLNTAAALPFQVDEHVEVGEEARL
+RHRYLDLRRPQPSRIMRLRSEVNRTARELLHGEGFVEVETPTLTRSTPEGARDFLVPARL
+APGSWYALPQSPQLFKQLLQVGGIEKYYQIARCYRDEDFRADRQPEFTQLDIEASFVEQD
+DVIALGEKIVKALWALVGVDVPTPIRRMTYAEAMEKYGSDKPDLRFGLELTDLTEYFKDT
+PFRVFQNEYVGAVVMPGGASQARRTLDAWQEWAKQRGAKGLAYVLIQEDGELTGPVSKNI
+SEEEKAGLAAAVGANPGDCVFFAAGKPKESRALLGAARVEIGRRCGLFTDAGDGVAAKDA
+DWAFVWVVDAPMFEPAADAVASGDVAVGAGAWTAVHHAFTSPKPEFADTFDTDPGSALAY
+AYDIVCNGNEIGGGSIRIHRQDVQERVFEVMGLSPEEANEKFGFLLEGFKYGAPPHGGIA
+FGWDRVVALLAGTDSIREVIAFPKTGGGFDPLTAAPAPITAQQRKEAGVDAQPEPKQAEA
+EPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001061.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001061.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf205f97dce7cc82c1bd0bef7c1c198ecc92e3da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001061.fa
@@ -0,0 +1,45 @@
+>0_1216
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAVAATLGLYLVPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRELLETALGSGWGWVAVAGAALAAAGAMLTLLTGISRTALAM
+AREADLPRPLARVHAGTGTPWTAQLTVAAAVVLLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDHGHRPARPRPLRVPRAVNVLGLALCLLLAFSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGG
+>1_944
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDD
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTLAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGV
+GGRAFVRAGRRGR
+>2_1593
+MLQRRLTLTHAVVIGLGSMIGAGVFTAIGLAAALTGGHPGLLYAALALALLTALCNALST
+AQLATVHPESGGAYVYGRRQLHPLAGFVAGWGFVTGKTASVAAMAATIGLYLFPDDAAAA
+RLTGVAAVVVLTAVAMAGVTRTAQATMAILVPVAAVLALAIGAGLALGAPSEADAFAGVA
+DSPVTGVLMGAGILFFAFAGYARVATMGEEVIDPRRSIPRAILIALGLTAGLYVLLTAAL
+FAGLGPTGLALSPAPVRELLETTLGATWGWAALAGAALAAAGAALNLLTGISRTALAMAR
+ESDLPRPLARVNARTGTPWVGQLTIAVAVILLLLTTDILTVVGFSSFGVLVYYAVANLAA
+ATLRGGEDGRDPALPRPLRVPRAVNVLGLVLCAVLAATLPPMAVVAMLAVFLVGVGGRAF
+VLAGRGRPGRRGAVAP
+>3_1490
+MTATSPAPRGLPLRGALAIGVGSMVGAGAFTSLGLAALLTGGHVGALAAALGLAVAVATC
+NALSTAQLAAVHPASGGTYVYGRRQIGPTAGFVAGWGFVTGKTASVAAMATTAGLYLFPD
+SPLAARLAGAAAVVILTAVALRGITRTAQATVAILVPVLAVLGLTIVAGLAGGRAAADTP
+VSAADPAGVLAAAGVLFFAFAGYARVATMGEEVEDPRRTIPRAVLGALAFTVVLYALLAA
+ALVAALGGTGLAASEAPVRATLEASLGAGWGWAAVVGAVLACAGAMLNLLAGISRTGMAM
+AREGDLPRPLARVDERTAVPWAGQVTVAVAVILLVLTTDVLTVVGFSSFGVLVYYAVANL
+SALTLRPEQRTLRVPRAVNVLGLGLCLVIAFTLPPASVAAMVGVFLIGLGGRWFVRSRRP
+DRIG
+>4_1173
+MTAALQRRLTLLHAVAIGLGSMIGAGVFTAIGLAAALTGGHPGLLYGALAVAAVAALCNA
+LSTAQLATVHPESGGAYVYGRRQLHPWAGFVAGWGFVTGKTASVAAMAATLGLYLFPDDA
+AAARWTGVAAVVVLTGVAMAGVTRTAQATLAILVPVLAVLVLAIGAGLAREAPGGSAAAL
+GVDSPVQGVLMGAGVLFFAFAGYARVATMGEEVIDPARTIPRAILIALAVTVALYLLLAT
+ALISGLGTSGLARSPAPVRDLLETALGSGWGWVAVAGAALAAAGAMLNLLTGISRTALAM
+ARESDLPRPLARVHAGTGTPWTAQLTVAAAVILLLLTTDILTVVGFSSFGVLVYYAVANL
+SALTLRGDDDGRRPARPRPLRVPRAVNVLGLALCLLLALSLPPMSVAAMAGVFLIGVGGR
+AFVRAGRRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001064.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001064.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e8c9004298c00b2b274e6e8f4376f1453d91d36e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001064.fa
@@ -0,0 +1,25 @@
+>0_1219
+MTTVTIEETAPAGALMLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGQLPWTLTQSDVAA
+DATGVAPAEQDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLTALDVPD
+>1_947
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
+>2_1590
+MEGLILAGEPFTPAELQALGSRGVVVPLVPGVWARPEAARRPGVRAEALWMLGGPVLAGG
+WTAIGSSAAWVLTGGAVPERLHAAVPHFHRLPAGGSPLPWTLTQSDVAAGPDGRAPAEED
+VLRIGPLRVTTPERTVEDLLLSPDPDAARTAAAVIAAHGAAGLRERLARHSRRSGVVAAR
+RRLDVLLGALEAAG
+>3_1485
+MHQGHGSRGGAAWELAGMTFTEPELRLLAARGTLEAVLPGVYRPVDVPSEPAGRAAALGL
+LGGPVLASGWTAVGPSAAWVHVGGPAPHRLHAAVPHFHRLPAGGAAPAWRLVQSDVAAGP
+TGAAPAEEDVQVLEGVRVTVPARTVEDLLLTGDPDDARRAARVIAAHGAEGLRDRLDRPS
+RRPGSVGARRRLRMLLDALGADG
+>4_1176
+MTTVTIEETAPTGALVLAGDPFTEPELQALGARGAVRPLLPGVWARPDAADDPAVRAAAL
+WTLGGPLLAAGWTAIGPSAAWILAGGAAPGRLHAAVPHFHRRPAGGGLLPWTLTQSDVAA
+DATGVAPAEHDVLRFGPVRVTTPARTVEDLLLSADPDAARRAAAVIGAHGAAGLRERLAR
+RTRRAGVVAARRRLGALLAALDVPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001075.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001075.fa
new file mode 100644
index 0000000000000000000000000000000000000000..001cede37cc730dad1a57375e4727ac98e414d36
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001075.fa
@@ -0,0 +1,25 @@
+>0_1231
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERHHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>1_959
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
+>2_1577
+MTVIGPRRLAPVTGPRGAVAPAPAPLPAAFRRALADLRTARPRPEVRLREIAAPAGQAPH
+AVALAAEVCGSPGADDVLATGRFVLLHDPSPAARWPGGFRAVTWIRASLEPDVALDQLAG
+AVAWTWLVEALERRHAEHTQAGGTATRSIAEGFGTLGTAPDATDIELRASWTPAPRDLGA
+HLEAWSDMIGAFAGLPPR
+>3_1472
+MTESGPRAPAPAAGGASGAFADALADLRAAHPRPEVRLRPIPDPPGLAPFAVTLAADVLD
+PHGAEADPLATGRFVLLHDPAGSPVWRGDFRVVTYIRASLEPDVATDHLAGAVAWDWLAE
+ALERRHAAHTEAGGTATRQLAEHFGTLALEPGWTDIELRASWTPGPRDLGAHLEAWSDMI
+CAFAGLPPLADDDVPAAVPLRP
+>4_1188
+MSVIGPRRLSAAPGAVEAPVPPGVFRRALADLRDARPRTEVRLREIPAPEGQAPFAVALA
+ADVCDGPGATGGVLATGRFVLLHDPAPDARWPGGFRAVTWIRASLEPDVALDQLAGAVAW
+TWLVEALERRHAEHSHAGGTATRSIAEGFGTLSAAPDTTDIELRASWTPAPRDLGSHLEA
+WSDMICAFAGLPPEHAADVHTAGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001077.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001077.fa
new file mode 100644
index 0000000000000000000000000000000000000000..814c2e974a23d15a9610979b9a673a6e2c93848e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001077.fa
@@ -0,0 +1,69 @@
+>0_1233
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIASITDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVTGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEALFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGQALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLERPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>1_961
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPDGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGAIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
+>2_1575
+MTFTPAPLAPFESLLPLVPDEVLTHVAATDHVLPGGAGTLVLLTLDNGQGPRRPATLGPA
+SLLELGRAVDAQAERARAGEVQALALTGVEGTFAAGADLSLIAGIEDRTVGRDLARLGHA
+VHDRIDAFPAPTLALVNGTALGGGLELALAADHRVVAADARGFGLPEVRLGLIPGWSGVW
+RVPHLIGPEAAVEVVLKNPLDNNRMLDARTAHGLGLMDEVAEGDLLEAGLAFAARIVAGD
+DAALAAVRDHRDRDVSDAAWDRALEAMEALQAGRPGRDLPARRALQELFAGARTRTREES
+AEAEAEALHGLIGSDEFRRTVYAFLDLLQRRAKRPVGDPGKELAREVTKVGVVGAGLMAG
+QLALVFAQHLRVPVVMTDMDQERVDRGLAGVRGQVEKMVSRGRITAEQGEALAGLITAST
+DKSVYADADVVIEAVFEELEVKRTVFRELEPIVREDAVLMTNTSSLSVAAMAEVLEHPER
+LVGFHFFNPVAQMPLIEVVRVAETSDEAVATAFELSRRLRKTGVLVHDAAAFVVNRVLLR
+MMGEVQASFDEGTDAHTADHALDPLALPMTPFTLLAMVGIPVAQHVSESLQAAFGAERFP
+VSANLQRLIDAGKTAIWAKDVRRDKVEEEAAGATGETIPAGTAALIERGSSPQTAEELRR
+RVEDALAEEIGLLLAEGVVAAPEDVDLCMILGAGWPLHLGGITPYLDDCGAAERVNGTRF
+HG
+>3_1470
+MSHTPAPLDQFEHLSTIAPDEILTRATATDHALPDGAGTLALITLDNGQGPRRPATLGSA
+SLLELARAVDEQAARASAGEIQALGITGVEGVFAAGADLALVASLPADAETGRALGRLGH
+AVYDRIDAFPVPTVALVNGTALGGGLELALACDRRVIAPEVKALGLPEVRLGLIPGWSGV
+WRAPHLVGPEAAVALLLTNPLDNGRMIGAADAVRLGLMDSLAEGDLLAAGLTAAADAVAG
+RTVQRTADVSDAAWDRALQAFGAAQSARPGRDLPARRHLEELFAGARTRTRAESAEAEAD
+ALADLIGSAEFRRTVYAFLGLVQGRAKRPAGDPGVEQAHTVHRVGVVGAGLMAGQLALLF
+ATALRVPVVMTDLDQERVDRGLAYVRSQLERSVTKGRMKAEDAEAVAGLITGATDVSAHA
+EAEFVIEAVFEELEVKRTVFRQLEQVVSPTAILATNTSSLSVAGMAEVLEHPERLVGFHF
+FNPVAQMPLVEIVRVAETTDAAVATAFELARRLRKTAVLVNDAAAFVVNRVLLRMMGEIQ
+NSFDQGTDAHTADHALDPLAFPMTPFTLAAMVGLPVAQHVSESLQAAFGAERFPVSENLQ
+RLIEAKKTAIWAKDVKSPEEAGGATGETIPADTAALIEQGDTPQTADELRVRVEDALAEE
+IGLLLDEGVVAAPDDVDLCMILGAGWPLHLGGITPYLDDCGASERVRGARFHQA
+>4_1190
+MTSVSLASFDHLPALAPDEVVTTVTVTDHALPEGAGTLALLTLDNGQGPRRPATLGPATL
+LGLGRVLDEQAARAAAGEIQALAVTGVEGTFAAGADLSLIAGLTDDVGRDLALLGHAVYD
+RLAALEIPTVALVNGLALGGGLELALAAGHRVVAADAKGFGLPEVRLGLIPGWSGVWRVP
+HLIGPEAAVDVVLKNPLDDNRMLDARAAHGLGLMDRIVEGDLLDAGLELAAALVAGDESV
+AAELAAHRDRDVSDAAWDRALAALERLQAARPGRHLPARRHLEDLFTGARTRTRAESAQA
+EADALGTLLHSPEFRRTVYAFLGLVQGRAKRPAGDPGRELAREVRKVGIVGAGLMAGQLA
+LVFARHLRVPVVMTDIDAERVERGLAGVRAQVEKMVSRGRLSAEDGEALAGLITADTDKA
+VYADADIVIEAVFEELEVKRTVFRELEGIVREDAILMTNTSSLSVAAMAEVLEHPERLVG
+FHFFNPVAVMPLVEIVRTEATTDEVVATAFELTRRLRKTGVLVHDATAFVVNRVLLRMMG
+EVQNSFDEGTDAHEADHALDPLALPMTPFTLLAMVGIPVAQHVSESLSASFGAERFPVSA
+NLQRLIDAGKTAIWAKDVRPDRRDEEAAGATGEQIPEATAALLEQGSTPQTSEELLRRVE
+DALAEEIGLLLDERVVAAPEDVDLCMILGANWPLHLGGITPYLDDCGAAERVNGRRFHPA
+AQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001078.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001078.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da96f15ceff383d5f0ea0e26d9894d9ef9c1a1d2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001078.fa
@@ -0,0 +1,25 @@
+>0_1234
+MTDPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRTGFAPTTAQRAAR
+DGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>1_962
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
+>2_1573
+MTDPAPVRPSLDLTPFERWEAVTLDGEHVGFLHRVLDGTLLTTRMGFAPTPAQRRARPEL
+PERYLAQSQVSFTADGTSWDWTSHEDSAGAQRVRIDRERAGLDADVLPSYAEYLLLAVAA
+ADGPVVVAARLEESSPLQGGLRMPRAELRPADAGDGDVSVTVVADGAALGAHLVRDGAVV
+ASDWGGGTASTPVAGRAEATEGLDEHVVTFSGMPLV
+>3_1469
+MSARYDLTPFETWEAVALDGVHAGFLHRRLADGILTTRMAFQPTGAQRRERADLPQRYLA
+QARVRFSADGSTWEVCDFEDSLTTQNVRIARERAGLGAEVVPSWAEHLLITAQRTPEHDG
+APYLRLEESSPLQGPVRMPPAVLRIGAREAVPAAGPAGSEAGQARPEGLRVEVVSEGHVL
+AVHWLGEPATEGRRPLVASDWGGGTVSVPVATAAEALEGLPADLHTFAQLPTD
+>4_1191
+MTHPAPRPTGAARFDLTPFERWEAVTLDDVHVGFLHRVLEDGVLTTRMGFAPTPAQRAAR
+GGLPERYLAQTQVGFTPDGDGWAWTTHEDSAGAQRVRIDRERAGIDAAVLPSYAEYLLLA
+RVAAEGPLAVDRLEEASPLQGGLRVPRAELRPADAGGSDVRVAVVADGVELGAHLVREGA
+VVASDWGGGTASTPVADQAAATAGLDAHVVTFAGLPIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001081.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001081.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0953244894a208530f91ffa24296e69e8c728a4e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001081.fa
@@ -0,0 +1,21 @@
+>0_1238
+MSIVRLYRESVGDDGARLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQAEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATAIERRTVERLRVEMTHQLAWRGLG
+EVEDVVEEVGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>1_966
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
+>2_1569
+MSIVRLYRETTNEDGSRLFEYREAWADVEGGEFVVHHGRVGHPGTVGEQPLADEAEGEEL
+LAAFLAQGAEEGFAEADPAGFALLPVAFRLRGREASDIERRNVEHLRVEVTHQLAWRGLG
+EVEDVTEEPGALVLAVRTPHARKAAAEIPVAARRADGVQPNKVEVRSAVQED
+>3_1465
+MSISRLYRDRTEEDGRRSFEYREAWIDPSGELFTVHHGRVGHPGTVGDQPLTSEAEGAEL
+MDAFLAQGEADGFAPADEDAFDVLEVAYRLRGRAITEIERRHGRTLREEVTHQLAWRGLG
+EVTDVVDGDGELVLVVRTPHAPKAAAEVPAAAKRAHGIQPNKVEVRRVDAPRTPAGAAPD
+ADGEG
+>4_1195
+MSIVRLYRETVGDDGTRLFEYREAWADAEAGEFVVHHGRVGQPGTVGEQPLADQVEGDQL
+LAAFVAQGAEEGFAEADPATFAVLPVAYRLRGREATVIERRTVERLRVEVTHQLAWRGLG
+EVEDVVEEAGALVLRVRTPHARKAAAEIPAAAKRADGVQPNKVDVRTAEQEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001084.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001084.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3d537f1a50dbb8bffdb9b33613452004ef8b2cc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001084.fa
@@ -0,0 +1,50 @@
+>0_1248
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>1_980
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
+>2_1566
+MAVIDTSTGVTGIGGTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEEG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIAGLTVEPEVCFAGPEDEPTGQRWRTRNAFTVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEAKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKRHSPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+RHAPATLVDAVLEDARIEPGQTVADLYGGAGLFSAYLADAVGPEGRVFSVEAAGQASKDA
+RRNLHGQPQATVLNGPTDKALGSWIKYPERTVADGGLEGASLDTVVLDPPRAGAGRRAIE
+RLLALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPATQ
+LAAVPAIVEI
+>3_1462
+MDTSTEVVAPGGVIEVEAGAMAHGGHCVARHEGRVVFVRHAIPGEIVRVALTEAEPGARF
+WRGDVVEVVRPSEFRRIHQWKLADSLRAHASGRLPVGGAEYGHIVVHHQRRLKAQVFRDT
+VARIAGVTIEPEALHAGHEDEPTGQHWRTRTAFAVTPQGRIAMHAHRSAVLLPVRNMPLG
+VHALDALALWDWDFTGAARVDVATPADGTQPLVLATPTPQTLADEARLGKLRTRIRQAAN
+ACPVDVSTGFAVPGPKKFSPTGIQRITGRTWVHETVSSERGGERTFRVTGDGFWQVHQHA
+PATLVDAVLEDVDPQPGEVIADLYAGAGLFSAFLSDAVGEEGRVYSVEASRQASKDARRN
+LLSLPQAGVLNGPTDKVLGSWIKEPERTTRDGGLDGDRLDAVVLDPPRAGAGRRAIERIL
+ALAPGRICYVSCDPASFARDLAWLREGGYEVERARVFDLYPDTHHLESVTLLRPAGEVEQ
+TTL
+>4_1205
+MAVVDTSTDVTGIGRTIEVEVGAMAHGGHCVARHEGRVVFVRHAVPGEKVRVALTEAEDG
+ARFWRGDVVEVLRPSEFRRIHQWKLADMLRAHASGRPPVGGAEFGHIVVPHQRRLKAQVF
+RDTVHRIADLAVEPEVCFAGSEDEPTGQRWRTRNAFAVTPQGHIAMHAYRSATLLPVRNM
+PLGVPALDALALWDWDFTGAARVDVATPASGSRPLVLVTPTPQTRADEVKLGRLRTRIRQ
+AANACGVDVSTGLALPGPKQFQPVKVERITGKTWVEETVESERGGTKRFRVTGDGFWQVH
+QHAPATLVDAVLEDARVEPGQVVADLYGGAGLFSAYLADAVGPEGRVYSVEASRQASKDA
+RRNLHDQPQASVLNGPTDKVLGSWLKYPERPVADGGLGGAALDTVVLDPPRAGAGRRAIE
+RILALEPGRIVYVSCDPASFARDLAWLRDGGYEVERARVFDLYPDTHHLESVTVLVPAAQ
+SAPAAAVVEI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001092.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001092.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f36e2ade84c3a07ed6340c96cc4b2c5d2f09e7f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001092.fa
@@ -0,0 +1,20 @@
+>0_1256
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>1_988
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
+>2_1558
+MREPQQHPVSDAPVDRPQDPAQGSDRVLFEERLTPSAGVWVVALMLASLTILVFAPIDLW
+FGVAAAVVFFGLEALLLLTTTPRIVVRERTLQVGRASIERRHVGEVTGHRGEDARRQRGP
+LLHGLAYVVVRGWISPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMVQEDPADEDR
+>3_1454
+MQDASATPDHHAPRTVAASADPVQYEERLSPSVGVWLVALLLAGLCIFVLAPVALWAGFL
+AAAVFFVVEAVVLLASTPRIVVRERTLQVGRAQIERRHLGAVTGHRGEAARAQRGPLLHG
+LAYVCVRGWISPVVRIQIEDERDATPYWLASTRHPEDLVAALGGRMAGEG
+>4_1213
+MRDPQQHPVADASRRAPGGAAAGPDPVLFEERLTPSPGVWAVALMLAALTILVFAPIDLG
+VGIAAAVAFFAVEVLILVATTPRIVVRERTLQVGRASIERHHVGQVTGYRGEDARAQRGP
+LLHGLAFVNVRGWIAPVVRIQLTDERDRTPYWLTSTRRPEELVAALGGTMARQEGTAEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001094.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001094.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cbf1237d4e3fbda80babe9019ad105ffda3105f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001094.fa
@@ -0,0 +1,40 @@
+>0_1259
+MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR
+FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN
+QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL
+IARAQAAERALKDARVPTLVYFYVNELDRAGHRDGVGSDRWLHALEEIDAAVRRLVDRVP
+AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADAALLEGVAHTAGEPRLVQLHFRSDA
+GPDVRARVRRAWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY
+DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
+>1_991
+MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR
+FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN
+QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL
+IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP
+AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA
+GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY
+DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
+>2_1555
+MSGPAVPVGVVPPERALRSVLTSAAAALGVPGCENALGVPASRRVVVALVDGLGRSVLKR
+FGGHAPTLRAAMADGGRVLQAAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPERDAVVN
+QLGGWDEATDPVAWQPRPTVFERAGAAGVDAVTVSLPAFEHSGLTRAGLRGGRFVAGRGL
+LARAQAAERVLKDAREPTLVYFYVNELDKAGHRDGVGSDRWLHALEEIDGALRRLVDRVP
+AGTVVLATGDHGMVDVPPTRRVDYAAADESGALADPALLEGIAHTAGEPRLVQLHFRPDA
+DADVRARVRRAWEDRFGAHAWVLTRDEAVAAGWFGTVVEERVRGRIGELLVAVHGDLALY
+DGRRVAPHAFEMVGQHGSPTRAEREVPLLTWRR
+>3_1451
+MTGPDAAAPAGPGLPPGPVPPERALRSVLTSAAAALGVPGCANALGVPVTRRVVVALVDG
+LGRGVLKRFSGHAPTLRAAMADGGRVLTAATPTTTAASLTSLGTGLDVGEHGVAGYDVLD
+PDRGVVVNMLGGWDEATDPLAWQPHPTVFERAVEAGVDAVTVSLPEFEHSALTRAGLRGG
+RFVGGRGLLARAGHAERVLADACVPTLVYFYVNELDKAGHRDGVGSRSWLHALEEVDAAL
+RRLVSRVPAGTVVLATGDHGMVDVAESRRVDYAALGDDGAPVRPGLLAGVAHTAGEPRLV
+QLHFAPTATPAEREGTRRAWEDAYGDQAWILTRDEAVAAGWFGERVADRVLPRIGDLLVA
+CHGELALYDGRRVSPRAFAMVGQHGSPTRAEREVPLLTWRR
+>4_1216
+MTGPALPAGVVPADRALRSVLTSAAAALGVPGCENALAVPAGRRVVVALVDGLGRSLLKR
+FGGHAPTLRSAMADGGRVLEVAVPTTTAASLTSLGTGLDVGEHGVAGYDVLDPDRDVVIN
+QLGGWDEATDPVGWQPKPTVFERAAAAGVDAVTVSLPAFERSALTRAGLRGGRFVAGRTL
+IARAQAAERVMKDARVPTLVYFYVNELDKAGHRDGVGSERWLHALEEIDAAVRRLVDRVP
+AGTVVLATGDHGMVDVPPSRRVDYAALDEAGELADPALLEGIAHTAGEPRLVQLHFRSDA
+GPDVRARVRRTWAERYGAHAWVLTRDEAVDAGWFGAVVEDRVRARIGDLLVAVHGDLALY
+DGRRVPPHAFEMVGQHGAPTRAEREVPLLTWHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001096.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001096.fa
new file mode 100644
index 0000000000000000000000000000000000000000..948c955029b12aa4f42e6b4d6b103c2f06c06789
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001096.fa
@@ -0,0 +1,85 @@
+>0_1261
+MGETEADRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAAAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGTVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASTGLVRTDPAIRLNASPSPGLAQRGPVSLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPADTL
+VSAVRDAVCHEQADAVVVLARLGLHQADDEPERLAHALADATREARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMAVLGALADYVHWRHQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSVRFETAEEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPPVDLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPERVTVLQAEVHVANAARRTD
+SARRALRGR
+>1_993
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL
+VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD
+SARRALRGR
+>2_1553
+MGDTEPVRDYPSHWEADVVLRDGATARLRPITPEDADELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHKDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAAREHGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAEARSVAELVAPESVAVVGASRDPQAVGSMVLRHILEGGFAGPVHAVN
+RAAGEVQGLTAHASLAEIGEEVELVVVAVPVDQVEALVPEAAAAGAAGLLVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAVRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGAKRRGVGVSTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFT
+RITRRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGAVDSMLDQTGVLEVHTHEAMLD
+LLMAVASQPLPTGRRVVLVADSLAVDRLARDAAAEAGLDVVATVGLAGSEQGVAPPAETL
+VASVREAVAHEQADAVVVVGRLGLHQEDDDPETVARALAEATAGARMPVLVCLTDVVSPR
+YAGATLGASGPVADDAEPGSLQPGVPFYPSPQQAMSVLGALADYVRWRGEEAGEPLEPAD
+VRLHAAEDLVEAAAARAEGTELVRLSAAETEELLGHYGIAVLPSARFETADEAVAAAERL
+GFPVAVKAVDPHLRHRLDLGGVRLNVVDAASLRRNVEQMRRVLAPFGVTELEVQAMAPAG
+QACMVTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAAKLEGR
+GGVPAVDLAALEDLVGRVSVLKDDLPQVARLRFSPVLASPEGVTVLQAEVDVANAAGRTD
+SARRALRGS
+>3_1449
+MAEPDTETAYPSQWEADVVLRDGATARLRPIREDDVDGLRALHAGQSESSIYLRYFTFKS
+ELSAKELERFTHVDHRDRVALVIERGGRILGVGRYDRYGDSDAAEVAFNISDAAQGQGLG
+SILMEHLAVAAREQGIRRFTAEVLPENRKMLSVFQDSGFEVARHFEDGVVAVEFPIDPTA
+RWRAVVESREHRAEARSVAELVEPESVAVVGASRDPHAVGSIVLRHILEAGFTGRVHAVN
+RAAEDVQGLTAHASLKDIGEPVDLVVVAVPVAEVDAVVAEAAEAGAQGLLVLTSGYADAG
+EDGLRAQRRLVARARARGMRVIGPASAGLVRTAPDVRLNASPSPGLASRGPVGVFSQSGA
+VGAMITAGMKRRGVGMSTSLSAGNRADVSGNDAMQFFEDDPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRALPPGHETRTTQAPEGAVDSMLEQTGVLEAATHEDMLD
+LLMAVATQPLPTGRRVTLVADSLALDRLGRDAAAVAGLEVVATHGLGGSEQGIAPTADDV
+VASVEAALAAGDTDAVVVVTRLGLHQDEDAAHEVAQALARVAEGATVPVLGCLTDVVSAR
+YGGARVGGAAAPAADAEPGALQPGLPLYPSPRKAMTVLGRLCDYVAWRREDAGEPIELTD
+VDVRAAEALVDRALERALGTELIRLTGAETEELLRIYGIGVLRSRRFTTPDEAVAAAEEL
+GFPVAVKAVDPYLRHRLDLGGVRLNLEDAESLRQNVRQMRAVLAPFGVTELEVQSMAPSG
+QPCMVTALEDPLLGPVVSFGMAGDATDLLGDWVHRVPPLTDQDVRRMVRSPRAAVKLDGV
+GGVPAVDLDALEDLLARVSCLKDDLPAVARLRFAPVLAAPTGTTVLSAEVDVANAAGRTD
+SARRALRAS
+>4_1218
+MGETEAVRGYPSHWEADVVLRDGATAHLRPISPEDAAELQRMHAGQSENSIYLRYFTYKS
+ELSAKDLDRFTHVDHRDRVAFVITRGGRLLGVGRYDRYGDSDAAEVAFNISDAAQGRGLG
+SILMEHLAVAARENGIRRFTAEVLPENRKMLSVFQESGFEVTRRFEDGVVAVEFPIDPTA
+RWRAVVESREHRAESRSVAELVEPASVAVVGASRDPQAVGSLVLRHVLEAGFTGAVHAVN
+RAAEDVQGLTAHRSLADIGEPVDLVVVAVPADEVEALIPEAAAAGAQGLVVLTSGYADAG
+AEGLEAQRRLVSLARAHGMRVIGPASAGLVRTDPAIRLNASPSPGLAQRGPVGLFSQSGA
+VGAMVSAGVKRRGVGISTSISAGNRADVSGNDAMQFFEADPHTAAVGVYLESFGNPRKFS
+RIARRLSRTKPVVVVRSDVTGRFLPPGHETRTTQAPEGTVDSMLDQTGVLEAHTHEAMLD
+ILMAVASQPLPTGHRVVLVADSLALDRLGRDAAAEAGLEVTATVGLVGSEQGIAPPAETL
+VSAVRDAVRHEQADAVVVLARLGLHQADDEPERLAHALADATRDARIPVLGCLTDVVSPR
+YRGATLGAAGPVDDDAEPGSLQPGLPFYPSPQQAMTVLGALADYVHWRRQEVGEPLEPTG
+LHPHEAEELVEAAAARAEGTELVRLSDEETETLLGHYGITVLPSARFETADEAVAAAERL
+GFPVALKAVDPHLRHRLDLGGVRLNVVDADSLRRNVEHMRRLLAPFGVRELEVQAMAPAG
+QACMLTALEDPLLGPVVSFGIAGDATDLLGDWVHRVPPLTDRDVARMVRAPRAAVKLRGT
+GGVPSVNLAALEDLVGRVSVLKDDLPQVARLRFAPVLAAPEGVTVLQAEVHVANAARRTD
+SARRALRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1248200ea4a3ebc6fa95c323260cdd2164f7a89a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001103.fa
@@ -0,0 +1,35 @@
+>0_1270
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLSWTPTVSIDEGLHRVAAYYRDR
+>1_1000
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADAGNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPEHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAALSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGAAEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
+>2_1544
+MSGFGYDVGLDEAGMPELVERLESRRVLVTGASGLLGAGVARVLADAGNDVVTLQRRPSG
+VAGARDVQGSVTDPAAVERAVAGVDTVVHVAAKVSVSGPEHEFEAVNVEGTRILLHAAQR
+HGARRFVHISSPSVAHAGDSIVGEGAGPASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDMQLTDRIVQRARAGRMPVLGTGAPLIDTLYTGNAVEAVVAAVSAADHH
+HGEALVVTNGEPRPVGELVRQIALAGGAEEPERHVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLDWTPSVSIGEGLHRLAAYYRAR
+>3_1440
+MGFEVHLGDDGLLQLAERVEHRRVLVTGASGLLGSGVARVLAEAGNPVTTLQRRPSGVPG
+AVDVLGSVTDPAAVERALEGVDTVVHVAAKVSVSGPEEEFAAVNVEGTRILVHAARRRGV
+HRFVHVSSPSVAHAGASIVGEGAGPADPEHARGPYARTKAAGELIALGADADDFRVLALR
+PHLMWGPGDLQLTDRIVQRAREGRMPVLGSGAALVDTLYTGNAVEAVVAAVSAVDHTHGE
+ALVVTNGEPRPVGELIRRIALAGGAPEPERTVPAGVARRAGALIERAWERDLFGVRSSGR
+GSADGEPPLTEFLAEQLSTSHWFDQRRTREVLDWTPSVSMDEGLLRLAAYYRDR
+>4_1225
+MSGFGYDVGLDAAGMPDLVERLESRRVLVTGASGLLGAGVARVLADADNDVTTLQRRPSG
+VPGARDVRGSVTDPAAVEEALTGADTVVHVAAKVSVSGPKHEYEAVNVEGTRILLHAAQR
+HGVRRFVHVSSPSVAHAGDSIVGEGAGAASPEHARGPYARTKAAGERLALAADRDDFRVL
+VLRPHLMWGPGDLQLTDRIVQRARAGRMPVLGTGAPLVDTLYTANAVEAVVAAVSAADVH
+HGEALVVTNGEPRPVGELIRQIALAGGATEPERRVPAGLARRAGALIERAWERDLFGLRS
+RGVGSDDGEPPLTEFLAEQLSTAHWFDQRRTREVLAWTPTVSIDEGLHRVAAYYRDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001105.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001105.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ae98a03b8e21ada00888b1df265352c8081a7ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001105.fa
@@ -0,0 +1,15 @@
+>0_1272
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>1_1002
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQAALWQD
+ETDRLTAGA
+>2_1541
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLPSGGALQFCGHHARAVEDALRPQAAHWQD
+ETDRLTAGA
+>3_1437
+MSITAVAEPAALTRADRCDRCGAQAYVRAVLPSGGELLFCGHHARGVEASLRPQAALWQD
+QTEELDGSTAA
+>4_1227
+MSITAVAEPAALTRSDRCDRCGAQAYVRAVLHSGGALQFCAHHARAVEDALRPQTALWQD
+ETDRLTAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001107.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001107.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1be74a15da42308f7595f2abb990aff4e47387c7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001107.fa
@@ -0,0 +1,33 @@
+>0_1274
+MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD
+VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC
+ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR
+WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGDPGDEERILTAASGRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALSPDDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP
+>1_1004
+MEAPTSLDAPVLPARGPEDLLAYVGHALGRLPEDSLVLLTLHDGRLRAVVRVDLPPEEVD
+VDAWACAVAEVCRRDAAADATLCLALPDGARATLTRPGWAAALDDALASAGRPLAAAWTC
+AHGRARPWWGSSIAEEGTLDPRAAPLSLHLMTRGSVWDRAAVSDPVPRRGPAAARPDDAR
+WRPPEQDAPPARRAWLAQWEPVLTGTARGRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGDPGDEERILTAASRRAPAWDRLDALRAGLRALVPVATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALSPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGRP
+>2_1539
+MWLSQWESVLAGERGAAGPVTAEGTAPVSGTEEHPSADAAVLGAPLTLPSWRDALVLHAA
+VRPGDPPPEPAERERFLIAGSEQAPPWERLDRLRAGLRRLVPAAPPPAAAQALALAGWVG
+WARGQGSDAAAHLAAAAELAPDDPFVTLMRRVVDTGCVAGWAAHPDTAWRPGA
+>3_1435
+MRPRTLEGMDHPPAVPSAVPAGVTPPHLPVLRARGVDDLLGYAFHVLGTEPRESILLVTL
+ARARLRAVVRVDRPGRETPPAARHWAEAVAAVARRDAAADAVVCVSLTGRAGGLEPPGWW
+PPLVRALRDRGIPAREGWGVVAGHAARWPVEPGAGPGPLEEVDPRHSDLSLHLIGAGSVW
+GLRAGHRSVPTPAALDPAAPDRPHWTAARARPEAPGPWLAAWERVLDGGGLPERPAGRAR
+LGAGLEHPARRDALLIAAAGAAADELPAAERAALLTGTRDPGPDWRRLDRLWDALRALAA
+DAPAPCAAPALALAAWICWARGEGTAAGAHLDVARRLAPRDPLVGVLRRILDAGAVCAWA
+ADPRRAWTPWDPQDPASGMRG
+>4_1229
+MEAPTSLDVPVLPARGPEDLLAYVGHALGRLPEGSLVLLTLRDGRLRAVVRVDLPPEEVD
+VGAWACAVAEVCRRDAAADATLCLALPDGARATLARPGWAAALDDALASAGRPLTAAWTC
+ARGRARPWWGSGVAEEGPLDPRAAPLSLHLMTRGSVWDRAAVPDPVPRRGPAAARADDAR
+WRPPEQDAPAARRAWLAQWESVLTGAARDRGAPAPAVLGSPLTRPAWRDGLLLHAAAPSG
+AATGEPGDEERILTAATGRAPAWDRLDALRAGLCALVPAATPAVAAQALALAGWVGWARG
+HGSDADAHLTAAAALNPGDPFVSVLRRIVAAGCVAGWATDPATAWRPDGGGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001113.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001113.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00c0bd9e106a33ed9660db44094cde8f892fd6b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001113.fa
@@ -0,0 +1,55 @@
+>0_1280
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRGRRAAPRRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGL
+WWPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAV
+DVGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTV
+EQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGR
+DGGAAGRTWRVETVDPR
+>1_1010
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWEPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVEGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAAPRRRALALRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTPESGTPARVPDAGAPGEDAAGEDAVD
+VGEALAAVGHARTAALIDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
+>2_1533
+MRDWDEADDGAVGRVGGGPETEPERTSELGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGHAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPEASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALVGRRGAAPRRGVLLAAGLATALAVGGGTAGLW
+WPAAPGSAAEGAPAEGAPEPAGTEPTGTPVDAARPADGTPESGTPARATDTGAPGEDAAG
+ADAVDVGEALAAVGQARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGL
+EVTVEQAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGED
+PEARDGGAAGRTWRVETVDPR
+>3_1429
+MEAEDAERSGGVPPVGRPATDDWFADGGRDVSAWADPPRGGEGPAAVEPGVGDVGSPAEL
+GPADRPPQAPGLRVVSRIGMGGQAEAWLVRREDGTECVLKVPRADGDPDAVAKEAAVYGH
+LRHPHLLRVLGTVDTDRGTGVLSERLPAGSLASMVHDAGPLRPGQAVTVLVPVAQALAHL
+HEHGVVHGDVSPGNVLFGVDGRPALADLGVARVVGGPRGRGGTPGFTAPEDEAGVGEGGA
+AADVYAWGALGWFALTGRAPGPREHRAPLPVLVPDVPVELALLLSAALDPDPAGRPGAAE
+AAVAAYDAAPPEPVPLHESAPAEVAHLLPTVVPPARPGGSGDARRSRPRAGGRRDAGRGR
+GGRKRRNRSPRSRGWHPVMLVGAAVLAGTVVSAAVGGLTDRPEDQGEGAGSRAVAAPPTS
+PTAAPANPRASVTPTGAADPKDAITPTRDGGVPSAAGTGPAAVLPAEDAAAALAAVAEGR
+TAALTDPDPARVDAYAVPDGPAWRRDRAIQDQLREGGSAFSGLVVTLEAVGRPRPAEAGG
+SGGAEAGWVVVPAVLRMSAHTVLDDAGSVVGEVPASEEDVSVTLVPGGEGRWRAAAVDPR
+>4_1235
+MRDWDEADGGAAGRVGGGPETEPERSSEPGTAAPRAPGWAPVRLLGAGAQAEVWLVEDGR
+GVRAALKVPRAGAAPDALAAEAQAGRVAHPHLLRVLGVVETDRGLGVLTEHRAAGTLQDM
+VQRVGPLSPGQAVTVLVPIAQALACLHREGVVHGDVSPANVLFGVDGSPALADLGVARVV
+GGASGAGATPGFAAPEALAAVQGAGAEPGASPAVGAPSDVHAWAALGWYALTGRAPGAAG
+HRAPLPVLVPEASPELALLLDAALSPDPAARPSAEEAAAAVYATARPEPVPLGEAAPAEV
+AHLLPTVLPGSGPTRRRRRRAGPGRRALARRRGAAPRRGVLVAAGLATALAVGGGTAGLW
+WPASLGDATEGAPEPAGAVPAGTSVDAARPADGTRESGAPARVPDTGAPGEDAAGEDAVD
+VGETLAAVGHARTAALTDPEPARLDAYAVPGGPAWENDRDLLRRLTDEGFAFSGLEVTVE
+QAGPARRAGDDALRVDAVLRTSAHTVLDRAGRVAAHREATAEEVVLVLRSGHGEGPEGRD
+GGAAGRTWRVETVDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001115.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001115.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85eb4896a3cfaca5b8b7bfaaec9706ecb946e596
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001115.fa
@@ -0,0 +1,35 @@
+>0_1282
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>1_1012
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVHWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
+>2_1531
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHAFNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLKVLSMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITVTQYVRPSKLHHPIDRWVKPQEFVEWSRRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLEHLAGEKTARQEASAVVAQMS
+>3_1427
+MTTAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNTVKGSGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDIASGRPLPLDMDEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHELNPSTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKEQELVTKSNLILGMGETDEEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVAWSQRAEEIGFAGVMAGPLVRSSYRAGKLYA
+QAMERLGREVPEHLAHLRGERTARQEAAAVVARMS
+>4_1237
+MSLAPEGRRLLRVEARNAEVPVERKPEWIKAKVHMGPEYIGLKNKVKSAGLHTVCEEAGC
+PNIFECWEDREATFLIGGDICTRRCDFCDITSGKPRPLDMEEPQKVAENIREMDLRYATV
+TGVARDDQKDGAAWLYAETIRRIHALNPGTGVEILPPDFGAVPELVQQVFDARPEVFAHN
+LETVPRIFKRIRPAFTYEKSLRVLTMAKADGLVTKSNLILGMGEEDHEIDQALVDLHEAG
+CDIITITQYVRPSKLHHPIDRWVKPQEFVQWSQRAEEIGFQGVMAGPLVRSSYRAGKLYA
+QAMQRLGRTLPENLAHLAGEKTARQEASAVVAQMS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001116.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001116.fa
new file mode 100644
index 0000000000000000000000000000000000000000..894b13a3fb811573328213881a24f7a307ebc4be
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001116.fa
@@ -0,0 +1,30 @@
+>0_1283
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
+>1_1013
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALVVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPGRRAMRGR
+>2_1530
+MTKNSQPPASSSGSTSADLKQVKAMQRDRRRRVKEETRAQRRDKRANRGPGIISQLKQAY
+AMTKANDPKVGLWMLLAFVGVLVLGLVIGLLLNNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVPEQPVAVNPKTQDVVYRAVGRPGVVLVTEGPSNR
+IAALVGKEEKAMRRFLPGVPVTVVEAGNGQGQVPLHELPRTLKSMKKALTAQEVQAVDKR
+VNALNVNRLPIPKGVDPMKARPSRRAMRGR
+>3_1426
+MAKNPSTSPSSSGSSSLKEVKAMQRDRRAQLKADAKAERAQKRANAGPGIISQLKQVFAI
+TRQQNPRLVLWMVLAFASVLVLGLVVGLLLHNWITWLLLAIPFGVLAAVIVMNRLGERAM
+FDRLEGQTGAAGATLSSLGRGWIVGEQPSAVNPKTHDLVYRAIGKPGVVLVTEGPASRVG
+KLVSKEQKAMERFLPGVPVHVVETGRGEGQIPLREVPKTLKALPKKLTAQEVSAVDKRLS
+ALGTQKPPIPKGVDPMRARPDRRGMRGR
+>4_1238
+MTKNSQPPASSSGSTSATLKEVKAMQRERRLREKEQAKAQRRDKRATKGPGVISQLKQAY
+AMTKAHDPKVGLWMLLAFLGALIVGLVIGLLLDNWITWLLIAIPFGVLAAVVILNRKARR
+AGFAQLEGRPGAAGAALSTLGRGWIVSEQPAAVNPKTQDLVYRAVGRPGVVLVTEGPSPR
+VAALVVKEEKAMRRFLPGVPVTVVESGNGQGQVPLHELPGTLKGMKKALTAQEVQAVDKR
+LTALNTNRLPIPKGVDPNKVRPSRRAMRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001118.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001118.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f4f20e94cc75dcd25a2a824daecae4e520bdb60
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001118.fa
@@ -0,0 +1,45 @@
+>0_1285
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>1_1015
+MFTSPADVLAYIKDEGIEFVDVRFTDLPGMQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVGAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>2_1528
+MFTSPADVLAYIKEEGIEFVDIRFTDLPGMQHHFNVPASTVDEDFFTTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICSVLAEVGLEVERSHHEVAAAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
+>3_1424
+MFTSVEDVLAYIKDEGVEFVDIRFTDLPGMQHHFNVPASTVDEDFFVTGQLFDGSSIRGF
+AGLAESDMQLIPDVTTAFVDPFRVRKTLAMNFSIVNPRTGEDYRRDPRGVAQRAEAYLAS
+TGIADTAFFAPEAEFYVFDDVRYESSARSSFYRVDSTEAHWNTSRDEEGGNLGHKTPRQG
+GYFPVTPVDKQADLRDEICAVLAEVGLEVERSHHEVGSAGQAEINYRFNTLTHSADDLQK
+FKYVVKNVAEMFGKSVTFMPKPVFGEAGSGMHCHQSLWLGGEPLFYDEKGYANLSDTARW
+YIGGLLQHASAVLAFTNPTVNSYRRLVPGFEAPVSMVYSQGNRSAGVRIPVTGSNPKAKR
+LEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPPEEAADIQKAPTSLE
+EALNALEEDHEFLLAGDVFTEELIRTWIDYKREMELTPLAARPNPYEFELYYSC
+>4_1240
+MFTSPQEVLTYIREEGVEFVDVRFTDLPGLQHHFNVPASSVDEDFFVTGQLFDGSSIRGF
+AGIAESDMQLIPDVATAFVDPFRVRKTLTMNFSIVNPRTGEPYLRDPRGVAQRAEAYLSS
+SGIADTAFFAPEAEFFIFEDVRYESSPRGSFYAVDSDEAWWNASREDEGGNLSHKTGLKG
+GYFPVSPTDKQADLRDEICAVLAEVGLTVERSHHEVGAPGQAEINYRFNTLTHSADDLQK
+FKYVVKNVANMFGKSATFMPKPVFGDNGSGMHCHQSLWNGGEPLFFDEKGYANLSDTARW
+YIGGLLKHASAVLAFTNPTVNSYRRLVPGFEAPVNMVYSQGNRSAGIRIPITGSNPKAKR
+IEFRAPDASGNPYLAFAAQLMAGLDGIRNRIEPAEPIDKDLYELPAEEAADIQKAPATLD
+EALNALEEDHEFLLAGDVFTEELIETWIAYKREMEIAPLALRPNPYEFELYYSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9007eda0fd4246b0de81941c6911c31c01a604aa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001120.fa
@@ -0,0 +1,45 @@
+>0_1288
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYEVPEAAAEDISALTTHERRVLGHVPLPGTLHDALRTAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>1_1018
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQGQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+QGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLIAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>2_1525
+MDRQQDYVLRTIEDRDVRFVRLWFTDVVGTLKSVALSPAEVENAFAEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGDGGQSSRMFCDVLTPDGRPAPADPRHVLRRVLEKASD
+MGFSCFMHPEIEFYLLTSDQPGPDGRPVPVDRAGYFDNVPGSDAADFRRDAVTLLESMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSEHPG
+SGMHTHISLFEGDSNAFYDPADEFRLSVTGRRFIAGLLRHSVEISAVTHQFVNSYKRLWG
+GGEAPSYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHDPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
+>3_1421
+MDRQQDFVLRTIEDRDVRFVRLWFTDVIGTLKSVALAPAEVEAAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPATFQILPWRGEAGQTSRMFCDVLTPDGRPAPADPRNVLRRVLDKASD
+MGFSCYTHPEIEFYLLASDRPGPDGRPVPVDSAGYFDHVPGGAAQDFRRDAVTLLEDMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVQTFRTIMKEVAARQGHYATFMPKPFGDQPG
+SGMHTHFSLFEGDSNAFYDPADEFRLSVTGRRFIAGLLKHSVEISLVTHQFVNSYKRLWG
+ADEAPAYVSWGHNNRSALVRVPLYKPDKAGSARIEYRGLDASANPYLAYALLLAAGLKGV
+EENYDLPEPASEDVGALTPQERRVLGHVSLPGTLHDAVRAAEESEFVADVLGEHVYEALL
+RNKRQEWDDYRVEITPYELRRYMTGL
+>4_1243
+MDRQQDYVLRTIEDRDVRFVRLWFTDVIGTLKSVALSPAEVENAFTEGLGFDGSSIDGYT
+RISESDMLLQPDPSTFQILPWRGDQEQSSRMFCDVLTPDGRPAPADPRHVLRRVLDRAAD
+RGFTCFTHPEIEFYLLQSDQPGPDGEPVPVDRAGYFDNVPGSDAADFRRDAVSLLEGMGI
+SVEFSHHENGPGQNEIDLRAADALTTADNVMTFRTVVKEVAAAQGTYATFMPKPFSHHPG
+SGMHTHFSLFEGDANAFYDPADEFRLSVTGRRFIAGLLRHSVEITAVTHQFVNSYKRLWG
+GGEAPSYTSWGHNNRSALVRVPLYKPDKAGSARIEYRGIDASANPYLAYALLLAAGLKGI
+EEGYELPESAAEDVSALTTHERRVLGHVPLPGTLHDALRAAEESEFVASVLGEHVFDALL
+RNKRQEWDDYRVEVTPYELRRYLSGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001123.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001123.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f50144f0f37f7b23788256323d1d7b9484a04192
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001123.fa
@@ -0,0 +1,35 @@
+>0_1292
+MSQRQNPVAPSSHNGPRPAGPTAPEPGSFAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGVERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>1_1021
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGNASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
+>2_1522
+MSHRQSTASPSSHNGPRPEGPAAPQPGSLAPVGTLTPGAPSPAPPVPASIPRPEYVGRAT
+ADEGNASDVYDAAGIERIRAAGRLAARAMEHTAAYIRPGVTTDELDRIAHAYLVEHGAYP
+SCLGYRGFPRSICTSMNEVICHGIPDSTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLEPGMVFTIEPMLTLGTIDWDQWDDGWTVVTRDRRRTAQFEHT
+LVVTDDGAEILTLP
+>3_1418
+MSTTARPTSQPSHNGPRPEGPPAPEPGSRAPLGTLTPGAPSPAPAVPASIVRPEYVGRAT
+ADEGNASDVYDTEGIGRIREAGRIAAQAMEHTAEHIRPGITTDELDRIAHEFIVAAGAYP
+SCLGYRGFPRSICTSVNEVICHGIPDGTVLEDGDIVNLDITAYKDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIKAVKPGREINVIGRAIESYARRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHNRLMVPGMVFTIEPMITLGGIDWEQWDDGWTVVTKDRRRTAQFEHT
+LVVTEDGAEILTLP
+>4_1246
+MSQRQNPAVPSSHNGPRPAGPTAPEPGSLAPVGTLTPGAPSPAPPVPAAIPRPEYVGKAT
+PDEGKASDVYDAAGIERIRAAGRLAAQAMEHTAAHIRPGVTTDELDRIAHAFLVERGAYP
+SCLGYRGFPRSICTSINEVICHGIPDGTVLEDGDIVNLDITAYLDGVHGDHNRTYLVGDV
+DEESRLLVERTEEALRRGIRAVKPGRQVNVIGRAIESYAKRFGYGVVRDFIGHGVGVDFH
+SGLVIPHYDAAPAHDRLLVPGMVFTIEPMLTLGTIEWDQWDDGWTVVTRDRRRTAQFEHT
+IVVTDDGAEILTLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001124.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001124.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e63cdb0ec58d6291cc2b75927a8b040c99fb90bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001124.fa
@@ -0,0 +1,20 @@
+>0_1294
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>1_1023
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
+>2_1520
+MHCPFCRHEDSRVVDSRSLEDGSAIRRRRQCQSCGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRASGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFADAIAELRAGTDERGRPAVQPRLFSR
+>3_1416
+MHCPYCRHEDSRVVDSRSLEDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVSSDDLAVLAQEVEEAVRASGNAEVDAHEVGLAILGPLRRLDQVA
+YLRFASVYRDFESLSDFEDAIAELRAQEGEAPGRPAVQPRLFSR
+>4_1248
+MHCPFCRHEDSRVVDSRSLDDGSAIRRRRQCQACGKRFTTMETTALTVVKRSGVAEPFDR
+SKVINGVRKACQGRPVTSDDLAMLAQEVEETVRATGNAEVDAHDVGLAILDPLRRLDQVA
+FLRFASVYRDFESLDDFEEAIAELRAGDGDDRGRPAVQPRLFTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001126.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001126.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f43b2f3901141cdab44e1e60d4d9e267244ec90
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001126.fa
@@ -0,0 +1,35 @@
+>0_1296
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLEDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>1_1025
+MGMRPGLTERLQVAEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGYDITTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYATLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDED
+>2_1518
+MEPIPGATARIEVTPDRAGRRADAVLAEVLGLSRSALADWFSRGLVRAESRTGRRDRVLA
+KSAKAVAGEVLAVDVPDDPDPLEVRAERVDALRILHEDEHLIAVDKPTGVAAHPSPGWAG
+PTVVGALAALGHDISTSGAPERQGIVHRLDVGTTGVMVVAKTEQAYAALKDQFRRRVPEK
+VYHALVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDGGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRLAAELGLTRQWLHAHRLSFPHPVTGEPVSV
+TSEHPDDLAHALARLRRDGS
+>3_1414
+MGLRPGLTERLAVTEDDAGRRADAVLADAFGVSRASLADLFSRGLVRAESRTGRRDRVLA
+KSAKAVAGETLAVDVPVDPDPLEVRAERVDAMTVLYEDDDLLAVDKPTGVAAHPSPGWFG
+PTVVGGLAGLGRRISTSGAPERQGIVHRLDVGTTGVMVVAKSERAYTALKDQFRERVPEK
+VYHAVVQGMPDPLEGTIDAPIGRDPNHHWRFAVLEGGRPSVTHYETVEAFGRATLLEIHL
+ETGRTHQIRVHTSALRHPCAGDLTYGADPRLAAELGLTRQWLHAHRLALPHPATGERLEI
+VSPYPDDLAHALRVLRGEDRGAAPDA
+>4_1250
+MGMRPGLTERLEVTEAEAGRRVDAVLADAFGVSRSLLADWFSRGLVRAESRSGRRDRVLA
+KSAKAVAGETLAVDVPDDPDPLEVRAERVDALSILYEDEDLVAVDKPTGVAAHPSPGWVG
+PTVVGALAALGRDISTSGAPERQGIVHRLDVGTTGVMVVAKTERAYTAMKDQFRERVPEK
+VYHAVVQGIPDPLSGTVDAPIGRHPGHHWKFAVLDDGRPSVTHYETLEVFGRATLLEVHL
+ETGRTHQIRVHTSALRHPCVGDLTYGADPRMAAELGLTRQWLHAHRLAFPHPVTGEPVTI
+TSPYPDDLAHALAALRGDAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001128.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001128.fa
new file mode 100644
index 0000000000000000000000000000000000000000..122dff8a4d4b2d8bf852d9f66be00555f3a0f640
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001128.fa
@@ -0,0 +1,25 @@
+>0_1298
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAGPAADTPEAAATPASAEESAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
+>1_1027
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APVADTPEAAETPSPVEEPAPAAAPEAADAAATSAAGVLAMAQRLHDEHVAAGEQRSTEL
+VAEAEATAARLVSDAEEQKARTLEALAEERAGLEGEVEQLRSFETDYRSRLTSYIEGQLR
+EIRAQKRVEPPTPTA
+>2_1516
+MALSWEDVVNKQFQPTKFREGYDQGEVDDFLDEIVGELKRLQGLNEQLTAENEALRAGGA
+VPDADAAVDAPVADADAAAVVDAGQSPAPAALADAEPGLEVEPTPSSADPASASAAGVLA
+MAQRVHDEHVAAGEQRRDELISEAEARAEALVAEAEETRTRTLEELAADKAGLEAEVEQL
+RGFETDYRSRLTAYIEGQLREIRSQERVEPAQRPA
+>3_1412
+MVLSWEDVVNKEFQLTKFREGYDREEVEDFLDEVVEELKRLTEENDRLRSDLDACREGAP
+AQAEASAPAAGEAAPALQAPAPVAPVEPSAPGEPVAPTDSATSAAGVLAMAQRLHDEYVA
+EGEQRRDRIIADAEAEATTVVRQAEETRTRTLSDLESRRKGLEADVERLRAFETDYRSRL
+TAYIEGQLREITAQERLEPAKGTV
+>4_1252
+MALSWEDVVNKQFQPTKFREGYDQTEVDDFLDEIVAEFKRLIALNEQLESENAELRAGGA
+APAAAPAADTPEAAATPASVEEAAPAAAPESADAAATSAAGVLAMAQRLHDEHVAAGEQR
+STELVAEAEATAARLVSDAEEQKARTLEALAEEKAGLEGEVEQLRSFETDYRSRLTSYIE
+GQLREIRAQKRVEPPTPTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001131.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001131.fa
new file mode 100644
index 0000000000000000000000000000000000000000..647ea88cd4a9ceb7803a8f9db77d4fab931f4ee0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001131.fa
@@ -0,0 +1,30 @@
+>0_1301
+MTAPATAGPTPTDPRAREIADALAAVHARIADAARDAGREAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALVLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+ADVIAGLPGLRLGGLMCVAPRGLDPEHAFRRLAALGARLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG
+>1_1030
+MTAPATAGPTPTDPRTREIADALAAVRARLADAARDAGREAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+TDAIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAHLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG
+>2_1513
+MSTPEQHPTPHDAAAETRTREIAAGLAAVRERIARAAREAGRADEPALVVVTKTHPAEDV
+VRLAGLGVAAVGENRDQEARPKAAAVAEALGDAAPRWHFIGQLQTNKAKHAARYASVVES
+VDRTELAEALSRALVLRREREPGVEVPDLECLVQVDVDDRADEDRPEGIGPRGGAAPEDV
+PALAAAIAALPGLRLGGLMCVAPRGLDPEASFRRLAALGEELRSAHPDASTLSMGMSADL
+ESAVRAGATQVRIGSDVLGARPAVG
+>3_1409
+MAEPLQDDPRVAEIAAGLDGVRRRIADAAAAAGRADLPELIVVSKTHPAEDVVALAGLGV
+RQVGENRDQEARPKAAAVAEALGGAGVPAPAWHFIGQLQTNKAKHVARYASAVHSVDRLD
+LVDALSRAVVLRREREGADAVSALDCLVQVDVDDRADEDRPEGIGPRGGAAPEDVPELAR
+AIAAADGLRLRGLMCVAPRAADPAAAFARLAALSARVRAEHPDADALSMGMSGDLEAAVA
+AGATHVRVGSDILGARGAVG
+>4_1255
+MTAPATAGPTPTDPRAREIADALAAVRARIADAARDTGRAAEPALVVVTKTHPAEDVVRL
+AALGVTDVGENRDQEARPKAEAVAAALGADAPRWHFVGQLQTNKAKYVVRYASVVESVDR
+PELAEALSRALLLRREREPEAAIPDLECLVQVDVDDRADEDRPEGIGPRGGARPEDVPAL
+ADVIAGLPGLRLGGLMCVAPRGLDPEDAFRRLAALGAGLRQTHPEATALSMGMSADLEAA
+VRAGATQVRIGSDVLGARDAVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001133.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001133.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bbead0a898a0cda75afedbbc929b89f60b471882
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001133.fa
@@ -0,0 +1,41 @@
+>0_1303
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPAQPQPAAQPQPAAPAQPQQAE
+RPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>1_1032
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAAQQQAAPQRAAAPAQPQPVPAQPQQAERPAVRGT
+VPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>2_1511
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPASPQAGQFQQAPQRPAQQAQPQQQAPAPQQHQAQPA
+QQEQPQQVQPQSVRGTVPLAPQQPQQTEQRRQQDLPTVVEPDLGAGSSDLDVPDFLK
+>3_1407
+MDTVAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLD
+VGRELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARI
+ARSLGALTIGVVTRPFTFEGRRRAGSAENGIDALRDEVDTLIVIPNDRLLSISDRNVSVM
+DAFRQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKA
+AELAIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDD
+ALGDEVRVTVIAAGFDKVDATSAPAAPFQQQAAPQRAAAPQQPAQQAQQAPVSQQAAPQR
+PSVPGTMPLNSSSAFGGAPAQPAATQQPAAPQQPAAPQRAQQDLPTVVEPEFGSSDLDVP
+DFLK
+>4_1257
+MAAPQNYLAVIKVVGIGGGGVNAVNRMIEVGLRGVEFIAINTDAQALLMSDADVKLDVGR
+ELTRGLGAGANPEVGRQAAEDHAEEIEEVLRGADMVFVTAGEGGGTGTGGAPVVARIARS
+LGALTIGVVTRPFTFEGRRRAGSAEAGIDALRDEVDTLIVIPNDRLLSISDRNVSVMDAF
+RQADQVLLSGVQGITDLITTPGLINLDFADVKSVMQGAGSALMGIGHAQGEDRAVKAAEL
+AIASPLLEASIDGAYGVLLSIQGGSDLGLFEINEAARLVQEVAHPEANIIFGAVIDDALG
+DEVRVTVIAAGFDKVDVTSAPAAPQAVQQQAAPQRAAAPTQPHPVPAQPQPAPAQPQPAP
+AQPQQAERPAVRGTVPLAPQEQQPRRQQDLPTVVEPDLGAGSSDLDVPDFLK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001136.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001136.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c93461c726fb96cbc70677f3a0efe3378566c89c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001136.fa
@@ -0,0 +1,40 @@
+>0_1306
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>1_1035
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEGDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAARRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
+>2_1508
+MPQTPDPARELRVVLAGGGTAGHISPMLAIARALESDDAGPVRCTMVGTASGMETRLVPE
+AGYELDLIERVPMPRRPSMDVVHFPARMRAAVAAAGRILAERRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRAAHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAQRRAARAALGLDPERTTVVVTGGSSGALAVNRTVRDSLDDLLGAGLQVFHLTGRDKAL
+TEADGTPLRREGYVQREYLDGMEQAYAAADLLVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALTVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAEEGARR
+>3_1404
+MTTPNDASRPLRVVLAGGGTAGHISPMLAIARALGRQDPSTVCTMVGTDSGMETRLVPQA
+GYELDFVERVPMPRRPSMDVVRFPGRFQASVRQAGEILRRRGADVLVGVGGYVSTPMYLA
+ASRAGVPVVVHEANARPGLANRVGALRAARVGTALPDTRLPKAQWVGMPMRPEISGLDRA
+AARDAARAELGLDPERTTVVVTGGSSGALNVNRTVRESLDDLLGAGLQVFHLTGRGKELT
+DEAGQRVTRPGYVQREYLDGMEKAYAAADLIVARSGAGTVCEIAAVGLPAVFVPLPVGNG
+EQALNARPVVDAGGALLVRDETFRADWVRRELIPLATDPQRLAAMGEAAARLGVRDADVR
+TADLVREAAREGARR
+>4_1260
+MTQTSHPSGPLRVVLAGGGTAGHISPMLAIARALEDDGGGPVECTMVGTASGMETRLVPE
+AGYELDLIDRVPMPRRPSMDVVRFPARMRAAVATAARILRDRRADVVVGVGGYVATPVYL
+AAFRAGVPVVVHEANARPGLANRIGALRATHVGTALPDTRLRGARWVGMPMRPEISGLDR
+AAAGRAAREALGLDPDRTTVVVTGGSSGALAVNRTVRAALGDLLDAGLQVFHLTGRDKAL
+TEDDGSLLVRDGYVQREYLAGMEQAYAAADLIVARSGAGTVCEVSAVGLPAVYVPLPIGN
+GEQALNARPVVEAEGALLVRDDAFGRAWVQRQLIPLATDPERLARMGEAAARFGVRDADV
+TMAGLVRSAAQEGARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..143a64a88888cbb12a4c05cd221f448dd546c29b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001142.fa
@@ -0,0 +1,25 @@
+>0_1313
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAEQVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
+>1_1042
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPAPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVIETNERLAEQVGNLEAPQNLAARADALG
+MVAPAGTASVDAGTGEFGGEAQAAQDGDVSATYVAPPADADVVRQGASAEGQDEIEGPRT
+LGGEDASAAADQDAADR
+>2_1502
+MTLHEEMSMAAHARIAEPLRHTGAPARPAPQERTPLSVVPAPLPRSRSGMTVLCVVVLLA
+ALAAVLVMNITMSNRQYALLDLRQEQQAVTEVNERLAEQVGYLEAPQNVAARADALGMVA
+PAGTASVDAATGEFRGEAQPAREGEISATFVAPPVNADAVRQGSAGSADADRGDIEGPRT
+LGAPAAAPGAAASDDRDASDR
+>3_1397
+MTAYEETGMSAQAWRDEARTAWPRTGATPEREHRQRTPLSVVPTPLPRSGSGVAVLCGLV
+LLVALGLVLVMNITMSNRQFTLLDLRAQQTTLTETNERLAEQAGYLDAPQNLAARAGAMG
+MVSPGATSTVDVASGAVAGPSTGAGSTTLPEGRIAPPADADLARQGEAQGQIPGPRTVDP
+AAPTAAPSGETAPTPAPTDAPAGR
+>4_1267
+MTLHEEMSMAAHARIAESLRPGSTPVAPARPTPQERTPLSVVPAPLPRSRSGVTVLCVLV
+VLAALAAVLVMNITMSNRQYALLDLRQEQQAVTETNERLAERVGHLEAPQNLAARADALG
+MVAPAGTASVDAGTGQFSGEAQAAQDGDISATYVAPPADADAVRQGTAGDGQDEIEGPRT
+LGGEDASAAPDQDAADR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001143.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001143.fa
new file mode 100644
index 0000000000000000000000000000000000000000..811060f2e42938ee3e08ecd1c229a585d752acc3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001143.fa
@@ -0,0 +1,35 @@
+>0_1314
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
+>1_1043
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAAERLGPLADRLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSAKVRAVEKIRTSRTTA
+>2_1501
+MDADQLRPEDRHVPVMRDRVVDLLAPAVQAALDAGRAPVAVDGTLGMGGHTEAMLTRFPE
+LTVIGIDRDAHAQALAAERLGPLAERLVPFHGTYDLVPEAMAAAGVEKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEHELRRIIRRDGEERFAGPIAR
+AIVRARAEAPIETTGRLVEVIRTAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRIAKRHLSAWAASTAPPGFPVVLEEHEPVVRTLTRGTE
+KPTEEEILENRRASSAKVRAVEKIRTSRTPA
+>3_1396
+MDPTQPLPRDRHVPVMRDRVVDLLAPAVEAAAAAGRTPVAVDGTLGMGGHTEVLLRRFPT
+LRVVGIDRDPNALAMAQERLGPLAERLVPFHGTYDQVPEALAAAGAERMDAALYDLGVSS
+YQLDARERGFAYSYDAPLDMRMDTTAPVTAADLVAELDEQSLRRIIRRDGEDRFAGPIAR
+AIVRAREEEPILTTGRLVDVIRAVVPVSAGNKGGHPAKRTFQALRIAVNEELDILDAAVP
+AVLDALEVGGRLVVMSYHSLEDRIAKRHLQEWAASTAPPGFPVELPEHRPLVKVLTRGTE
+KPTEEEIEENRRASSAKVRAVEKIRTSRTTA
+>4_1268
+MDAGQPRPEDRHLPVMRDRVVDLLAPAVQAALEAGRTPVAVDGTLGMGGHTEALLTRFPH
+LRVIGIDRDVHAQAMAVERLGPLAERLIPFHGTYDRVPEAMAAAGVTKVDAALYDLGVSS
+YQLDDRERGFAYSYDAPLDMRMDDTAERSAATLVAELDEQELRRIIRRDGEERFAGPIAR
+AIVRARDEAPIETTGRLVEVIRSAVPVAAGATGGHPAKRTFQALRIAVNEELDILDAAVP
+AILDALHVGGRLVVMSYHSLEDRITKRHLSAWATSTAPPGFPVVLEEHEPVVRVLTRGTE
+KPTEEEISENRRASSARVRAVEKIRTSRTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001145.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001145.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5575235a149d5757e45dc34600a3cc296b4652e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001145.fa
@@ -0,0 +1,20 @@
+>0_1316
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>1_1045
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
+>2_1499
+MPLSEHEQRMLDQLEHQLRTEDPRLATQMADTRRDPVPVKRVVLGAVLAVVGLLVIVMGV
+ANQLVPVGVLGALVVGAGIFLVTTRPRGGRAAGADRPGPGRGGRPGGGRPEGGRPGGDFM
+GRLERRWDARREQGD
+>3_1394
+MPLSDHEQRVLDELERQLHADDPSLASQLSTPRGPAPVRRIVLGAAMMLAGLAVVLVGVS
+THLVVVGVLGAVLLGGGILVLTSRRVSASRAPGAPVAGDGGPHAGRRRGGLMDRLDREWD
+SRGRADT
+>4_1270
+MPLSEHEQRMLDQLEQQLRTEDPRLATQMADTGRHRLPVGRVVAGAVLAVVGLLVVVLGV
+ANHAILLGVLGVVVIGAGIFLLTTRPRAVASGASGPEARRSGAPRRQGGGDFMGRLERRW
+DERRAGGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001146.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001146.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05f96c19f23e1308fc5b81f1948df9f382731106
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001146.fa
@@ -0,0 +1,44 @@
+>0_1317
+MSETAPAAPRDEATILHVDMDAFFLSVELRERPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQATAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>1_1046
+MSESAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSALGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPQRTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEQVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPVRLVGVRAERLGDEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
+>2_1498
+MSDTAAAQARPEASILHVDMDAFFLSVELRERPDLTGRPAAVAAPSGRSVVLSASYEARA
+YGVRSAMPLAHARALCPPLVVVPPRQDVYRSVSADVMALLGQVTPVLEQLSVDEAFLDVA
+GARRRLGPPARIGGLIRRRVREELGLPCTVGAAGVKFVAKMASTAAKPDGLLVVPPERTL
+EFLHPLPVGRLWGVGPKAAEALRRRGMATIRDLAAADPEQLERAFGAAGRSWAQLSRGID
+PRPVAPRPAARSIGADHTFDVDPLDVAGVDLEVLRLCHRVAARLRAEEVAAGAVTVRLKD
+PDGRVRSRTARLARPTTTAHGLLGPARRLVAELHAQRPHPVRLVGVRAERLTDADEPAPE
+QEALFGGSGFGDDDAAEGGAGDWAGAEAAADAVARRFPTAAVRPASLLRRAAGRPDTRRD
+VPGP
+>3_1393
+MSAPDPGPAPSSPPPPRREPSILHVDMDAFFLSVERRERPELRGVPAAVAHPEGRSVVLS
+ASYEARAYGVRSAMPLAQARALCPPLRVTPPRQELYRSTSARVMDLFGRVTPVVEQLSVD
+EAFLDVAGARRLLGPPERIAALIRERVRAELGLPCTVGGAGVKFVAKMASTAAKPDGMLL
+VPPQCTLAFLHPRPVGALWGVGPQAARRLRERGVETIGDLAARDPRWLREAFGAAGAAWA
+ELAAGRDPRPVAPREPARSVGADHTFDVDARDPAALDREVLSLCHRVAARLRSGGHTAAA
+VTVRVKDPALATRARTVRLPAPTASGRVLHAHAGPAVAGLLTERPHPVRLVGVRAERLSD
+AEAHGAVQEALFAPEGHEGPTDDAGWRRAEEAADAVARRFPGAGVRPASLLGPPEGS
+>4_1271
+MSETAPAAPRDEATILHVDMDAFFLSVELREQPDLEGRPAAVAAPSGRSVVLSASYAARA
+YGVRSAMPLAHARALCPPLVVIPPRQQLYRAVSAEVMAVLADVTPVMEQLSVDEAFLDVA
+GARRRLGPPEHIGHLIRERVRSELGLPCTVGGSAVKFVAKTASTAAKPDGLLIVPPERTL
+DFLHPLPVGRLWGVGPKAAERLARRGVATIGDLARVDPARLEASFGAAGREWASLARGID
+PRPVAPRPAARSIGADHTFDVDPVDVAGVDPEVLRLCHRVAARLRAEGVTAGAVTVRLKA
+PDGSVRSRTARLARPTATGHDLLGPARRLVRELHAERPHPIRLVGVRAERLGGEADQPPA
+QEALFGGPAWGTEGEASEAGDWAGAEAALDAVARRFPTAAVRPASLLGRREARADARRDA
+PRPGPGGPDRE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001149.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001149.fa
new file mode 100644
index 0000000000000000000000000000000000000000..676601a1f8a4a5b01571d33ea20df6178812c433
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001149.fa
@@ -0,0 +1,40 @@
+>0_1320
+MPRSAVPHTPVRSRCLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTTPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRAVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>1_1049
+MPRSAVSHTPVRSRRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDTLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAVGTYTVQPNDGWWIIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKTPASTAPATTPASAPASTAPAAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIIRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGIAFIKYVQDRTPTLDQ
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
+>2_1495
+MPRSSVSHTPSRRLRHALAGGAVPLLLLTGLPAQAQAQEAPVHTVRPGDTLTAISAAHGV
+PLVDLFRLNGLDHESIIYPGDAIRLTGEAAPAAAAGTYTVQPDDGWWIIARRTGVSAAEL
+QRLNGMSASTMLHPGMVLTTAGKAAAPAPTPAPPRCSLAPATRDVVRYAVVSGDSMWGIS
+QRFEMSIPRLRELNGLTRSSMLHPGQVLVISDGTLEVEPVSDVQPIGDTFLGRTYPAHVT
+ASANENLRLLQSVPQPSPEQMREIVRETAVRMDVDPRLALGHAYTESRFRMASVSPANAI
+GAMQVIPITGEFASELVGRELNLLDPYDNAVAGVAYIKYVQDRTPTLDTGIGAYYQGLGG
+VLQGGLSAEGRTYVATVRAAMAMF
+>3_1390
+MPPARKVTPLMPQPAAPRASATTARRSLGLVAGGVVPLLMTGALPVAAQAAEAAHAAPRT
+HTVRAGENPYRIAEAEGVRLSDLLRLNGLRADSVIYTGQVLALTGAPAPAAAPGTVEVER
+GEGWWQVSRRAGVDAAVLQRINGLGARSMLHPGQILLTEAPARPTTPATPVAAAPAPVRQ
+AAPTTYTVRNGDSMWSISQRVEVSIPRLRELNGLTWRSVLHTGDVLVIADGTEQAPVIDG
+PVGSTFLSTTYAPHVTASANDNLRALQAVPQPSPAEVQALVRQTALELGVDPALALGHAY
+TESRFQHASVSPGNAIGAMQVIPITGEFASQLVGRELNVLDVRDNVTAGVVLIKYLQEHT
+DTVDQGISAYFTGLGGSDDPVKQQEARNYVARVKAAAAMF
+>4_1274
+MPRSAVPHTPVRSHRLRSVLTGGAVPLLLLTGLPAQAHAQEAAVHTVRPGDSLTRISAAR
+GVSVADLLRFNGLGLETVLYPGDELRLTGAAAPAPAAGTYTVQPNDGWWVIARRTGVSAA
+QLQRLNGMSASSMLHPGMVLTTQRTAAAPKAPASPAPTTTPATAPASTAPTAAGGTVRYT
+VVSGDSLWGISQRFEVSIPRLRELNGLTRASTLHPGDVLVISDGTLEVEPVSAVQAVGDT
+FLGRTYAPHVTASANENLRLLRSVPQPTPEQMQQIVRETAERMGVDPRLALGHAYTESRF
+RMASVSPGNAVGAMQVIPITGEFASELVGRELNLLDPHDNAVAGVAFIKYVQDRTPTLDE
+GIGAYYQGLGGVLDSGLNPEARDYVAKVRAAMAMF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001152.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001152.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8580697618f12ff322087731deaa6cf4fea6df49
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001152.fa
@@ -0,0 +1,30 @@
+>0_1324
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
+>1_1053
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAAVGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDHDLP
+LLIDHGRSAVAAMTTH
+>2_1490
+MDRPVPPVEPAPPAVPAPAVDPVHLPLRLAPGSGAGADRCVVVLHGFTSGPDSVRAWAEG
+IAAGGSHVSVPLLPGHGTRWQDLAATGADEIRGAVRETVDRELSRHRHVVVAGISMGGAL
+ALDAAAHRPVSAAIVVNPALRFASPLAPLAPALAPFVPSVAPIANDIADPDARELAYPRT
+PVAGVAAVGRIQRAARRALPRITAPVTVFRSARDAVVPAASHRTLLRGLRRAPVDVVPLP
+RSRHVATLDYDLPLLIERSRAAVEAATRA
+>3_1386
+MTRLRPAAPDRRPAPGVDPAQRPFRLPATSLPGVAVVMLHGFTSGPDSVRAWAEGVAAGG
+AAVHVPLLPGHGTRWEDLGTTDADELRAAVRDAVDAALATHRRVVVAGISMGGALALDAA
+AHRDVAGVLVVNPALRFGSPLAVAAPLLRHVVPSVPSIAGDIADPDARELAYERAPVAGV
+AQVGRIQTAARRGLGRITAPVTVFRSAEDAVVPERSHHTLLRGLTAAPVEVVRLLHSRHV
+ATLDRDLPLLVARSRDAVAAAAR
+>4_1278
+MPRPVAVAPEDLPLRLMPAAPARRDHCVVLLHGFTSTPASVRAWAEGLAAGGSPVSVPLL
+PGHGTRWEDLAATGADEIRAAVRAVVDLELARHGRVVMAGISMGGALALDAAAHRPVAGV
+LVVNPALRFASPLAPFAPLLAPFVPTVAPIADDIADPTARERAYPRTPVAGVAALGRIQR
+AARRALPRITAPVTVYRSARDAVVPASSHRTLVRGLRQAPVEVVGLPRSRHVATLDYDLP
+LLIDHGRSAVAAMTTH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001160.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001160.fa
new file mode 100644
index 0000000000000000000000000000000000000000..32c7664e3f11f770705b619a3653b43afea727e0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001160.fa
@@ -0,0 +1,20 @@
+>0_1332
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>1_1061
+MSSIPEGLKYSAEHEWIAKAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
+>2_1482
+MSSIPEGLKYSAEHEWIAEAGQAGTVRIGITDFAQDALGDVVYVDLPEVGSEVTAGTAVG
+EVESTKSVSDIYAPVTGTVAAVNEDLDGEPGLVNSAPYEGGWLFEVTLADEAQLEGLLDA
+EGYASHTS
+>3_1377
+MSSIPEGLKYSTDHEWAQDAAEPGVVRVGITDFAQDALGDVVYVDLPSVGDEVTAGAAIG
+EVESTKSVSDIMAPVSGTVTAVNEELDGEPALVNSAPYEGGWLVEIKLSDPAEVDGLLDA
+AGYAAHVG
+>4_1286
+MSSIPEGLKYSAEHEWIAEAGAAGTVRVGITDFAQDALGDVVYVDLPEVGTEVTAGTAVG
+EVESTKSVSDIYAPVSGTVAAVNDELDGEPGLVNSAPYEGGWLFEITLADEAQLEGLMDA
+EGYASHTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001170.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001170.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eddedb943241897ac794f805467f9193053bbbf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001170.fa
@@ -0,0 +1,40 @@
+>0_1367
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFEHFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESRQDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>1_1107
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWTGELPT
+DEELTAFERFERTHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQEVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
+>2_1454
+MTETEIKKGLAGVVVDTTAISKVNPDTNSLLYRGYPVQDLAAKLPFESVALLLWNGELPT
+DEELAEFQRFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAAVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLQSAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPLFIASRITGWTAHIMEQRAA
+NALIRPLSSYDGPEQRELPAG
+>3_1361
+MTETEIKKGLAGVVVDTTAVSKVNPETNSLLYRGYPVQDLAAQLPFEAVALLLWNGELPT
+DAELEEFQRFERAHRALDPEVKAAVDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAKALFAAFPAVVAYDQRRRRGQEVVEPRADLDYAQNFLWMSFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTEMFTPIFIAARITGWTAHIMEQRAA
+NALIRPLSAYNGPEQRELPGK
+>4_1316
+MTETEIKKGLAGVVVDTTAISKVNPETNSLLYRGYPVQDLAAQLSFEAVALLLWTGELPT
+DEELAAFERFERAHRALDPKVKQAIDLLPTDCHPMDVGRTAVSVLGANHPKAEDSSPEAE
+LEKAQALFAAFPAVVAYDQRRRRGQDVVEPREDLDYSQNFLWMTFGEEAAPEVVDAFRVS
+MVLYAEHSFNASTFTARVITSTLSDLHSAVTGAIGALKGPLHGGANEAVMHTFDEIGIRK
+EESREDAAARAKAWMEDALAQKKKVMGFGHRVYKNGDSRVPTMKAALDRMIEHYGREEML
+GLYDGLEQAMDEAKQIKPNLDYPAGPTYHLMGFDTELFTPIFIASRITGWTAHIMEQRAA
+NALIRPLSAYDGPEQRELPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6a61a8566ae436bc81827951b0ae48e8e5e5177f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001171.fa
@@ -0,0 +1,35 @@
+>0_1369
+MSADPAPRGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRWLEAQG
+VRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPAL
+DVHPPKPGARLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVD
+DVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMAGAARSTPA
+LFVNACGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLG
+HASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>1_1109
+MSTDPAARGSGEAEARGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERYRRW
+LEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPLAVRSAARVLAAVRGLHRFWALEGLTP
+ADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVV
+GLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVT
+RSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVV
+QELLGHASVTTTQVYTLVTVDSLREVYSAAHPRAR
+>2_1452
+MSTDPAARGSGEAEARGSRGGRGAESALAAPFRRHLEHLAVERGLAANTLAAYRRDLERY
+RRWLEAHGVRAPADVDPGHVSGFLRALGTGEDGGRPFAVRSAARVLAAVRGLHRFWALEG
+LTPADPARDVHPPKPGDRLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARIS
+EVVGLDVDDVVGLAQTGDDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMT
+GAARSTPALFVNARGGRLSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADV
+RVVQELLGHASVTTTQVYTLVTVDSLREVYAAAHPRAR
+>3_1360
+MSASPELHRALDRHLDHLAVERGLASATLAAYRRDLGRYLAWLEASRVDRPADVDPGHVA
+GFLSALGTGDDGGRPLGARSAARVLSAVRGMHRFWALEGLTPTDPAADVAPPRPPERLPK
+ALPVETVTRILEAVPTAEPADLRDRALLEFLYGTGARVSEAVGLDVDDVVGVAGDRGAGR
+GDDDRLPVVRLFGKGSKERLVPVGSHAADALAAWLVRGRPALAAAATRPVPALFLNLRGG
+RLSRQSAWSILKAAAERAGVAQDVSPHTLRHSFATHLMQGGADVRVVQELLGHASVTTTQ
+VYTRVTAEALREVYASAHPRARWTT
+>4_1318
+MSPHAPQTSALAAPFRRHLDHLAVERGLAENTLAAYRCDLARYRRWLEAAGVRAPGDVDP
+GHVAGFLQALATGDDGGRPLAVRSAARVLAAVRGLHRFWALEGLTPADPARDVHPPKPGD
+RLPKALPVEQVTALLEAVPVDTPAGLRDRALLEFLYGTGARISEVVGLDVDDVVGLAQTG
+DDGGQPVVRLFGKGSKERVVPIGSYAAAALDAWLVRGRPTIMTGVTRSTPALFVNARGGR
+LSRQSAWAVLKRAAERAGLEADVSPHTLRHCFATHLLAGGADVRVVQELLGHASVTTTQV
+YTLVTVDSLREVYSAAHPRAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001173.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001173.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5eaf25c17284900dd1a921460d6898522e955f6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001173.fa
@@ -0,0 +1,55 @@
+>0_1371
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRVTADHAALRLAQEAGAVVDEGDNGTHDLVLSRSVTASGDGTRSRATAGGRS
+VPVGLLSEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPREGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPDLAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>1_1111
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDTMDETPGAVSLVEAAQQAVLAAPGDDPELAAAAARLAEAAVVLTDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTAAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
+>2_1450
+MIEHLRISGLGVIGEATVDLDPGLTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGAA
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADDGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGAEAQRRALDAFGGAELAASLRAYRADHAAVSAA
+RRERDELTAHRQERAREAEALQRSLEEIDLAEPLAGEDAELRELIRRLEDVEELRAASGE
+AHARLAGAEMDALEETPGAVSLVEGARQAVLAAPGDDPALAAAAERLAEAAVVLTDIAAD
+LARYTADLDTDAASDLDAAQSRLAELTRLQRLYGPELEDVIGWAETQRPRLDELQGDSGR
+LEELEGELERLESALRERAAALTALRTAAAGRLEEAVTQELHALFMPDASFHVDLAPVGG
+DGLGPHGAEDVALALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLSAEERVEELARMLAGHGDSAAAREHARELLEASARERG
+>3_1358
+MIDWMQITGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGRRADAGAVRRGSR
+RAAVDAGVRLPADHPALSLAVEAGAVLDDAGDGSADLVLSRSVTASGDGTRSRAGLGGRA
+VPVGVLAEVGSALVAVHGQNDQVRLQSAAAQRHALDAFGGPQLVAAAAAYRADHTAYVAA
+RRERDLLVERQQERAREAEALQRGLEEIDRAEPEAGEDETLRALIRRLEDVEELRAAADG
+GHAHLAGPDIESGDDLPGAITLVESARAAVQAAPGDDPELAAAAGRLAEASVILGDIAAD
+LARFSADLDGDAVSDLDAAQTRLAELSRLQRLYGPELTDVLAWAEAQRPRLEELQGDSGR
+IDELEADLARLDASRRERAAELTTLRTAAAGRLEQAVTAELHALFMPDASFHVSLVPLDD
+GDPGPHGAEDVALALRPHAGAEPRPLGRGASGGELSRVMLALEVVLAETDPVPTFVFDEV
+DAGVGGEAAVSIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPEAGVTTSDVV
+TLGQQERVDELARMLAGHGDSAAARAHARELLEASAAERA
+>4_1320
+MIDHLRISGLGVIGEATVDLDPGFTVVTGETGAGKTMVVTALGLLLGARADAGAVRRGSS
+RAVVDAGVRLPEAHAALALAEDAGAVLDEADEGVRELVLSRSVTASGEGTRSRAAAGGRT
+VPVGLLAEIGATLVAVHGQNDQVRLQGADAQRHALDAFGGAELAAALRAYRADHAAWTAA
+RREREELTAHRQERAREAEALQRSLEEIDLAEPQEGEDEELRALIRRLEDVEELRAASGE
+AHARLAGPDVDAMDETPGAVSLVEAARQAVLAAPGDDPELAAAAARLAEAAVVLSDIAGD
+LARYTADLDADAASDLDAAQSRLAELTRLQRLYGPELADVIDWARTQRPRLDELQGDSGR
+LEELEAEVDRLDAALRERAATLTALRTEAAERLETAVTEELHALFMPDASFHVGLTPVAG
+DGLGPYGAEDVTLALRPHAGVEPRPLGRGASGGELSRVMLALEVVLAATDPVPTFVFDEV
+DAGVGGEAAVRIGARLARLARHVQVIAVTHLPQVAAYADRHVRVEKNSDPAAGVTTSDVV
+TLTADERVEELARMLAGHGDSAAAREHARELLESSARERG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001176.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001176.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e5f34d3f30328dad95979036faf3f09fc61ac6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001176.fa
@@ -0,0 +1,30 @@
+>0_1374
+MSTTFFDGHDGLLCDLDGVVYAGDGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAEAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QCPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAADALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEASADPRRG
+>1_1114
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
+>2_1447
+MSPTLPRGHDGLLCDLDGVVYAGGGAVPGAVETLTALAERGVPVGFVTNNASRAPESVAE
+HLRSLGVPARPEQVFGSAPAGVDLLEETLGARTGRVLVVGSDYLRQVVRDRGFEVVAASQ
+DRPDAVIQGFDPGVGWAELAQAAYAVNAGAAWVATNLDASIPRAEGIAPGNGALVGAVGQ
+ATGTAPAAAGKPEPLLFRTAARALGLTRPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ENAGSAPEADRPTWIVEDLPALLSEPDGQAGTADGRRG
+>3_1355
+MTDPAASTFFGGHDGLLCDLDGVVYAGGEAIPGAVETVSALAERGVPVGFVTNNASRPPE
+AVAEQLRRFGLEVSPSHVFGSAPVGVDLLEERLTAAGHEGPARVLVVGSVHLADLVAARG
+HHVVETAAERPDAVLQGFDPRVDWSRLAEAAYAVNAGAAWVATNLDLSIPRAEGVAPGNG
+ALALAVTQATGVIPVAAGKPEPRLFHTAAAALGLQAPLMVGDRLDTDIRGGNAAGMETVL
+VLTGVGSRHAAGEAPEEDRPTWIVDDMTALLGEPAEAARG
+>4_1323
+MSATFFAGHDGLLCDLDGVVYAGGGAIAGAVETLSTLQERGVPVGFVTNNASRAPESVAE
+HLRTLGVPAQAGQVFGSAPAGVDLLEETLGRRTGRVLVVGSAYLRAVVEERGYEVVASAA
+QRPDAVIQGFDPGLGWADLAEAAYAVRAGATWVATNLDTSIPRAEGIAPGNGALVEAVGR
+ATGTAPVAAGKPEPRLFRTAAEALGLARPLVVGDRLDTDIRGGNAAGFDTVLVLTGIDTR
+ETAAAAPGPDRPTWVRAHLPALLAGGAEAFADPRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001177.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001177.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ef50b182fd0c9866d3d9ac7ead2a78571368a0a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001177.fa
@@ -0,0 +1,36 @@
+>0_1375
+MTGKELDRGTLKEINGLDERAASWVAKHLVMAGRYLDVDPTLAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRNRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAAAEPTLVPRQEAVAQPPAAVDTPDEVDPNQLSLFDALEAPEADER
+>1_1115
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
+>2_1446
+MAEDTPRGRRDDRRSPGDGAGRSRGGSGDARRFGGPRDGRRSGGSGEGRSGQDRRDRSSE
+GFRGGRSGDGPRRERSSDGPRRERSSDGFRRDRSSDGPRGERSGDGPRGPRAGGDRRQSG
+AGSARGGFEGRRGGERREGAGGERRDRRSASSSPRWEGRGQDRTERTERRERPAHNPRDL
+RAANRVDQERSPDIDADVTGQELDRGTLKEVNGLDERPASWVAKHLVMAGRYIDVDPALA
+FQHALAASRKGGRLSRVREAVALTAYAAGEYADALREFRTYRRMTGDDTHVAAQVDSERA
+LGRPAKALQLAAEIDTARLDRAARVELAMVVSGIREDAGDLQGAHDALQIPELDRRRGYP
+FSPRLFQRQADVLLLLGRADEARLWARAVRVAEKALGIGGFAEPEIVDVDTEPVDDRRER
+GPSPRERRYAENAAPAAEEVPDTPEADDEVAADADTEAPASTESELDAPPAAVAQADEVD
+PNQMSLFDELDGGEGEGR
+>3_1354
+MAERSAREPRDDRRGDGHDGTRSGTPRGRRDGDGGRRQGEGRPFRPHRDGEGVGRSRNVG
+GRDGAAPRPGRPERAQRERPAHSPSDLRAANRVDQQRSPDIDGDVTGKELDRGTLKEIGG
+LDERPATWVAKHLVMAGRYIDEDPELAFQHALAASRKGGRLARVREAVALTAYAAGEYHE
+ALREFRTYRRMTGDDTHIAAQVDSERALGRHEKALQLAGEVDTSRLDRAARVELAMVVSG
+VREDLGDLEGALAALKIPELDRRRGYPFSPRLFQRQADVLTALGRTQEAAVWQRSVHVAE
+RALGIGGFAEPEIVDVEVEPAEDDRPVRGHRERHTGPRVSDASQSSAESAPVGEGSAEEH
+GQAAPAERES
+>4_1324
+MTGQELDRGTLKEINGLDERPASWVAKHLVMAGRYLDVDPALAFQHALAASRKGGRLSRV
+REAVALTAYAAGEYADALREFRTYRRMTGDDTHIAAQVDSERALGRTEKALQLAAEVDAS
+RLDRAARAELAMVVSGIREDAGDLQGAHEALQIPELDRRRGYPFSPRLFQRQADVLLALG
+RRDEARLWARAVRVAEKALGVGGFADPEIIDVDTEPVEDPRDRRPSPRERRHERYAAEAG
+AEPTADGSPAEEPEAATEPTEAPRPEAAAEPPAAVDAPDEVDPNQLSLFDALEAPEADER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001178.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001178.fa
new file mode 100644
index 0000000000000000000000000000000000000000..61749cd0f1f75b083adc903d7ce748568653120e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001178.fa
@@ -0,0 +1,45 @@
+>0_1376
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKNMAGADLGEA
+>1_1116
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAKMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTALAHGEETTTKVIEASHAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDALAGRHLLVRRGKKSMAGADLGEG
+>2_1445
+MAPDNEERAARLRAQANDPSFENVWQELLWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAASLHLGHLVQLLTLRRLQLAGHRPMALVGGATGLIGDPRQTSERVLNSQETVAGWVES
+LREQIQPYLSFEGENAATMVNNLDWTAGMSALDFLREVGKNFRVGTMMKKEIVAKRLNSE
+EGISYTEFSYQVLQGNDFLELYRRHGVSLQTGGSDQWGNLTAGTELIRKVEGVPAHALGT
+PLITNADGTKFGKSEGNAIWLDAAMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQKRLAWEVTSLAHGEEATTKVIEASQAVFGGGDLGEVDAETLGAIL
+SELPQADRTQWEGEPGTVTAVELLVSTGLVGSKSEARRTVKEGGASVNNERVSDADRVYT
+REDALAGRHLLVRRGKKNMAGADFGSQDADRG
+>3_1352
+MAETTVTRAERLRQQANDPSFENVWQELTWRGLVHVSTDEAALEEALAGEPISYYCGFDP
+TAPSLHLGHLVQLLLMRRLQLAGHRPVALVGGATGLIGDPRQTSERVLNTREVVQEWVES
+LRAQIEPYLAFEGDNGARMVNNLDWTASMSALDFLREVGKNFRVGTMVKKEIVAKRLHSE
+EGISYTEFSYQVLQGNDFLELYRQHGVTLQSGGSDQWGNLTSGTELIRKVEGAHVHALGT
+PLITNSDGTKFGKSEGNAIWLDADMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAAKVDAEPFRREAQKRLAWEVTALAHGEEAARTVIDASAAVFGGGDLSEVDVDVLSAVL
+AELPQADAAQWGAAGKPTAVELLVSTGLVSSNSEARRTIKEGGASVNNVKVADAEQVFGA
+DEALAGRYLLVRRGKKNMAAADLRSGE
+>4_1325
+MAPQNEERAARLRAQANDPSFENVWQELRWRGLVHVSTDEAALEQALAGEPVSYYCGFDP
+TAPSLHLGHLVQLLTLRRLQLAGHRPYALVGGATGLIGDPRQTSERVLNSQETVAAWVES
+LRAQIEPYLSFEGENAATMVNNLDWTAGMSALDFLRDVGKNFRVGTMVKKEIVAKRLNSD
+EGISYTEFSYQVLQGNDFLELHRRHGVTLQTGGSDQWGNLTAGTELIRKVEGTHAHALGT
+PLITNADGTKFGKSEGNAVWLDAEMCSPYAFYQFWLNTADADVVDRLKVFTFLTRAEIEE
+YAQKVADEPFRREAQRRLAWEVTALAHGEETTTKVIEASQAVFGGGDLTTVDPDTLTAVL
+AELPQADRTQWEGEPGTVTAVELLVSTGLVASRSEARRTVRDGGASVNNVRVTDADQVFT
+RDDAFAGRHLLVRRGKKNMAGADLGEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001180.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001180.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b7c4c7487af9fdc6557569cfa834fec01f46f0b1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001180.fa
@@ -0,0 +1,50 @@
+>0_1378
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPHAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALEPLRRWADTPG
+SVVDAR
+>1_1119
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVAAELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVRLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVMAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
+>2_1443
+MTENPEARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHAA
+GLLGAEDLEGMIAALDRLETDVRSGAYAPADSDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGLVATVDALLSQVQAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARTAVSPYGSGALAGSSLGLDPEAVAAELGFDSAVWNSID
+GTASRDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVKLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLAGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFETERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+EEYAAISPALTPQVREVLSTEGSLNSRDAQGGTAPAAVAAQVEALERTLEPLRRWAQTPG
+SVVDAR
+>3_1350
+MSENSTPRHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLTADELAGMIDALDRLEADVRSGAYAPAESDEDVHGSLERGLIERAGAELGGKLRAGR
+SRNDQVATLGRMFLRDHARVVARGVLATVDALVEQAEAHPFAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFTRDLQRLVDWDARAAVSPYGSGALAGSTLGLDPNAVAAELGFDSAVWNSID
+GTAARDVYAEFAWVAGMIGVDLSRISEEVIFWATKEAGFVRLHDSYSTGSSIMPQKKNPD
+VAELARGKAGRLIGDLAGLMATLKGLPLAYNRDLQEDKEPVFDAVDTLELLLPAVSGMIA
+TLSFNTERMAALAPQGFALATDIAEWLVRQGVPFRVAHELSGEAVQVAESRGVELWDLTD
+EEYAGISAHLTPAVREVLSTEGSLNARRGQGGTAPEAVAEQLAALKAALEPLRAFAASAG
+SVVDAR
+>4_1327
+MTENTDARHGTNEGALWGGRFAGGPSEALAALSKSTHFDWRLAPYDIAGSRAHARVLHTA
+GLLSADDLDGMIAALDRLEADVRSGAYTPAASDEDVHGSLERGLIERAGPELGGRLRAGR
+SRNDQVATLGRMFLRDHARIIARGVIATVDALLDQARAHPYAPMPGRTHLQHAQPVLLSH
+HLLAHAWAFARDLQRLVDWDARAAVSPYGSGALAGSSLGLDPNAVATELGFESAVWNSID
+GTAARDVYAEFAWVAAMVGVDLSRISEEVIFWATKEAGFVTLHDAYSTGSSIMPQKKNPD
+VAELARGKSGRLIGDLTGLLATLKGMPLAYNRDLQEDKEPVFDAADTLELLLPAVSGMIA
+TLEFQTERMAELAPQGFALATDVAEWLVRQGVPFREAHELSGEAVKAAEARGVELWDLTD
+DEYAAISPALTPQVREVLSTEGSLASRDAQGGTAPTAVAAQIGALEDALAPLRRWADTPG
+SVVDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001184.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001184.fa
new file mode 100644
index 0000000000000000000000000000000000000000..28c856c7bf9d99769adcded6ee1ae3a33403f784
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001184.fa
@@ -0,0 +1,35 @@
+>0_1382
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRTLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAAEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>1_1123
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
+>2_1438
+MTPAPTPAPAAVRHFLVDTDLTPGEQAEVLDLAAQMKTDRFAHRPLAGPRTGVVFFDKTS
+TRTRVSFAAGIAELGGSPLIVNPGESQLGHKESVADTARVLERMVGIIVWRTFAQSGLEE
+MAAHSRVPVVNALSDDYHPCQILADLLTVREHLGGTQGRVLAYLGDAANNMAHSYLLGCA
+TAGMHVRIAGPAGHLPAEHVVAAARERAAETGGSVLVTTDAAEALDGADVVVTDTWVSMG
+QEDEKEARLALFRDYQVDAAAMARAGSDAIFLHCLPAYRGYEVSAEVIDGPQSVVFDEAE
+NRLHAQKALMAWLLYRSGLAEDPR
+>3_1346
+MTAAPGTDVPVRHFLVDTDLSPAEQAEVLDLALEMKADRFRHRPLAGPQTGIVFFDKTST
+RTRVSFAAGIADLGGTPLIVNPGESQLGHKESIADTARVLERMVGVIVWRTYAQSGLEEM
+AAHSRVPVVNALSDDYHPCQLLADLLTVREHKGRTRGLTMAYLGDAANNMANSYLLGGVT
+AGMHVRVAGPEGFLPDPAVVRAAEERAGETGGSVLVTTDAAAALDGADVVVTDTWVSMGQ
+EDEKEERLRLFADYRVDAAAMARAASDAVFLHCLPAYRGYEVTEDVIDGPQSVVFDEAEN
+RLHAQKALMAWLLYRSGLAQDPR
+>4_1331
+MTPAAAVRHFLVDTDLTPAEQAEVLDLAAQMKADRFRHRPLAGPRTGIVFFDKTSTRTRV
+SFAAGIAELGGTPLIVNPGESQLGHKESVADTARVLERMVGVIVWRTFAQAGLEEMAAHS
+SVPVVNALSDDYHPCQILADLLTVREHLGGTAGRNLTYLGDAANNMAHSYLLGCATAGMH
+VRVAGPEGHLPAEDVVAAARQRAAETGGSVLVTTDAVEALAGADVVVTDTWVSMGQEEEK
+EARLALFRDYQVDAAAMARAADDAIFLHCLPAYRGYEVTAEVIDGPRSVVFDEAENRLHA
+QKALIAWLLYRSGLAEEPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6719cd86fc9c763e6afa69f748cc73185550b478
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001189.fa
@@ -0,0 +1,35 @@
+>0_1387
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>1_1128
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GTYAMDLPFTPGTEGSGEVVALGEGVDAALLGARVATATATGAYAEHFTAPADRLLAVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHVVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
+>2_1433
+MPHASSPAVPRTHHAVVVAETGGPEVLRWTQADVPAPGPGRVLVRTAAVGLNYIETYQRA
+GVYPMDLPFVPGTEASGTVVGLGEGVDPTLLGARVATATAQGAYAEHFTAPADRLLTVPE
+GVDLADAAALPLQGMTAHYLCRSTFPVEEGQTVVVTAGAGGVGLLLTQLAAARGARVITT
+ASTEAKRELSRAAGAAAAVDYPELAATVDRLTDGHGAHAVFDGVGKDTFETSLRVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGGLYVTRPSLVHYTRTEEETRGRSDELFAAWAAGELD
+VRIGERIPLAEAAAAHAALESRATTGKVLLTLG
+>3_1341
+MSTHAEIPARHHAIIAEEVGGPEVLRWTETAVPTPGAGEVLVRTAAAGLNFIETYQRSGV
+YAVPHPFTPGSEGSGVVVALGPGVDEALRGARVATAAGRGTYAEHFTAPADQLLHVPAGV
+DLADAAALPLQGMTAHYLCRSTFPVEPGHVVALTAGAGGVGLLLTQLAAARGATVITAAS
+TEDKRALSAAAGASAAVPYAELRQTVLDATGGEGAHAVFDGVGADTFEDSLASLRVRGTL
+VLFGGASGQVPPFDLQRLNSGGGLYVTRPSLAHYTRTAEETAWRGRELFDAWSAGALDVR
+IGARVPLAEAGRAHTLLASRATTGKVLLPLS
+>4_1336
+MTTANTPAVPRTHHAVVVSATGGPEVLQWTETEVPSPAPGHVLVRTAAAGLNFIETYQRS
+GVYTMDLPFTPGTEGSGEVVALGEGVDAGLLGARVATATATGAYAEHFTAPADRLLTVPE
+GIDLAEAAALPLQGMTAHYLCRSTFPVEEGHTVVVTAGAGGVGLLLTQLATARGARVVTT
+ASTEEKRELSRGAGAVAAVDYPDLAATVAELTDGEGAHAVYDGVGKDTFDTSLEVLRVRG
+TLVLFGGASGQVPPFDLQRLNAAGSLYVTRPSLVHYTRTGEETRWRGGEVFGAWASGELD
+VRIGERFPLADAAAAHAALESRSTTGKVLLTLS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001190.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001190.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6de6aa6eb410f21e033a0ee2929d876b26848c11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001190.fa
@@ -0,0 +1,45 @@
+>0_1389
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLHQRVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>1_1130
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
+>2_1431
+MSTDPYVPGVGTDAAVIEHVVLDLDVRLAANRVSGTAVLSVRLTRQSRRIELDLHRLRVS
+KVGAAVDGRALPASFSQPRRWPSRLVVDLGESRPEGTLVELTVAYAGTPTPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPVSRSTADITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLTQPVPAYLLTVQIGRYRLVDAAAPADGLPPLRLVASTRTEQRARAALATQPAM
+MAAFIAAYGPYPFEEYTAVVADDVLEIPLEAAGMSLFGTNHLDGSWESERLIAHEMAHQW
+FGNAVTLGRWADLWLHEGFACWSEWLWAEASGRSSIASMARRAWQRLAEDPVEHVLTEPG
+AAEMFEDWVYKRGALTVEALRVLLGREVFGSMLRAWVDEHRFGTVDTAGLRAHVHAWAPR
+AQVTPEQVDELFEAWTRRPELPPFPG
+>3_1339
+MSTDPYIPGVGSDTATIEHLRVELDVRLASNRVAGVAELHVRLCRQSDTVELDLHRLAVD
+GAAGTHDGRPLKVRATTPRNRPHRVVVHLGASLPEGSLVVLRLSYSGHPRPRRSPWGTIG
+WEELTDGVLVAGQPHGASTWVPCIDSPAVRQTADITVTCDAGYLPVANGRGTRLRSRGSR
+ETWRWVMDRPVPAYLLTLQIGRYRQVTAPGSGTPESAAAGGVPPLRLVVSPRLQARAEAA
+MAGQGRMMEAFTAAYGPYPFDDYAAVVADDVLEIPLEAAGLSLFGVNHLDGSWESERLIA
+HEMAHQWFGNAVTLGRWSDLWLHEGFACYSEWLWAEASGRAALRHEAKQAWHGLKRQGED
+LVLAAPGAADMFDDRVYKRGALTVLAVRTLLGDAVFGEMLRDWVARHRFATVDTPGFRAH
+VLAWAPRADVAPEDVDALFDAWTLRPELPAFPG
+>4_1338
+MSTDPYVPGVGTDAATVEHIALDLDVRLAANRVSGTAVLRVRLTKQSRRIELDLYRLRVS
+RVDAVVDGRAVASSFTQPGRAPSRLVVDLDESRPEGTLVELTVVYAGTPTLRRSPWGTIG
+WEELTDGVLVAGQPHGASTWLPCVDSPTSRSTAEITLTCDAGYLPVANGVGAPVRTRGSR
+VTWRWRLDQPVPAYLLSVQIGRYRLVDAAPPAEGLPPLRLVVSPRTEQRALRALAPQPAM
+MATFIDAYGPYPFEDYTAVVADEELEIPLEAASMSLFGTNHLDGSWESERLIAHEMSHQW
+FGNAVTLGRWSDLWLHEGFACWSEWLWAEASGRSSITSMARRAWQKLAAHPVEQALAEPG
+PEEMFEDWVYKRGALTVEALRHLLGTDLFGSMLRAWVREHRFGTVDSLGLRTHVHAWAPH
+AGVSRAQVDELFDAWTLRPELPPFPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001192.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001192.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0d56eb6083f82cb955d9820813854e900878abbe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001192.fa
@@ -0,0 +1,80 @@
+>0_1391
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVALPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS
+EARAAATALAAQRHGAVQR
+>1_1132
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGVGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVAEAAADVAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQALAMVALANPIASQYRYLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSAEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHDPRPVDWQDAIAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPEIVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEVS
+EARAAATALAAQRHGAVQR
+>2_1429
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPSDELRGPIVVGQVLSKEPEP
+QKNGKTINWCTVRVVPEGAEQTLTGEGIDPSGVQGVVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASVRELGIGDDHDGILVLSTLGLDPEPGTDALEVLDLQGEAA
+EINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAALTPPAADDAGHPVRIADDAPIYGAP
+GATRFVARTVSGVDASRPTPPWMAARLRLAGIRSISLPVDISNYVMWELGQPLHFYDAQK
+LAGEIVVRRARAGETLRTLDDKERTLDPEDLLITDDSGPIGLAGVMGGLATEVTDATTTI
+VIESANFDPISIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTAEPG
+VTDVGTRPELAVVEMAADFPTALVGVEYTADEVAETLRALGAQVEAAEAADGAAPRLRVT
+APSWRTDLRIPEDLVEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGHT
+EVLAYPFVSAEQNRRFGVDSEEQGEALEMVALANPISSQYRYMRLSLLPGLVEIARRNLG
+RGFRDLALYEAGLVFLPGTQLGSASIPPRAAHPAPEVLADLEAGIPAQPWRVAGLYAGHD
+SAPGPDHAPRPVDWQDAVSGALAVADVLGVELAVRQGRHHAFHPGRVAELVVLGERGDQV
+VGVAGELHPQWLEAEDLPARTSVWELDLDALCAAAPPAVVAVPLSTYPMSTQDVALVVEE
+AVVAGDVRASLAEGAGELLESVELFDVYRGPGVPEGSKSLAFSLRFRAPDRTLTAEEASE
+ARAAATALAAQRHGAVQR
+>3_1337
+MRIPLDWLREFAQVPADATAEDVLADLVTVGLEEEDVHRPSDELTGPLVVGQVLTREPEP
+QKNGKTINWCSVRVVPEGAEQTLTGEGIDPSGVQGIVCGAHNFEVGDKVVVCLPGAVLPG
+DFRISPRSTYGHVSAGMMASARELGLGDDHDGIIVLGDMGLDPEVGTDVVDLFHLREEAA
+EVNVTPDRSYAFSIRGIAREYAHATGTAFTDPAAAVTAPEANDAGPAVTLADGAGIYGVP
+GCDRFVARVVEGIDPAAATPPWMAARLRLAGIRPHSLAVDVSNYVMWELGQPLHFYDADR
+LTGGITVRRAAAGETLRTLDDKERTLDPEDLVIADESGAIGLAGVMGGAATEVSEGTTRV
+LIESAHFDAVSIARTRRRHRLPSEASKRNERGVDWEIADEAAERAVQLLVELAGGTPAQG
+VTDVGTRPEPVVVELDPEYPARRIGVDYPRERVVELLTGLGASVEDAGDLLQVTAPTWRH
+DLRIPEDLVEEVARLDGYANIPSTLPVAPPGRGLTRAQVHRRRVADTLAAAGLTEVLDYP
+FVSEGQNRLFGSATPEEGAAQRMVRLANPISSEFGWMRTTLLPNLLETVRRNVSRGFKDV
+ALFEVGAVFLPGDGALGSPSNEPIGVKPSAETLAELDAGIPAQPRHVAGAFAGHEAAPGA
+GFAPRAFDWQDPIAAALAVGRAVGVELTVVQGTHQAFHPGRTATLSLPDGTAVGVAGELL
+PAWLEDADMPARTGAFELDLDAVLAAAADRVVARPLSTYPASQQDVALVVADDVVAGDVR
+ATLAEGAGELLEEVALFDVYAGKGVPEGHKSLAFSLRFRAPDRTLTADEASEAREAATAL
+AAERHGAVQR
+>4_1340
+MRIPLDWLREFVPVPAEHRAEDVMADLVRVGLEEEDVHRPAAELQGPIVVGQVLSKEPEP
+QKNGKTINWCSVRVVPEGAAQPLTGEGIEPSGVQGIVCGAHNFEVGDKVVVTLPGAVLPG
+DFRISPRKTYGHVSAGMIASSTELGMGDDGTDGIIVLGDLGLDPEPGTDARDVLDLHGEA
+AEINVTPDRGYAFSMRGVAREYAHATGVPFTDPAAAVHPPAADDAGPAVRIDDDAPIHGE
+PGATRFVARTVSGVDATRPTPPWLAARLRLAGIRTISLPVDISNYVMWELGQPLHFYDAD
+TLSGEIVVRRARAGETLTTLDGKERELDPEDLLITDDSGPIGLAGVMGGAATEVTDATTT
+IVVESANFDPVSIARTRRRHRLPSEASKRNERGVDWEVADEAAERAVQMLVELAGGTAEP
+GVTDVGTRPQPAVVEMAADFPSALVGVAYTTDEVVETLRALGAEVAVTEAADGAAPRLTV
+TAPSWRTDLRIPEDLAEEVARLRGYDAIPSVVPVAPPGRGFTRRQAQRRRVSAALAAAGL
+TEVLAYPFVSEEQNRRFGADSDAQGQVPAMVALANPIASQYRHLRLSLLPGLVETARRNL
+GRGFRDLALYEMGLVFLPGAQLGSATIPPRAVHPSPEVLADLEAGIPAQPWHVAGLYAGH
+DSAPGPDHAPRPVDWQDAVAGALDVADVLGVELTVRQGRHHAFHPGRVAELVVVTEHGDR
+VVGVAGELHPQWLEAEDLPARMSVWELDLDALCAAAPETVVAAPLSTFPVSTQDVALVVD
+EAVVAGDVRATLAEGAGELLEAVELFDVYRGAGVPEGRKSLAFSLRFRAPDRTLTAEEAS
+EARAAATALAAQRHGAVQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8c67d364d621af6ac976fd4f335f9d70bbd3edf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001196.fa
@@ -0,0 +1,37 @@
+>0_1396
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
+>1_1137
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
+>2_1425
+MRWEAQTLRSESGAQRAAAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNAV
+PAASAMPFRWTVNPYRGCTHACRYCYARSTHAFLDLDAGEDFDRQIVVKVNVAQVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYSLMPGIIEALADSGTPFSVLTKGTLLARDVPLLQ
+AASRSVPVQVSLSLAMLDPAVAAAVEPGTPSPAARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDRDLDALMRALAAAGAARVMPGALHLRPGAKEWYLRWIRQEHPDLLAGYEQMYARSA
+YAPESYRRTLARAAGEAAARHGLTRGGAHGIRREDGPVARPVPRSTPVAVPAPAAPAQPA
+LF
+>3_1329
+MRWEAQTLRTGGGAQRPGAGTPAGSPATLPLPGLQRIVSPPEFAGVTFHEVLARSALNKV
+PASSAMPFRWTVNPYRGCTHACVYCYARGTHRYLDLGPGEDFDRQIVVKTNAPEVLRAEL
+SRPGWTREPVALGTNTDPYQRAEGRYRLMPGIITALADTGTPFSILTKGTLLGRDAPALQ
+AAAAQTSVQVGLSLALLDPSLAAAVEPGTPSPAARLRLISRLAEAGVEVSVMAMPLLPWL
+TDSDRQLDRLMAALADAGAHSVLAGTLHLRPGAREWFLGWIDREHPHLAADYRRMYARSA
+YAPQAYRRVVSQAAREAAARHGLRHGGAHTITREDGPGPRGGASAPLSAPAGTTGAEQAD
+TAADAVRPVIAQPTLF
+>4_1345
+MRWEAQTLRSEGGAQRATAGTPAGSAALLPLSDLQRSVTTPEFAGVTFHEVLAKTALNSV
+PSASAMPFRWTVNPYRGCTHACRYCYARSTHTFLELDAGADFDRQIVVKVNVAEVLRAEL
+ARPTWGREAVALGTNTDPYQRAEGRYALMPGIIRALADSGTPFSVLTKGTLLARDVPLLQ
+AASRQVPVQVSLSLAMLDPAIAAAVEPGTPSPTARLRLIERLAAAGADVTVMAMPLLPWL
+TDGDREIDALMRALADAGAARVMPGALHLRPGAKEWYLDWIRREHPDLLAGYEQMYARSA
+YAPESYRRMLTRMAGEAAARHGLARGGAHGIRREDGPPARRRPASRPSAPAAQPALF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001203.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001203.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bfc043de01f9ae45662ac11d68a3453ade6b6e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001203.fa
@@ -0,0 +1,20 @@
+>0_1405
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAAVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>1_1146
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
+>2_1417
+MAQSRRPDPVDPREAPAAPAPEGPRTGGRAPVAALVVAAALALQAAALLWLAGDAIAHLG
+DGVLPAGARVMLIVIYVLLGLWILVTSVALLRGRAWSRGAATAVQLFGVLLSSRLLSVGE
+PVVGGVLLAVSGIALVTLFSRPVTAHLSQAAREPSAE
+>3_1320
+MSSSIPASPSGRRRMPAQAVVVAGVLGLEALTLVWLAVDGVAHLGAGALPTAAGVFLVVV
+YVLLAAWVGAVCGGMVRGRRFSRGAAVAIQLFAVILSTWLMSIGAPIAGGLLLVGSGAAL
+LCLFSGAVQAHLAGPDAGRPDAGRPDVG
+>4_1354
+MAQSRRPDPVAPSESSGADATTVPPRPGRGLPVAVLVVAAALVLEAGALLWLAVDAVVHA
+ADGVLPAGARVMLVVIYALLTLWILATAVALLRGRAWSRGAVVAIQLFGVLLSSWLFSVD
+AAALGGPLLAVSGVALLTLFTTPVTRHLTPAPEASTDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001205.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001205.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec9078f59805a497ff7a00b8993c41afb6ea633c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001205.fa
@@ -0,0 +1,50 @@
+>0_1407
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
+>1_1148
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
+>2_1415
+MVSSLAQDPLTSHPDLADEDRSWLQLLVGDWQLVADLALADLVLWCPAPRPDPAEGFVAV
+AQVRPFTAPTLFHRDIVGSRARADLRAVVASTWSGGERPEGAGPVETPDGTLQVRLWPVV
+RRGRVVAVLSAHGDPNGRPSRSVIEENYIRTADSLLDMMQHGRWPAPEESAGLWAGGTPR
+VGDGLVVLGPDSVARFTSPNAVSALRRLGIGATLEGHRLTDVLAGTDAARQPSEEGTWAV
+LTGLRAGRREVQSRGASLTVRSVPLLGPDGWHGALLLLRDVTELRRQEQRLVSKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEADRALRQAMRRVDTIALVHQTLSEEIDGQVPVD
+DLLKRQFRLAVEVSGDGRPLEAAASGEFGELPSHVTTPLALVLNELAANAVEHGTAPAGG
+RVELHAERELTPAGSVLVVSVTDGGSGVQDGWSPGEFQPAADGAGLGLRIVQTMVEGDLR
+GTLRWERLPDGGTRVVLRIPTA
+>3_1318
+MVSTIASDPLNTHPDLGAEDRAWLQQLVGDWQLIADLALADLVLWCPLPVEVDGTGHLAM
+AQVRPFTAPTLFHRDIVGSRARADLRALVDRVWAAGAPADGTGPLVEPGATLKVRLWPVV
+RAGRVVGVVSAHEDPRTRPARSAVEDNYRTSADTLLDMVQHGRWPNPEDPPAYWIGGTPR
+VGDGLVVLGDDSRATFTSPNAVSALRRLGLPTTLAGHSLTELLGGTEAARRPVEEGSWAM
+LNGQRAGRTEVQANGATLTVRSVPLRNRDGWCGALIMLRDVTELRRQEQRLISKDATIRE
+IHHRVKNNLQTVGSLLRMQARRSDSPETGRALRQAMQRVDTIALVHQTLSEQIDAQLSVD
+ALMARQFRLAVEVAGDGRPLGTRVEGTFGELASHVVTSVALVLNELATNAVEHGTGEEGG
+VVSLQAHREDTPAGDVLVFSVTDGASVEDGPGEGFVPQPAPNGLGLRIVHSLVEGDLRGS
+IQWRRMPDGGTRVTVRLPVE
+>4_1356
+MVSSLAQDPLTSHPDIGDEDRAWLQRLVGDWQLVADLALADLVLWCPVPRRDEAGGFVAL
+AQVRPFTAPTLFHRDIVGSRARADLRAVVGQTWHGGERAEGAGPVEAPGGTLQVRLWPVV
+RAGRVIAVVSAHADPNGRPARSVIEENYSRTASTLLDMMQHGRWPAPEEPSGLWAGGTPR
+VGDGLVVLGPDSVAEFTSPNAVSALRRLGIASTLEGHRLTDVLASTEAARVPTDEGTWAV
+LTGLRAGRREVQSGGASLTVRSVPLLGPDGWQGALLLLRDVTELRRQEQRLLTKDATIRE
+IHHRVKNNLQTVGSLLRMQARRTSSPEAERALRQAMQRVDTIALVHQTLSEEIEDQVPVD
+GLLQRQFRLAVEVAGDGRPLQVAVTGEFGELPSHVTTPLALVLNELAANAVEHGTAPGGG
+CVGLHADRESTPAGTVLVVSVTDGGPAAPDGWVPGESPRAGEGSGLGLRIVHSLVEGDLR
+GTLRWERSDDGGTRVVLRLPLT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f4993859dd2c82f59f4c20c0e503cc06e685fc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001210.fa
@@ -0,0 +1,31 @@
+>0_1412
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
+>1_1153
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPAAELTRVLGLG
+AGLAGLGLLAWWAVGLTGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAASPTHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFA
+PHAGVDGPRP
+>2_1410
+MQRITEPARRGRAALSEADGHRADGHRVDTVDAVGLVVLALAAPALLIGAAALLEPGEGA
+ASSELVRLLGLGAGIAGLGLVAWWAVGLLGLVLATVGRRTGRLGFARLGARLTPALLGRV
+AGAVLGAHMLAAPAAWAEQPAVGPVPDAGQTVSHAAPASTTASAPAAVPEAAWTPRTPVP
+APPGATAARNLSDRPTVTVRRGDCLWDIAAAELGPDATPREIDARWRRWHEANRRVIGDD
+PHLLLPGTVLTAPVFSPHAAPQEGLAMTPRPRTTPTTTRPQEPAMTALAARPPSPPSTAA
+PAVSPGTPTVAPTVPPPRCCTVPPTARPCCPAARRSPAGPPSSRAGRSCVGSAPWPR
+>3_1313
+MSFVASQPPAAGVHAPRASALDVAALAVLAAAVPALGWAAATLLGPAAPTPDAALGRALG
+LGAAGLGLALAAWWALGLLGLAALALGRRTGHRGWSRLGERMTPALLRRAGAAVLGAQLL
+AAPAAWADAPPAPSAAVVDASWTSAAASPTLPDAAWTPGAPPTPQPGSPAAPRDTGDRPT
+VTVRAGDCLWDIAADELGPDATPREVDRRWREWHRHNRDLIGEDPNLILPGTVLTAPDFT
+PHVQRGGTP
+>4_1361
+MERSTSPAGPAPTRPVDAADAVGLTVLLLAGPGLLACAAALLQTGTSAPGAELTRVLGLG
+AGLAGLGLLAWWAVGLIGLALVALGRRAGRPAWARLGRSLTPALLGRVAGAVVGAQLLAA
+PAAWADAAHPVPDASWTVAAVPAHATGVEAPAPDAAWTPRPPAPAPPGAGTGRADPDHPT
+VTVRRGDCLWHLAAAELGPDATPREIDARWRRWYEANRRVIGDDPHLLLPGTVLTSPVFT
+PHAGVDGPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001215.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001215.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e0236d7f21697e5f8639235acf346a2f45be15a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001215.fa
@@ -0,0 +1,55 @@
+>0_1417
+MTTVDPQPPRPPRVAVVAVIVALVLALSGCTQIPQSSEVRSADPVDGASAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GDGDYQIQVEVDSEIDEYGLRTVAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYIVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVETAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISAGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
+>1_1158
+MTTVDPQSPRPPRLAVVGVIVALMLALSGCTQIPQSSEVRSADPVDGATADADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTIAPPGTTRAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADAERRHRMREQLELTLRGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVRSVQVGIDAATGGLVYVQGSSVTPVGGAPDVTALDPVRPTM
+SGDRSRFAFVTGDRTAVHVAGTDGSLREVLRGTGLTVPSLDLLGWVWAADRGTTSRIRAV
+SAQPGGQERIVTATWLRPGERIVDLRLARSGARAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAAKPDERVVPRIVSVDGTVRELNPLGGLRG
+ISAGDDGAYYAETEEFVFLLVGSSWRAQELDRGVRDLSFPD
+>2_1405
+MSPTRPTGPRRARRLAGVGLAAALALALGGCTQIPQSSDVRSAEPLDGATAAPEAPQFRP
+PGPSADDTAEDVIRGFLLAGTSPQDDYAVAREFLDGPAAARWAPGQRTLVYSAQPRITRG
+EGTGNYQVQVEVDSEIDEFGLRTIAPEGTTRAWQVSVQERPEGMRITATENGTLLSQSQF
+GQLFAPHELAFYDTAQRYAVPDVRWFVNRGTTVTAVTRALLRGPAPYLTGAVETAFPLRT
+GADLAGPTVPVDEDGVAHVDLTEAAAEGADADRRHRMREQLEITLLGLQSVSDVRVTVDG
+AELSASGENPPPPVQDEPTTGSVQVGIDSATGDLAYFQGMSVGPVGGAPDVSALDPVDPT
+MSRDRSRFAFVTRDRTAVHVAGTDGSLREAMRGTGLTSPSIDGLGWVWAADGAETSRVRA
+VPAEPGQEARIVTATWLRPAERIVDLRVSRSGARAALLVDDGDRRTVRVAGIVRGSDGVP
+SALTEPILLPSTGRAASVEWAGDTNLLVSPRAATPDERVVPRIVSIDGTVRELNPLGGLT
+GVSAGDGGALYAETDELVFLLVGSSWRAQELERGVRDLSFPG
+>3_1307
+MRPSGPARPRRRLCAAALAGALALAGCAQIPQSSPVRSGAPLDVGSRAADAPQFRPPGPA
+EDATAEQLVRGFAQAGIAPEDGYAIARQYLSAEASDGWEPDRGVVVYSGEPTVTRGLGEG
+TYEVQLEVESEVDEFGQRTMAPPNTTQAREVTVEEVDGVLRITGVQDGVLLSRSQFAQLY
+APHPLYFFDQSQAFAVPDVRWFVNRGTAVTALTRALLRGPAPYLTGAVATAFPLRTGADL
+TGPSVPVAEDGTAAVDLTGATVDGADPARLSRMREQLERTLTGVSGVERVEVTVEGRSLT
+SSAPSGSVPSARIGEDPGTVQVGVSDAGELVFFQGLDAVPVGGLPSVADLGPEDPAMDRE
+RRRFVFLDRTRTVLHGVGTDGGEHRLLDGGRLTAPSLDSSGWAWTVDRARSSRISVVRAD
+GSEPARVVTTPWLAEGESIVALHIGPAGARAALIVDDGQQRTLRVAGVVRGGDGVPTALT
+PPVYIPTLDPPDDVEWMGDGSLVSTPLAPDAETRVRPEVVSLDGTSRQLNPLAGLTGISA
+REEGTLYAETAEDVFLLVGSSWRAQDVATPVHDLAFPD
+>4_1366
+MTTVDPQPPRPLRVAVFAVIVALVLALSGCTQIPQSSEVRSADPVDGATAAADAPQFHPP
+GPAESDTAEEAIRGFLLAGTSPQDDYAVAREFLDGPAATQWTPGQRTLVYSAEPRITRGD
+GAGDYQIQVEVDSEIDEYGLRTVAPPGTTQAWAVTVQERPQGMRITSTENGTLLSQAQFG
+QLFAPHELAFYDTAKRYVVPDVRWFVNRGTTVTAVTRALLRGPAPYLAGAVDTAFPLRTG
+TDLAAPTVPVDDDGVAHVDLTQAAAEGADADRRHRMREQLELTLTGLQSVKEVEVTVAGA
+QLSTSGDDGPAPVQTDPAVGSVQVGIDTATGGLVYVQGTSVTPVGGAPDVTALDPVRPTM
+SGDRSRFVFVTRDRTAVHVAGTDGTLREVLRGTGLTVPSLDLLGWVWAADRETTSRIRAV
+PAQPGGQERIVTATWLRPGERIVDLRLSRSGAQAAMLVDDGQRTTLRVSGVVRGSDGVPN
+ALTEPILLPSSGSEDSVEWAGDTNLLVSAYAEKPDERVVPRIVSIDGTVRELNPLGGLRG
+ISVGDDGAYYAETEELVFLLVGSSWRAQELDRGVRDLSFPD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aa5b00cbe78afbb903a83719f31bcdb8a4d56c30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001221.fa
@@ -0,0 +1,35 @@
+>0_1426
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>1_1167
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
+>2_1398
+MRQNVAMALTELALRHPVRRFARREVDFRRRILTMAVVNRTPDSFYDDGAAFALEAAVDQ
+ARAAAEAGAEWVDVGGVPFAPGPALDPGEEARRVVPLIAALRGEAAEHSEAVAGLILSAD
+TFEPAVAEAAIAAGADVVNDTSGLVHADLGRVVAASQAHLVLTHSLAHVHGPRAVVPRPR
+YGDVVAEVREHLLRTVERAVALGVPEERIIVDPGHDLNKNTLHTLEITRRLDEIAGLGLP
+VLAAVSNKDFIGESLDQHRHERLAGSLAAAVACVHGGARILRMHDAAASVSAARLLECVF
+GWREPARLVHNMGEANPAPDRTSLAEHRAGRVRAGGTR
+>3_1298
+MPTPSVPLAHPVHRFAHHEIDFRRRIVTMAVVNRTPDSFFDDGAGFAFDAALAQVHTAAD
+AGAEWVDVGGVPFAPGRELDPAEEAARVAPFVAAVRAGRGEGASEAARRLILSADTFQPA
+VAEAAIDAGADVVNDTTGLYYPDLGRVVAASNAHLVVTHSLAHVSGPRTVVPRPRYDDVV
+AEVREHLLRTVDRAVALGVPEERIIVDPGHDLNKTTVHTLEVTRRLDEIADLGFPVLAAV
+SNKDFIGESLDRHRHDRLAGTLASAAFCALAGARILRMHDADASVSTAHMLECILGWREP
+LLAVHNTGDVNPAADRTTPADRVPADRPPAAVPAPTHDPEEARP
+>4_1375
+MSREGNIVLPGRTVTVRRRWLNGRVPTPSVPLVHPVHRFAHHEIDFRRRIVTMAVVNRTP
+DSFYDDGAGAVLEDALAQAHAAADAGAEWVDVGGVPFAPGAELDPTEEAARVVPLIAALR
+SGDGAGSSEASRRLILSADTFQPAVAEAALAAGADVVNDTTGLFHADLGRVVAAAGAHLV
+VTHSLAHVRGPRAVVPRPTYGDVVREVRDHLRRTVDRAVALGVPEERIIVDPGHDLNKNT
+RHTLEITRRLDEIATLGLPVLAAVSNKDFIGESLDRHRHERLPGSLAAAAACVYGGARIL
+RMHDADASVSAARMLECVFGWRQPARLVHNMGAENPPPDRSTLAGHRAHRGGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001226.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001226.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46cce8f220fc97032603dcaab9a86df9d1355420
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001226.fa
@@ -0,0 +1,29 @@
+>0_1431
+MAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGGFDSEGAEAMTARRHAEQRAA
+AAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVVLSTHPERDWERMQAAHPDH
+LACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRNLLLYAAPAARRNTVVDVTGLAEQK
+LRALDAHLSQHPDVDAMRRHVLAQMAEHHRHAAGPAAGPGHAEAFHLVTVNGPGTIAGF
+>1_1172
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFSAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPGTIAGF
+>2_1393
+MTTPITPAALAAEHGWRTVLAVGAHPDDLDFGAAATLAGLSAAGLRVELCVVTDGDAGGF
+DSEGPEAMTARRHAEQRAAAAVVGAHEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDVV
+LSTHPERDWELMQAAHPDHLACGEAVVRAAYPAVENPYAYPELAAEGLEAFKIRHLLLYS
+APAARRNTVVDVTGLEDVKLRALDAHISQHPDVAAMRRHVLAQMTEHHRRAAGPAAAPGL
+AEAFHLVTVNGPGTISGF
+>3_1293
+MSAVPESLPTPADLAVRHGWRTVLAFGAHPDDLDFDASATLAGLAAAGVRVELCVVTDGD
+AGGFDSDGPEAMTARRHAEQRAAAAVIGAADVHFLGERDGHLEPTHEVRRRIVELMRRVR
+PDVVLCPHPERDWESMQASHPDHLACGEAVVRAAYPAVENPYAYPELADAGLDAFRIRHL
+MLYTAPAARRNLTVDVTGLEDVKLRALDAHVSQHPDAPAMREAVRAKLTRRHREAAGPDA
+PAGSGEAYHLVTVNGDGVIAGF
+>4_1380
+MTTTLTTPAALAAHHGWRRVLAVGAHPDDLDFGAAATLAGFRAAGLHIELCIVTDGDAGG
+FDSEGPEAMTARRHAEQRAAAAVVGAAEVHFLGERDGHLEPDHGVRRKLVALMRRVRPDV
+VLSTHPERDWERMQAAHPDHLACGEAVVRAAYPAAENPYAYPELAAEGLEAFKVRNLLLY
+AAPAARRNTVVDVTGLAEQKLRALDAHLSQHPDVDAMRRHVLAQMAEHHRRAAGPAAAPG
+HAEAFHLVTVNGPSTIAGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001230.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001230.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f0bb4cf96482943faa4a83a7c031c6dccb98465
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001230.fa
@@ -0,0 +1,41 @@
+>0_1435
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLVLGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYASQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITSVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>1_1176
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+LAGLSWAVVGIWGAIAVIAIIAAVWLRRTDPGRRTPAQQAVRASSR
+>2_1389
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVIKPLQTLMIPASVIAGILGLVLGPNVLGWL
+PFSTQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGSFASYGVLIYASQVAIGALVALL
+VLQPLFSTPDSFAALLFAGWAGGFGSAAAVGQAYAANGDMTVTSLAYTSATVGMIVGVVG
+GIIQAKIGARRGHAKEFAGLTSIPDELRTGVLDQVQERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVTWITAVWPNIVGEDGPKLIIPAFAVAFILGLIGRVVFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIASIAPTVVVDYWQPLLVLFVIGLALALFLGLVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIAAILAAIWLRRTDPGVRSPAQQAVRAASR
+>3_1288
+MTWFQGVWPSIVGPEGPKLMIPAFAVAFVLGIIGRLLLQVTKTATFLDSASLNSVSGTAT
+DILIVCGIASIAPKVVLDYWQPLLILFVVGLALAVLLGLVVAPHVMTESWFEKQLFTWGW
+ATGAVATGVAMLRIVDPKLKSGTMEQFGVAYITVVPVEIAAVSFVPLLIIAGLSWAVVGI
+WDAIAEAAIIAAVFLVRSDPARKSAVPA
+>4_1384
+MQEQFTAWSVLVDAGLIGALLAVGTLARAVITPLQTLMIPASVIAGILGLALGPNGLGWL
+PFSSQLGTYGSILIVIVFVCIALTDDFDVRKIGRPVGAFASYGVLIYSSQVAIGALVTLV
+LLQPLFDAPDSFAALLFAGWAGGFGSAAAVGQAYAANGDATVTSLAYTSATVGMIVGVVG
+GIIQAKIGAQRGHAREFAGLTSIPEELRTGVLNQVEERPVIGRHTFSAASVESLAFQVGV
+VAMIAAAAHGVVSWITAVWPSVVGEDGPQLIIPAFAIAFLLGLIARVLFQATKTAKFLDP
+GSLNSVSGTATDILIVCGIAAIAPTVVVDYWQPLLLLFVIGLALALFLGIVVAPRVMTDA
+WFEKQLFTWGWATGAVATGVAMLRIVDPKLKSGTMEQFGVAYIPVVPVEIAAVSFVPLLL
+IAGLSWAVVGIWGAIAIIAIIAAVWLRRTDPGRRTPAQQAVRASSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001234.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001234.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae5d1ff1efee9818400e7f1b9f09893260dd40c2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001234.fa
@@ -0,0 +1,30 @@
+>0_1462
+MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP
+RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL
+DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPVVRGCPLCRWPADPAGVPGAPTAPGPS
+AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW
+AF
+>1_1181
+MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP
+RPVDAADLGTGLLPGDLGRPRAGALARRLGDVAPGLRLYAHHGPVPVLVGQATVAVGSVL
+DADLAAHALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGAPTAPGPS
+AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW
+AF
+>2_1384
+MPAAPSSALSDALSSAEPGAVRPEVEPGPPGAGWEPPVDVHVAGLDAVGVAVAHALAGAG
+AHRMALWDPRPVDAADLGTGLLPGDLGRPRARALERRLLDVAPGLRVYAHHGPLPVLVGQ
+ASVAVGDVLDADLAAQALAADHPLLPVHVGPRAVTVGPWCAPDVVGCPLCSLPADPVGPP
+GRRSARGRATSSGESGAAAVDALTAQRAAVLVADALRAGPSAGVVRADRASGRTRRARVR
+PRAGCACDPDALAWGT
+>3_1284
+MATTDAHGPRESGLLADPAGIQVAGLGPAGGALAAALAAGGVAALALWDPTPVGASDLGL
+GLLPADLGRPRDRAWEARLSRTWPALPVYAGAGTRPGALGAATVAVDLPGLPDLAARAIA
+AQHPLLPVRTDLHGVSAGPWTGGGAPGCVLCTEDVPGTALTAPPAAPPRRDPGAAREPGH
+ALRAVVLALDVLTGRRDATSAVLRVDAATGRLTRIPVRTRPGCGCADLLAGDGTGDDWAA
+ALAAVEESLDGALADARP
+>4_1389
+MRTVAETVTTVPHDAAASALEPGAWAPPTDVHVAGLDAVGAAIAHALAGAGALRLALWDP
+RPVDAADLGTGLLPGDLGRPRAGALERRLGDVAPGLRVFAHHGPVPVLVGQATVAVGSVL
+DADLAAQALAADHPLLPVTVGPRAVTVGPWCAPGVRGCPLCRWPADPAGVPGVPTAPGPS
+AHRGQVDGLAALRAAVLTVDALRTGPAPGVLRADRVTGRTRRVKVRPRPGCACDPDALGW
+AF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001236.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001236.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e12ec486f2528dbf34546dc853979bfa9f470c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001236.fa
@@ -0,0 +1,35 @@
+>0_1464
+MASCPPSSSDPTVAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>1_1183
+MASCPPSSSDPTAAPPLALPLAREELDRGAVARLDPGHLAASWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVIDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGV
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELARLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
+>2_1382
+MPVPDPAAPAPEPRHDPAPAPAPAAPLALPLAREEVDRGAVARLDPGHLAAAWEREGTEV
+LWLQGGRAPVADGRLRFTTPSGPVPPQAAYLGRGTAADLGPGGRERAVVAVALEPPAVLP
+PDAAAALGDAAWVGLRDAAAALSDADAGLFVAAVANANWHAAHRFCSFCGGATAVEAAGW
+VRRCEACGREHFPRTDPAVIVAVTDPDGRILLGRNAAWPAGRYSCLAGFVEPGESLEHAV
+VREVAEESGVTVADPRYRGSQPWPFPRSLMLGFTAQAPAGAEPVADGTEILSVRWFEREE
+LAALAREGEITLPGAVSIARALIEDWYGGTLPDAQTLIT
+>3_1282
+MPVPSAPDAVPAALPHLTLAREALDRSGAEREDPGLLGRLAADPATGVLHLVGGRAPVRD
+GALVLVPPAGPFPPEAVFLGRRLTDAAAPSAAGRPLVLVARESAPGSSGDGGPTRPAEPT
+DAPTRDPLAGAAWLGLRDVAAGLSDADTGLFVEAVAIANWHAGHGFCSRCGGRTDTESAG
+WVRRCRDCSARHFPRTDPAVIMAVMDDQDRILLGSNAAWPAGRHSCLAGFVEPGESLEHA
+VAREVLEEAGIVVVDAAYRGSQPWPFPRSLMVGYRAHALPGQEPVADGHEIRSVRWFTRD
+ELAAEVRAGAVTLPGAVSIARALIEDWYGGTLPDPTTLIS
+>4_1391
+MASCPPSSSDLTAAPPLALPLAREELDRGAVARLDPGHLAAVWAREGTEVLWLQGGRAPV
+ADGRLVFTAPSGPVPAEAAYLGRGTAADRGPHGREREVVSVAVEPPAALPEDAATALADA
+VWVGLRDAAAALSDADTGLFVAAVANANWHATHRFCAFCGGVTDVEAAGWVRRCRDCSRE
+QFPRTDPAVIVAVTDPAGRILLGRNAAWPEGLYSCLAGFVEPGESLEHAVVREIAEESGI
+TVTQPRYRGSQPWPFPRSLMLGFTALAPAGAEPVPDGEEILSVRWFEREELAHLAREGDV
+TLPGAVSIARALIEDWYGGTLPDAQTLIT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001240.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001240.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6c48757aa8ea8163c684792ab1425f51e520e34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001240.fa
@@ -0,0 +1,20 @@
+>0_1468
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREAMPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>1_1187
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGHAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREATPRTPAGRVDLPRARWEPDDGAARAIR
+AIADRIVSGPGARMRP
+>2_1378
+MTTPPADPRPVPDGPLTLGEGLEAVARLVPAGRAVSYGDLAGLLGVGGPRQAGRAMAKSA
+PGTPWWRVVSADGSLPGELARRAAVEHAREGTPVRPGGRVDLPRARWEPDEAALGAVAAI
+AARIVSGPGARMQA
+>3_1278
+MSPVPSTPPDPDPHLPTDGPVTLGEALAAAARLIPSGRAASYGALAGLLGRGGPRQAGRA
+MAESEPGTPWWRVVRADGSLPEPLRRQARERWAAEGTPVRGSGTVRDQRVDLAQAGWEPD
+AAARAALADLAARVG
+>4_1395
+MTDHPVLPGARHRDDGPLTLGEGLEALARLVPPGRAVSYGGLAGLLGVGGPRQAGRAMAE
+SSPGTPWWRVVRADGSLPPELAARAAVEHEREGTPRTPAGRVDLRRARWEPDDGAARAIR
+AIADRIVSGPGARMGP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001252.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001252.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9bc35992ae1ab4adb9b67e14fef7008a047aa83e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001252.fa
@@ -0,0 +1,40 @@
+>0_1480
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
+>1_1200
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGVETAEREERA
+>2_1366
+MSDLSQTSEIRAGAPALPADHPLRTQDPARSTAASPLVRALRGQRPDRHPVWFMRQAGRS
+LPEYREARAGIGMLESCLMPDLVREITLQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGRAVRTAEDVAALPVLEDSALDVIREAVSSTVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHGDPEAWAALAGWAATVSGQFLRAQLEAGASAAQLFDSWAGSLA
+AEDYLEHVQPHSRAALAHVDDLAGPGVDGGAPLLHFGTGTGEFLHHLRDAGASAVGVDHR
+LTLSEAHRRLSERPGPDGRTVVPLQGNIDPALLAAPWPVVEAHVRDVVASGAAAPGHVVN
+LAHGVPPETDPTVLTRVVELIHSLPVPEREGQDPAPPAGAAAGEGRA
+>3_1258
+MSAMTTPPGLPAEHPLSTADPARSTADAPLVCALRGRRPHRHPVWFMRQAGRSLPEYRKA
+REGVGMLESCLRPELAAEITLQPVRRHDVDAAIFFSDIVVPLKLAGVGVEIVPGVGPVLD
+HPVRTAEDAAALPELEDSALDVIREAVSRTVAELGPTPLIGFAGAPFTLAAYMVEGRPSR
+DHLGPRRMMHGDPQTWAALAAWAATVSGQFLRAQLEAGASAAQLFDSWAGSLSAADYRKH
+VQPHSAAALSAVSDLAGPGVEGGAPLLHFGTGTGEFLDLMRDAGASAVGVDHRITLAEAH
+RRLSSRPGPDGRAAVPLQGNIDPALLGAPWEVLEAHVREVVASGAAAPGHVVNLAHGVPP
+ETDPEVLTRVVELIHSIPVADGAEK
+>4_1407
+MSALSQTPETPAAVPALPAEHPLRTEDPSRSTVASPLLRALRGQRPDRHPVWFMRQAGRS
+LPEYRRVREGIGMLDSCLMPDLVREITMQPVRRHDVDAAIFFSDIVVPLRLAGVDVEIQP
+GVGPVLGQAVRTADDVAALPVLEDAALDVIREAVAATVAELGPRPLIGFAGAPFTLAAYM
+VEGRPSRDHFGPRRMMHADPETWAALAGWAATVSGQFLRAQLESGASAAQLFDSWAGSLS
+ADDYLEHVQPHSTAALAHVADLAGPGVPDGAPLLHFGTGTGEFLHHMRDAGATAVGVDHR
+LTLAEAHRRLSANPGPDGRGAVPLQGNIDPALLAAPWEVLEAHVRDVVASGAVAPGHVVN
+LAHGVPPETDAAVLTRVVELIHSLPVPEREGQDPAPGAETAEREERA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001253.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001253.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00be1c7cecdc987dc6ce180751a4959d97160ce6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001253.fa
@@ -0,0 +1,45 @@
+>0_1481
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHAAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAVCPAHEDEGGAARIA
+>1_1201
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEADAAGV
+EAARAGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELRKGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
+>2_1365
+MADVVTVFSLVASHQHLDLDTVARLSAGATGVGPALPGSGAAGAVVLATCNRVEIYAEAD
+ESGVEAAREGLVAAVAAHSSLPDEAVRSAFRVLDSEATARHLFEVGAGLDSAVVGEREIA
+GQVRRALSMARESGTASGSLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLTEELRG
+LADDDAKAAFWADASVLLIGTGAYAGTTLAQLAERGATAVAVHSASGRAEQFVEDRGGWA
+LALGGGAVAGAVAEADVIIGSSGGERQISPERLQELREDVDRPLTVVDLALSRDFDPAVG
+DLPDVDLITLESVRLAAPEQARAAVAEARVLVDGAVAEYRAAQRGRSADASIKALRRHTL
+AALDREMERVRARHGCTAAAEEVEFALRRMVNQLLHEPIVRAKRLAAEGRLDRYEDGLEA
+VFGIEPPGSTSSPAERPDAGCPAHEDEAGTARIA
+>3_1257
+MDVAVTVFSLVASHKDLSLDTVARLSAGSAGVGSALASSTDDGAVVLATCNRVEVYADAR
+DADAARERIVAAIAEQSGLPEDAVRSAFRVLDDDASARHLFEVGAGLDSAVVGEREIAGQ
+VRRALVDARDAGTATGSLTRLFESATRTAKDVGSHTALGATGRSVVSVALDLAEELRGLT
+DAMARRTFWQEANVLLIGTGAYAGTTLAQLADRGAQAVGVHSASGRAAQFVADRGGWALA
+LGGADVAGAVAEADVIIGSSGGDRQISPERMAGLRRGAERPVTVVDLALSRDFDPAVGEL
+EGVDLITLESVRLAAPEQAQAAVAEARGLVETALEEYTSARRGRTADAAIKALRGHTMAA
+LDREMERVRARHGCTAAADEVQFALRRMVNQLLHTPSVRARELAAQGRLDEFEHALEVLF
+DIPVPGTRPADAPGDACPATEADDARRTA
+>4_1408
+MTVFSLVASHHDLDLDTVARLSAGATGVGPALPGSGAAGAIVLATCNRVEIYAEADGAGV
+EAARTGLLSAVAASTSLPDEDVHTAFRTLDADATARHLFEVGAGLDSAVVGEREIAGQVR
+RALTAAQEAGTASGPLVRLFESATRTAKDVGSRTALGAAGRSVVSVALDLAEELRGLTDA
+AAQRDFWAGATILLIGTGAYAGTTLAQLADRGATTVGVHSASGRAEQFVADRGGWALALG
+GEAVAGAVAEADVIIGSSGGERQISPERLQELREGGRRPLTVVDLALSRDFDPAVADLPD
+VDLITLESVRLAAPEQAQVAVAEARALVDDAVEEYRAAQRGRSADAAIKALRRHTLGVLD
+RELERVRARHGCTAAAEEVEFALRRMVNQLLHEPSVRAKRLAAEGRLDRYEDALEAVFGI
+EAPGRPAPAVGTVEAACPAHEDDGGAARIA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001255.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001255.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf92324ee2ad863fb7e421a4041d747d5624bd08
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001255.fa
@@ -0,0 +1,15 @@
+>0_1483
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVSDGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>1_1203
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLADAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
+>2_1363
+MEIRIGVQHVGREVVIESEQPAEEVRSLVDAAVADGSTLVLADAKGRQVVVPGDRIGFVE
+INAKKSGPLGFAAS
+>3_1255
+MEIRIGVQHVGREVVLESDHTAQEVRALVDAALADGTTLALTDTKGRQVIVPADRIGFVE
+IGAKKSAPLGFAAV
+>4_1410
+MEIRIGVQHVGREVVIDSEQSADEVRSLVDAAVADGTPLVLTDAKGRQVVVPGDRIGFVE
+IGAKKSGPLGFAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001256.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001256.fa
new file mode 100644
index 0000000000000000000000000000000000000000..456f8ec6e664d71959c4980162449525c74934d6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001256.fa
@@ -0,0 +1,50 @@
+>0_1484
+MTPHALGLRGPADPTLLERLAALRTELELPPAFPAPVLAEAEAAAREVHAGLTGSPDHAD
+RTALPFVTVDPAGSTDLDQALLLTPADDDGILVRYAIADVPAFVTPGGAVDGEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDREHPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
+>1_1204
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARVRSRAQLT
+YGQVQAFLDARPGAQAPATPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVLVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDADAVAAFRERTRALGVPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPAEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHASGAPAPAWVRS
+ALPELPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWSHSSR
+>2_1362
+MPHRAVALRGRPDPALIERLAALRTELELPAGFPPEVLEEADAAARDVLAALASDPAYAD
+RTDVPFVTVDPAGSTDLDQALYLEAADGDAITVRYAIADVPAFVAPGGAVDVEARRRGQT
+VYLPDGRVPLHPEALSEDAASLLPDRERPAFVWTFVLDAAGAVVDTSLERARIRSRAQLT
+YAQVQAFLDALPDAKAPAAPRPGLDEADHAAHRGWDAPLRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVHVAEDGRHCLVQRAPLPAEDHNAQLSLMTGMAAARLMLEAGVGILRTM
+PAPDAEAVAAFRSRTRALGAPWEEGQDYGAYLRTLDPADPGHLAVLHEATSLFRGAGYTA
+FDAHAEDPELRTPPSEPEQAALAAPYAHATAPLRRLVDRFVLALCHAHATGAPAPEWARA
+ALPEVPALMTESSRRTSAADRAATDLVEAAALQDHVCAELEGIAVRRVKGGAEVWLLDPA
+VTLRVPGEAEPGTRVRVRIEGVDRASGEVTASGVDWPHSSR
+>3_1254
+MPHHALEVRGGPDAALAARLRALRAELDVPGEFPADVLTEAERAAAEVPGRVAADPDRAD
+LTAVPFVTVDPAGSTDLDQALHLQAGPGRDELTVRYAIADVPGFVAPEGAVDAEARRRGQ
+TVYLPDGRVPLHPEVLSEDAASLLPEVERPTFVWTFVLDAEGAVASTDLVRARIRSRAQL
+AYPQVQALLDDDAAPEAADWPAEVRASLALLPEVGARRTAQEAARGGASLSMPDQEISVV
+DGAYTLVQRVPLAAEDHNAQLSLMTGMAAARIMLEAGVGILRTMPAPDPDAVDAFRARTR
+ALGLPWGEELDYGAYLRTVDPTDPRGLAVMHAATTLFRGAGYTAFDRGSVDPALRALPED
+PEQAALAAPYAHTTAPLRRLVDRFVLVLCHAHVAGEPVPDWVRRALPDLPALMAESGRRA
+SAADRAATDLVEAALLAARVGSVLEGTAVRTSEKGTDVQLTDPAVSLRVPGRAEPGTVVR
+VRVDAVDVAAGKVTASGVDWPHSAR
+>4_1411
+MSSHALGLRGPADPALLERLAALRTELELPSAFPTPVLAEAEAAAHGVHVGLAGSPDHAD
+RTALPFVTVDPAGATDLDQALLLTPSDDDGILVRYAIADVPAFVAPGGAVDAEARRRGQT
+VYLPDGRVPLHPEVLSEDAASLLPDRERPAFVWTFLLDAAGAVVETGLERARIRSRAQLT
+YGQVQAFLDAQPGAQAPTTPRPGVTDADRAAAEGWPAEVRDSLALLPEVGRRRAAQEAAR
+GGASLNLPDQEVRVTEDGAHELVHRAPLPAEEHNAQLSLLTGMAAAELMLAAGVGILRTM
+PAPDTDAVAAFRERTRALGAPWDEGQDYGAYLRSLDPADARHLAVLHAATGLFRGAGYTA
+FDAQAEDPALRTPPDEPAQAALAAPYAHATAPLRRLVDRFVLALCHAHAIGAPAPAWVRS
+ALPALPALMADSSRRASAASRTAADLVEAAALESRVGAELEGIAVREAKDGTEVWLLDPA
+VSLRVPGSVPAGTRVRVRIEGVDRASGAITAAGVDWPHSSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001259.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001259.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9cce915b1b3699f17b619cbbc2dceb93981ff99e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001259.fa
@@ -0,0 +1,59 @@
+>0_1488
+MGIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDLATAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVAVAD
+RPDGAVVVPLAAPDGKTLAGLQRGDEIELTDARGAHRRLEVERVSGEGVLVRADKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>1_1208
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GLPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARDPSGIVTEPSRVWLAAGPHDAVATAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEEIVLARSLEPVPAVDTPPYRIGLTLAQAFA
+DAAVGDRVSLDDGRIGARITAVSADEITLEVTQAGPRGAKLKAEKGVNFPDTHLAIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
+>2_1358
+MDIDLTTELTALRDRLLSAEAEHADLISRVRDRHRASARNLVHYVALRGTDLRPLQDALS
+DVGLSSLGRMEAGVLGHVDAVLAAARALDGEDAPSPDDDALTPARGREILARDADRLLGP
+ARPDRAARIMVTLPSEAAQDPDLVARMAEAGMDLARVNCAHDDEAAWAAMIEAVRACATP
+ERPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPARTPAGLVTEPSRVWLAAAGAADAPAGA
+VVVPVTEAGAEVLAGLAAGDEVELTDARGSHHVLTVEQAGAAGALVRADKTVYWGTGLAV
+DTPRGTLTVGELAPLEQSMRVRRRDQVVLTRSLDPVPAASAPPYRIGLTLAQAFEDVAVG
+DRVSIDDGKIDAVVRAANADEITLEVTEAGPNGTKLKAEKGVNFPDTALSIPALTDEDLA
+HIPFVARHADMVNLSFVRSAEDVAQLIDALAAEDATDVDITLKIETVGAFEQLPRMLLEA
+MRWRDVGVMIARGDLAVEAGFERMAELQEEILWLCEAAHVPAIWATQILESLAKTGLPSR
+AEITDAAMAQRAEAAMLNKGPYIEEAITALGDILGRMGGHARKKRDMLRRLESWSL
+>3_1250
+MSTLPENAPDSRPTAESPVVAPGAAVTELIEAIDALRARIVAAEQAHAERLDRVADRHRA
+SARNLVHYVTLRGEDLRPLQDALSAVGLSSLGRMEAGVLGHLDAVRTALHPLGGRPAPDP
+ADDDPLSPAEGRALLAANAESLLGPSRPGRETRIMVTMPSEAATNAALVQGMADAGMDLA
+RVNAAHDGEAAWAAMVANIRGVARDGGRPAPRICMDLAGPKLRTGPLEPGPGVVKVKPRR
+DVDGTVLERSRVWLGEADAPEAADAVVLPLDPAGSGHSPVLSALRPGDHAMLTDARDSDR
+TLHVLAATEAGVLLACRKTVYWHTGLEVDTPRGTLVVGALPSVPQAMRVHAGDEIVLTRS
+MDPRPAVSEGPFTIGCSLPQAFQDVRPGERVLIDDGKITGEVVSNDGEAITLTVTEAGPT
+GAKLRAEKGVNFPDTDLRLPALTDEDRSHLPFAAAHADVVNMSFVRSPADVAALIDALDA
+EDARGVGVSLKIETVGAFERLPAMLLEAMRWNDVGVMIARGDLAVEAGFERMAELQEEIL
+WLCEAAHVPAVWATQILETLAKQGLPSRAEITDAAMAQRAEAAMLNKGPYIDEAIGALSD
+ILTRMGGHADKKRDMLRRLRSWSL
+>4_1415
+MGIDLTTELTALRDRLLSAEAEHADLISRVRERHRASARNLVHYVALRGTDLRPLQEALS
+DAGLSSLGRMEAGVLGHVDAVLAAARALDGDPAPAPEDDALTSAEGRAILARNAASLLGP
+ARGDRDARIMVTMPSEAATDPELVARIAEAGMDLARVNCAHDDEQAWAAMIAAVRRCAGA
+GRPAPLVAMDLAGPKVRTGPIEPGPRVVKVKPTRDPSGTVTEPSRVWLAAGPHDAVAAAD
+RPDGAVVVPLADPEGTTLAVLQRGDEIELTDARGAHRRLEVEQVDGEGVLVRAEKTVYWA
+TGTALTTPHGPLEVGPLPPLEQSMRVHEGEQIVLTRSLEPVPAVDTPPYRIGLTLAQAFA
+DATVGDRVSLDDGRIGTRITGVSDDEITLEVTQAGPRGAKLKAEKGVNFPDTHLDIPALT
+DEDLAHIPFAARHADMVNMSFVRSAEDVAQLIDALEAEDAPDVDITLKIETVEAFRQLPR
+MLLEAMRWRDVGVMIARGDLAVEAGFARMAELQEEILWLCEAAHVPAIWATQVLESLAKT
+GLPSRAEITDAAMAQRAEAAMLNKGPYIDRAVTVLGDILGRMHGHASKKRDMLRRLESWS
+L
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001268.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001268.fa
new file mode 100644
index 0000000000000000000000000000000000000000..10a6c0e1934969d2c636fb7722477a6ab80e2a45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001268.fa
@@ -0,0 +1,30 @@
+>0_1498
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGDAAHTPTFDQLLLDGRRPGDAARPAADVASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIDLPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWSPLVDWIRGTLVERGMISPE
+DPDLFHLVDTAEEAVACVLRSAGRADA
+>1_1218
+MAPDEHPLDGDVAEPEHVRRGGQVLRGEAERTPTFDQLLLDGRQPGDATQPAADIASTTS
+EAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVIT
+GGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQG
+FIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPED
+PDLVQLVDTAEEAVACVLRSAGRADA
+>2_1348
+MDPDQHPRTDAVPAPERVRRGGQVLRGEAARRPTSDQLLLDARRPGDALPPAADLASTTS
+EAWRVLRIQAEFVEGFGTLAGIGPAVSVFGSARTPEASPEYALAREVGARLAEAGFTVIT
+GGGPGSMAAANRGAHEAGGESVGLGIELPFEAGLNEWVHVGVDFRYFFARKVMFLKYAQG
+FVVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVDSTFWGPVVDWIRGTLVERGMISPGD
+PEIFHVVETAEEAVDCVQRVCGPGAP
+>3_1240
+MTDKPDPARADRVDRHRVHRGGQILRGDAAASPTFDQLLLDARRAPAGKTRTPSTSSTSD
+AWRVLRIQSEFVEGFGTLADLGPAISVFGSARTGEGTDEYALGVEIGRRLAEEGWAVITG
+GGPGAMESANRGADEAGGVSVGLGIELPFETGLNPWVGIGVDFRYFFARKVMFLRYAQGF
+VVLPGGFGTLDELFEALTLVQTGTVTRFPVVLVGTEFWGPLVDWIRGTLTARGMISPGDA
+DLITVVDTAEEAVAHVSATCGGARA
+>4_1425
+MAPHEHPSGGDVAAKPQRVRRGGQVLRGEAARTPTFDQLLLDGRRPGDATQPAADIASTT
+SEAWRVLRIQAEFVEGFGTLAGLGPAVSVFGSARTPEGSAEYALAHEVGTRLARAGYTVI
+TGGGPGTMAAANRGAHEAGGESVGLGIELPFETGLNPWVHVGVDFRYFFVRKVMFLKYAQ
+GFIVLPGGLGTLDELFEALTLVQTGTVTRFPVVLVDRGFWGPLVDWIRGTLVERGMISPE
+DPDLVQLVDTAEEAVACVLRSAGRADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001269.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001269.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f0df7a2da8094acd453df826dad56cfa7a7fda6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001269.fa
@@ -0,0 +1,30 @@
+>0_1499
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>1_1219
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAAQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
+>2_1347
+MTQITPEEPHGAHARDEAAPRRPRAAPGDDLIVLENVNKHFGDFHALKDIDLRIPRGQVA
+IVVGPSGSGKSTLCRTINRLETIDDDGGRILLDGQPLPAEGKQLAQLRAEVGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRKADAERHAMELLERVGVAQQAKKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPESFFTAPQHERARDFLGKILAH
+>3_1239
+MSEITSGTVHGSTAASGPAPAAASDALIRLEHVNKHFGEFHALKDIDLAIPRGQVAIVLG
+PSGSGKSTLCRTINRLETIDDDGGRILIDGRPLPSEGRELARLRAEVGMVFQSFNLFAHK
+SILENVTLGPIRVKGRKKAEAERHALELLERVGVAHQAKKMPAQLSGGQQQRVAIARALA
+MEPQALLFDEPTSALDPEMVQEVLDVMVGLAREGMTMVVVTHEMGFARKAGDRVVFMADG
+EILEDTDPESFFTRPQHPRAQEFLGKILVH
+>4_1426
+MTQITPEQPHGAHLPDEAGVRRRRGAAGDDLIVLEGVNKHFGDFHALRQIDLRIPRGQVA
+IVLGPSGSGKSTLCRTINRLETIDDDGGRILVDGRPLPTEGRQLAQLRAEIGMVFQSFNL
+FAHKSILENVTLGPIKVKGKRRADAERHAMELLERVGVAQQARKMPAQLSGGQQQRVAIA
+RALAMEPKALLFDEPTSALDPEMVQEVLDVMVQLAEGGMTMVVVTHEMGFARKAGDRVVF
+MADGAILEDTDPDTFFTNPRHERAQDFLGKILAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001270.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001270.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2021e44452357911323e8fd9a31b15be6962c09f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001270.fa
@@ -0,0 +1,30 @@
+>0_1500
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>1_1220
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGERLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEKDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVDFAGPYFVAGQDLLVRADDTAITGPESLEGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWEKALESNTEGTGYTYDETLNSGEDAEFEPCA
+>2_1346
+MFRKKLLTLSAVTAAAALSLTACSPSAQQGGGEGSGSASAGGSQSAGSGEGLRIGIKFDQ
+PGLGFREGSGAPTGFDTDVARYVADKLGVAEGDIEWVQTPSANRENALENGEVDMIFATY
+SITDARKERVDFAGPYFVAGQDLLVRADDTEITGPDALDGKNLCSVTGSTSAQKIKDQFA
+SGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGNTFTTERYGV
+GIAKGDDRCEDINDAIKEMKDSGAWKESLDANTEGTGYEYDEALNSGADAEFESCS
+>3_1238
+MARSRILSVAAVAAAAALSLSACSPSSSGGSGSASSASGSTAAQSGSSDTLRIGIKYDQP
+GLGFREGQNAPTGFDTDVARYVAGKLGVAEDKIEWVQTPSANRENALENGEVDMIFATYS
+ITDARKQRVDFAGPYFVAGQDLLVRQDDTSITGPDSLNGKNLCSVTGSTSAQKIKDNYAS
+GVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAATDANKGKFKVVGQPFTTERYGVG
+LQKGSDKCKDINEAIKAMKDSGEWEKSLKANTEGTGYEYSEDKNSGADAEFEPCA
+>4_1427
+MLRTKLLTLSAVTAAAALSLTACAPSSSQGGGGDAAGSSSAGESTSSGSGESLRIGIKFD
+QPGLGYREGSAQPTGFDTDVARYVADKLGVAEQDIEWVQTPSANRENALENGEVDMIFAT
+YSITDARKERVAFAGPYFVAGQDLLVRADDTAITGPESLDGKNLCSVTGSTSAQKIKDQF
+ASGVNLVEQGGYAECVTYLESGQVDAVTTDDIILAGLAAADANKGKFKVVGNTFTTERYG
+VGLPKDSERCEDINEAIKEMKDSGEWKKALESNTEGTGYTYDETLNSGEDAEFEPCA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8041ee01d83410a7ab2757583c29c0e83676b67f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001271.fa
@@ -0,0 +1,25 @@
+>0_1501
+MESISSLLADYGADIPLAFWMNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>1_1221
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
+>2_1345
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRAIGTAYVN
+VVRNTPLTIVMLLGVLAVWGQLKITFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDVMVAIFLTFAIGFCLIVIPIGLLTTWASDKWAVAR
+>3_1237
+MESLSTLVEQYGAAVPQAFWMNIRLAALATLGAFVLGVLLALCRISPVPSLRAVGAGYVH
+IVRNTPLTIIMLIGVLAVWGQLKVTFAPDFKVNFFVYAVLALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARAIGLGFLPAARLVILPQALRGAITPIGNTVIALTKNTTVAAAASVAEASG
+LMKTMIEFRPDAMVAIFLTIAIGFCLIVIPIGLLTTWASDKWAVSR
+>4_1428
+MESISSLLADYGADIPLAFWTNIRLAFLATLGSFVLGVVLALFRISPVPSLRALGAGYVN
+VVRNTPLTIIMLLGVLAVWGQLKISFSSDFTLNFFIYAVIALSLYHAAFMCEAIRSGVNT
+VPLGQAEAARSIGLGFLPAARHVILPQALRGAITPLGNTVIALTKNTTVAAAASVAEASG
+LMKRMIEFSPDLMVAIFLTFAIGFCLIVIPIGLLTTWASEKWAVAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001272.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001272.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca8ce694891140090b2c11eae691b62ae4166089
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001272.fa
@@ -0,0 +1,30 @@
+>0_1502
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
+>1_1222
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLHYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
+>2_1344
+MSSQASVLFDAPGPLARRRILIANLVALAAVLALAVAVLMRMADADQLEARRWTAALDAN
+AWTNYYLPGLQFTVQAAAIAVLTSVVFGLVLGFLRLAPFAPVRGAAGLVVEFFRAVPVLI
+MMVFFYQVFAQVARTGVIAPADGPYYAVIVALTLYNGSVIAELVRSGVRSLPKGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQSLVVAALIFIVINFLLTWVATRLSRRLSSRTAGDAGAPTTPVVGAPTDKPA
+>3_1236
+MSAQASVLFDAPGPATRRRILIVNLVALALVLAVAVVVGMALQDRGQLEPRRWLAALDAN
+AWTNYYLPGLQFTLQSAGIAVVTSVVFGLVFGFLRLAPVAPVRWLAAVVVEFLRAVPVLV
+MMVFFYQAFALAARGGAINAADSPYYAVIVGLTLYNGSVIAELVRSGVTGLPKGQREAAA
+AIGMTPNQSLRLVEVPQALVAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGQG
+NILQTLVVAAVIFILINMLLTWLATLLSRRLSSRTSGRTKPHAGSTAVTIGKD
+>4_1429
+MSAQASVLFDAPGPIARRRILLANLVSLAAVLVVAVLVLIQMNATGQLSGRRWLAAVDGN
+AWRNYYLPGLQFTLQSAGIAVVSSVVFGLVFGFLRLAPVGPVRWLAAVVVEFFRAVPVLV
+MMVFFYQLFAQVARSGAIQPQDGPYYAVIAALTLYNGSVIAELVRSGVRSLPRGQREAAA
+AVGMTSTQSLRLVEVPQALIAMLPSLLSQFVVILKDSALGYLIGFFELLQYARQLGSGNG
+NILQSLVVAAMIFIVINFLLTWAATRLSRRLSSRTAGDASAPTTPRVGAPTDTAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001273.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001273.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3ac9a3804fccb394181b83c44827c9683f6a449
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001273.fa
@@ -0,0 +1,40 @@
+>0_1503
+MSLTPNTLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA
+VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA
+LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV
+EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL
+HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS
+PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV
+SREAVHACLAALTAWLAG
+>1_1223
+MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEHALRALGGLEVRRFGDA
+VVARTALGRPTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA
+LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV
+EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL
+HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRAVLEGAGVDWDAQVRIDDAS
+PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV
+SREAVHACLAALTAWLAG
+>2_1343
+MTETSAPALPDLADPGLDVAELTAVLLDVPSVSGDEGPLADAVETALRALGGLEVRRFGD
+AVVARTDLGRDTRVILAGHLDTVPLPTVPGSRGTVPSAWEGDVLYGRGAVDMKSGVAVQL
+ALAGRYGRADGPAPAHDVTWVFYDHEEVASDLSGLARVARQAPELLEGDFAVLLEPTDGV
+VEGGCNGTCRYRVSFSGVAAHSGRAWRGENAIHKLGAVLTALAAHEPATVTVEGLDYREG
+LNAIRVAGGVAGNVIPDAAHVDVNYRFAPDKTLEQAHARVREVLEGAGVDWDAQVRIDDA
+SPAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH
+VHRAAVHACLDALDAWLAG
+>3_1235
+MTDAVAPVLPDLAAADLDVAALTATLLDAPSVSDDEGPLADAVEAALARLPRLGVRRFGD
+AIVARTELGLPGRVILAGHLDTVPLPTAPGARGTVPSAWEGDVLYGRGAVDMKSGVAVQL
+ALAGLFGRADGPDPVHDVTWVFYDHEEVDSARSGLARIARQAPELLEGDFAVLLEPTDGV
+VEGGCNGTCRYRVRFEGVAAHSGRAWRGDNAIHKLGALLSALAAYEPATVTVEGLDYREG
+LNAIRVSGGVAGNVIPDAAATEVNYRFAPDKTLEQAHAHVREVFAAAGVDWDAQVEVTDA
+SPAARPGLDRPAAAAFVAAVGGEPMPKYGWTDVARFSELGVPAVNFGPGDALLAHTDDEH
+VERAAVERCRDALEAWLRG
+>4_1430
+MSLTPVSLPDLADPDLDVAALTATLLDVRSVSGEEGPLADAVEQALRALGGLEVRRFGDA
+VVARTALGRSTRVILAGHLDTVPLPTVPGSRGTVPSAWDGDVLYGRGAVDMKSGVAVQLA
+LAGRFGRADGPTPVHDVTWVFYDHEEVSSDLSGLARVARQAPELLEGDFAVLLEPTDGVV
+EGGCNGTCRYRVTFSGVAAHSGRAWRGDNAIHKLAPVLTALAAYEPATVTVEGLEYREGL
+HAIRVAGGVAGNVIPDEASVDLNYRFAPDKTLEQAHAHVRTVLEGAGVDWDAQVRIDDAS
+PAARPGLDRPAAAAFVAAVGGEPQPKYGWTDVARFSQLGVPAVNFGPGDALLAHTDDEHV
+HREAVHACLAALAAWLAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001275.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001275.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0b0774aabd8df54e579e519b1d1b12666428c30
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001275.fa
@@ -0,0 +1,45 @@
+>0_1506
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDQEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPAAKIGRPRQIYVGE
+QLRQYPQR
+>1_1226
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSALSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
+>2_1341
+MTQNESVRLTVGEQSLDLGVERATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDEGILRYRGYAIEDLAANSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYEIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRTIQSDGIKPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILSKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+PLRQYPQR
+>3_1233
+MSEIESARLTVGEKTLDLGVEKAAEGNDGIVVAPLLKETGKVTYDPGFMNTANAKSAITY
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKEALEAWETNILRHNMVHEDL
+KMFFNGFPRDAHPMPVLSSSVSALSTFYADSLDPKDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNNLNYVENFLRLCFGVPAEEYEIDPDMVKALDLLLMLHADHEQNASTST
+VRLVGSTDANLFASVSAGINALYGPLHGGANEAVLNMLRRIQAEGIKPEDFMEKVKHKED
+GVRLMGFGHRVYKNYDPRAKIVKKTAEDILAKLGGNDELLEIAMRLEEKALADDYFVERR
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELTEDPATKIGRPRQIYVGE
+QLRQYPQR
+>4_1433
+MTHHESVRLTVGEQSLDLGVEHATEGNNGINIAPLLKETGDVTYDPGFMNTANAKSAVTF
+IDGDQGILRYRGYAIEDLAEHSSFMEVAYLLIYGELPESKETLEAWETNILRHNMVHEDL
+KLFFNGFPRDAHPMPVLSSSVSGLSTFYPDSLDPHDPEQVHISTVRLLGKLPVLASYAFK
+KSLGQPFMYPHNSLNYVENFLRLCFGVPAEEYDIDPDVVKALDLLLMLHADHEQNASTST
+VRLVGSTQANLFASVSAGINALYGPLHGGANEAVLNMLRKIKSEGITPEDFMEKVKNKED
+GVRLMGFGHRVYKNYDPRAKIIKKTAEDILGKMGGNDELLEIAQRLEEKALADDYFVERK
+LYPNVDFYTGVIYKAMGFPEKMFTVLFALGRLPGWIAQWRELMEDPATKIGRPRQIYVGE
+QLRQYPQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001276.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001276.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07617dda5b2edcc4fb9134a758411dd7b626840c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001276.fa
@@ -0,0 +1,40 @@
+>0_1507
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDDLRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARDV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPQLVATLINTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGELADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>1_1227
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADGLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGAGGDGYVRVA
+ITATDEAVARAAARLTARGPRTG
+>2_1340
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPELIRRALTEAADAHGYPTTHG
+TADLRRAVVDWYARRRGVAGLDPEAVVPTVGSKEFIAWLPTLMGLGAGDVVVHPEAAYPT
+YAMGALIAGAEAVAADDLASLAPEVRERVRLVWTNSPANPTGAVLDAAALKRVVDDARAL
+GAVVCGDECYAELGWDEWDGELVPCILSEEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPGLVATLVNTRKHAGMIVPAPVQHAMAVALADEGHVAQQKDRYRRRRDALRAALEASG
+HAVDHSEAGLYLWTRRADTDPAAATEQDSWDLLGELADLGIIAGPGVFYGAGGHGYVRVA
+ITASDEAVEQAARRLAARGPLRR
+>3_1232
+MLTLPDYPWDTLAPYRERAAAHPEGTVDLSIGTPVDPTPALIRDALTAAADAHGYPTTHG
+TAELRQAVVDWFARRRGVPGLDPEAVLPTVGSKELIAWLPTLLGLGAGDVVVFPATAYPT
+YAIGAQIAGAEAVAADTLAELDDDVRSRVRLVWTNSPANPTGAVLDAAELRAIVDDARAL
+GAVVCGDECYAELGWDEWEDRVVPCILAPEVSGGDLTGLLSVYSLSKQSNLAGYRAAFVG
+GDPELIAPLTNTRKHAGMIVPGPVQHAMAVALRDDAHVAAQRDLYRERRAALKAALESAG
+YAVDHSEAGLYLWTRRADLAPGQGTAQDSWDLLGELAELGIVAGPGVFYGAAGHGHVRVA
+ITASDEAVAAGAARLTARGPLPR
+>4_1434
+MLTLPDYPWDTLTPYRERAAAHPDGVADLSIGTPVDPTPALIRRALTEAADAHGYPTTHG
+TDALRRAVVDWYARRRGVSGLDPAAVVPTVGSKEFIAWLPTLLGLGAGDVVVHPEAAYPT
+YAVGALLAGAEAVAADDLDALAPEVRERVRLVWTNSPANPTGAVLDAAALRRTVDAARGV
+GAVVCGDECYAELGWDAWDGAVVPCILSDEVSGGDLTGLLSVYSLSKQSNLAGYRAAFAA
+GDPELVATLVNTRKHAGMIVPAPVQHAMAVALADDAHVAEQKDRYRRRRDALRTALEASG
+HTVDHSEAGLYLWTRRADLDPADATAQDSWDLLGDLADLGIIAGPGVFYGGDGYVRVAIT
+ATDEAVARAAARLTARGPRTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eddf3511386f14d31dd3d5ed70a9e70c79c341b3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001277.fa
@@ -0,0 +1,15 @@
+>0_1508
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>1_1228
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
+>2_1339
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPEEWADYYKANVEFFDDLGSPGGAAKLGMIAKDHPIIAALPPQNADA
+>3_1231
+MTYVIALPCVDVKDKACIDECPVDCIYEGERSLYIHPDECVDCGACEPVCPVEAIYYEDD
+VPEEWADYYKANVEFFDDLGSPGGAAKLGQIAKDHPLISALPPQGEGA
+>4_1435
+MTYVIALPCVDVKDKACIDECPVDCIYEGERMLYIHPDECVDCGACEPVCPVEAIYYEDD
+TPDEWAEYYKANVEFFDDLGSPGGAAKLGMIAKDHPIISALPLQNADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001284.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001284.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e059dc1df845833377fe2f9c4e5af455e2a26327
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001284.fa
@@ -0,0 +1,40 @@
+>0_1517
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLTGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
+>1_1237
+MTPPGWPPRARRAPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHVHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGETVAAVGNGGGQGHLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTAEEVDGFAIPLDVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRPVGDDAFRMSRLV
+NDHNVGDRITVQWRTASGEVREAEAVLQPALVN
+>2_1328
+MSVPPGWPPRRRRSPLALAISFFGVLGALVLAVGVTLLVAGRMVDVVGAPDPVVSARESA
+PPDAGALAQELAGAHEGVAVDWDAPAHAGSELDPGLAVDHAPGILLVETVLGQRMGTGTG
+MVLTPEGLALTNYHVVEDSSEVFVVEADTGERHTATVLGRDAEHDVAVLDVHGVTDLPVA
+SVSLDPVRRGDEVAAVGNGRGQGHLTAVRGTVLGTDRSIMAASQGSDEYARLTGLIQTDA
+DVVPGYSGGPVVDDDGQVVGVTVAASDGTGAQEVDGFAIPLGVALGVVDQVLSGEETDTV
+SIGADGALGIMVAADPEAGVVVMQVDADSAAEAIGLVPGDVVLAVDGQAVEGNASRMSRL
+VNDHNVGDRITVTWRTASGEVREAEAVLQEAVVN
+>3_1222
+MAIAVFGVLGAVVLAVGLTLLAGGRLIAAVGAGSSSSAAAPSGPQVTTRSLDALAASLDH
+AHAGIAVPAADAPPADGSLDPGERVRRAPGVLLVETRLEAMQGTGTGMVLTSDGLALTNY
+HVVEDSTAVSVVVADTGARHAATVLGRDAKNDVAVLQIDGVSGLTTTSVSRDPVRPGEAV
+AAVGNGGGQGYLTSVGGEVLRVDQSILAATEGTDDFERLTGLIQTDADVVPGYSGGPLVD
+GEGQVVGVTVAASEGRTAAQVDGYAIPLSTAFDVVAQVLSGEETDSVSIGADGSLGISVA
+GSRDGVEVLSVDRGSAGEELGLRPGDVITAIDGRTLDGNATAMSRLVNDHEVGDRLSVQW
+RTADGEARQGEAVLQKARHN
+>4_1444
+MTPPGWPPRARRSPLAFVIALFGVLGALVLAGGLTALLAGRMVDVAADSAPTVPAAEAPA
+REAGELAAGLTHIHDGVAVDWSASAHDGSSLDPGQPVADAPGILLVETALGARTGTGTGM
+VLSPDGLAVTNYHVVEDSSEVHVVVADTGARHTATVLGRDAEHDIAVLDVEGVSDLPVAS
+VSLDPVRRGDQVAAVGNGGGQGYLTAVRGTVLGTDRSIMAAAEGTDQYARLSGLIQTDAD
+VVPGYSGGPVVDDAGQVVGVTVAASDGTTADEVDGFAIPLEVAFDVVDQVLSGEETDTVS
+IGADGALGIMVGADPDVGVVVMQVDAGSAAEQIGLVEGDVILEIEGRAVGDDASRMSRLV
+NDHNVGDRITVQWRTADGEVREAEAVLQPALVN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001285.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001285.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d7bbb955f28766032e4fceb0a5c48967732ff457
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001285.fa
@@ -0,0 +1,20 @@
+>0_1518
+MATTHMKSTPVHTVGELPQVGSPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGGDYGVRM
+TDGPLEGLLARAVVMVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>1_1238
+MATTHMKSTPVHTVGELPPVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLEDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
+>2_1327
+MATTHMKSTPVQTVGDLPEVGAPAPDFTLTGADLSPVTLQELRGRRVILNVFPSLDTGVC
+AASVREFNSRATDLEDTTVLAVSADLPFAAARFCSAEGIENVRSGSVFRSSFGDDYGVTM
+VDGPLEGLLARAVVVVDAEGVVRHAQLVPEITEEPDYEAALAAAQA
+>3_1221
+MATTHFKGTSVHTVGELPEVGSAAPEFTLTGSDLSSVTLADLKGRTVVLNIFPSLDTGVC
+AASVRRFNQEAAGLEDTTVLAVSADLPFAAGRFCSAEGIENVVTGSVFRSDFGTAYGAEL
+ADGPMRGLLARAVVVVDAEGTVAYTELVPEITTEPDYEAALAVVRG
+>4_1445
+MATTHMKSTPVHTVGGLPQVGAPAPDFTLTGADLSPVTLRELRGRRVILNIFPSLDTGVC
+AASVREFDSRVADLGDTTVVAVSADLPFAAARFCSVEGIDHVRSGSVFRSSFGDDYGVRM
+TDGPLEGLLARAVVVVDADGVVRHAQLVPEISEEPDYEAALAAARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001288.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001288.fa
new file mode 100644
index 0000000000000000000000000000000000000000..395ff791fe50321458263a003c3f4d8bb0201609
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001288.fa
@@ -0,0 +1,19 @@
+>0_1521
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>1_1241
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMAAWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
+>2_1324
+MTGVTAADGLDLSGMAAWLRHQADEEIVHANKFIDHVTDRGSDAAGDLSSRPLLNWFLEE
+QIEGEATPPL
+>3_1218
+MSIDKDLTRKFNEQITLEFEASMVYRQLAIAADMQDLSGMAAWLRHQADEEIVHANKFID
+HVVDREASAVIGAIPAPDVPEHITPVQIFEAALAHERKVSEAIRELYRAAEAAGDLSSRP
+LLNWFLEEQIEEEATVGEIVGQLKLVGEDGSGLLRIDSALGARPVETTENAG
+>4_1448
+MKLTDDLLQKFNDQITLEFEASMVYRQLAIAADDLDLSGMASWLRHQADEEIVHANKFID
+HVADRDSFPTIGAIPAPPVQAGLSALEIFRAALAHEQKVSEAIRELYRATESAGDLNSRP
+LLNWFLDEQIEEEATVSEIVGQLELVGDDGSGLLRIDGRLGSRPVETTENDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001290.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001290.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a5a2c1a1e4587aa9c17f6e91e39bd4510a71eb6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001290.fa
@@ -0,0 +1,30 @@
+>0_1523
+MNTTAAASDPSDAPLASTRIGEGPRGVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLI
+VEDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>1_1243
+MNTTAAASDPSDAPLASTRIGEGPRRVAFLHGLLGRGRNFTGPAKELGDDFTVELIDLPD
+HGASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPDLVDRLI
+VEDISPRVSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRR
+TAGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVFDHPVLWLAGAESDYVQDEDVPRM
+KELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>2_1321
+MTISDQGSPRRLPDSLERVSTPDPSASAAPSDAALASDVIGDGPHRVAFLHGLMGRGRNF
+TGPAKALADDFTVELLDLPDHGRSPWTDRVDYQEIADRVAEHLRAGLAADGPVHVLGHSM
+GGKVAMVLALRHPDLVDRLIVEDISPRLLPQATDEFVHLLGTMLRMDLDSYESRAEADAV
+MAKHVHDARVRGFLLQNLRREGGRFAWQPNVAMLFEHLEAVGSFPDPAAPEDPDRVFDRP
+VLWLAGANSDYVRDEDVPRMKDLFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
+>3_1215
+MPTWSRASLSRVNTTAASAPSDAPLASTRIGEGSRRVAFLHGLMGRGRNFTGVATALADD
+FTVELIDLPDHGQSPWTDAVDYQDMADRVADHLRAGLAADGPVHLLGHSMGGKVAMVLAL
+RHPELVERLVVVDISPRMSPSATGEFVHLLGTMLRMDLASYTSRAEADAAMAEHVHDARV
+RGFLLQNLRREDGHFAWQPNVRMLFEHLDEIGAFPDPVVPEDPDRVFDRPVLWLGGADSD
+YIRDGDAPEMKALFPRVVRVTVRGASHWVHADQPEAFVSAVRTFLTAD
+>4_1450
+MNTTAASAPSDAPLASTRIGEGPRRVAFLHGLMGRGRNFTGPAKELGDDFTVELIDLPDH
+GASPWTDRVDYREIADRVAAHLRAGLAADGPVHLLGHSMGGKVAMVLALRHPELVDRLIV
+EDISPRLSPQATDEFVHLLGTMLRMDLDAYDSRAEADAAMAEHVHDARVRGFLLQNLRRT
+AGHFAWQPNVAMLFEHLREIGSFPDPVVPEDPERVVDHPVLWLAGAESDYVQDEDVPRMK
+ELFPRVVRVTVRDAGHWLHADQPEAFVSAVRTFLTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..af4ee1cf57283f518df584286d0eff2ba3760c62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001291.fa
@@ -0,0 +1,30 @@
+>0_1524
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPVLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>1_1244
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGALEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
+>2_1320
+MPAPEARVTVAVSTAVFGVRPDPSGAPRLHVALVPRMREPFLDRWALPGTWLAADEELAD
+AAARVAAETVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPSHGGGLD
+VAGLPAGVHVRWQRADAPPAMAFDHAEILTAAVARLRADLPRAGVAHALLGPSFTLAELR
+AVHEAVLGRTLDAANFRRATLATGVLEETGEVRAGTRHRPPKLYRYRPADGAPPPAAPDD
+PGDLS
+>3_1214
+MPVAEARVSVAVSTAVFGVRPDAHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPTLDDDGAAPASRPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRDGTPHRPPKLYRYRPAGPGTDPNPAGP
+DASR
+>4_1451
+MPVAEARVSVAVSTAVFGVRPDPHGVPRLCVALVPRMREPFLDRWALPGAWLGADEELAD
+VAARVAAECVPGPVRRLEQLAAFGAVDRSPTGRVLTVAHWALSPALDDDGAAPASSPDPD
+VAGLPIGVHVRWHRADAPPALAFDHAQILAAAVARLRADLPRAGVGHALLGPSFTLAELR
+AVHEAVLGRGLDAANFRRATLAAGTLEETGEVRGGTPHRPPKLYRYRPAGPGTDPDPAGP
+DARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001292.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001292.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dff5f6779ef6f34773939701cb72ed989b05d414
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001292.fa
@@ -0,0 +1,45 @@
+>0_1525
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVAEPART
+ALERMLAVAPKQSAAQSAGAGT
+>1_1245
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
+>2_1319
+MTATPETTASVARTLTLVARDPARGSACSSDLTTGPWAFDAGLPAYGPGASQDDAIPADA
+PVQGRIPEEYQQASDEELHARIAAAKAALGDRAVVLGHFYQRDEVVRHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPEQAVILPNLAAGCSMADMADLDSVQDAWEQL
+EEVYGTEPDADGRVPLLPVTYMNCSAALKGFVGERGGIVCTSSNASAVLEWAFERAQRVL
+FFPDQHLGRNTGRAMGIELERMPMWNPRLPLGGNTEETLRDARVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVRVIVHPECPLPVVEAADESGSTDHIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPDAVADPARA
+ALERMLAVAPRQSVAQGAGA
+>3_1213
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPAAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRMPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALREAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPVSVADPART
+ALERMLAVAPKQSAAQSAAQSAGAGT
+>4_1452
+MTTPTGTTASVARTLTLIDKDAARGSSCSPDLTRGPWAFDAGLPAYGPGASQDDAVPADA
+PVQGRIPEEYQRASDEELHARISAARQTLGERVVVLGHFYQRDEVVQHADFVGDSFQLAR
+ASQGRPEAEAIVFCGVHFMAETADLLSTPDQAVILPNLAAGCSMADMADLDSVEDAWEQL
+EAVYGTEPDDDGRVPLLPVTYMNSSAALKGFVGERGGIVCTSSNASAVLDWAFERAQRVL
+FFPDQHLGRNTGRARGIPLEQMPTWNPRLPLGGNSEDALRDAKVLLWHGFCSVHRRFTVA
+QIEQARAEHPDVQVIVHPECPLPVVEAADSSGSTDFIVKAIQAAPAGSTFAIGTEINLVQ
+RLAAQHPEHTIFCLDPVICPCSTMYRIHPGYLAWVLEELVAGRVVNRITVPASVADPART
+ALERMLAVAPKQSAAQSAGAGT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..443f428da7c10aacb3e58e67e3c9b59ce5a3caec
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001310.fa
@@ -0,0 +1,23 @@
+>0_1574
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGDTVDEVLFVPYGETAEAAFRAALGHLEAPQTT
+DDEGDTGR
+>1_1289
+MQLTIAPGDITATHADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVEEVLFVPYGDTAEAAFRTALDRVERG
+>2_1243
+MELLIAPGDITATTADVVVNAANSTLLGGGGVDGAIHRRGGPEILAACRRLRETELPDGL
+PVGQAVATTAGRLPARWVVHTVGPVWAKTIDKSATLASCYRESLRVAAELGARSVAFPAI
+SAGVYGWPMDDAARIAVTTCREVAAQGAGSVERVLFVPFGERAEAAFRAALDAPDETGAP
+AAS
+>3_1152
+MKLSIAPGDITATHADAIVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPDGL
+PAGQAVATTAGRLPARWVIHTVGPVWAKTIDKSDTLASCYRESLRVARELGARTVAFPAI
+SAGVYGWPMDDAARIAVETSHAMADEVGDVVEEVLFVPFGDRAEAAFRAALEHLT
+>4_1503
+MQLTIAPGDITATRADAVVNAANSTLLGGGGVDGAIHRRGGPEILAECRRLRETDLPEGL
+PAGQAVATTAGRLPARWVIHTVGPVWAETIDKSDTLASCYRESLKVAAGLGARTVAFPAI
+SAGIYGWPMEDAARIAVETCHAMADEVGGTVDEVLFVPYGETAEAAFRAALGHLEDPQAT
+DDEGDTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001313.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001313.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ee3eee447cc27d8f8bb2ca994af6aef693b5da41
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001313.fa
@@ -0,0 +1,51 @@
+>0_1577
+MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGI
+TFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLILGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVQIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAA
+LAWITVPLISEYVLDLESPLLSDAAIAIVVGLILFLLPAGGGAGRGVRLLDWEAAKDLPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIASVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISIASMTLLVWVFGL
+>1_1292
+MESRSIPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLTGGENVKRIIGLVAGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVIFPLGVPAEESDGGI
+TFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLVLGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDDALTGDEAAGQVDRPAAPASAPGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDEVPGGRDLIATELARLGRMSAPEAKVLAVFVLAA
+LAWITVPLISEYVLDLKSPLLSDAAIAMVVGLILFLLPAGGGAGRGVRLLDWEAAKELPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGFGDIPVWVLVVIAAVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISLASMTLLVWVFGL
+>2_134
+MSSSLAFEGRAVAGAAVWMAVWWMTEAVPIPVTSLLPIVRFPLFGMGTMAEVASPYANSV
+VFLVMGGVILGLATEKAYLLENHDDDMQFGRWMLVGVPWAIVMLLIAWVVLTKLVFRAEV
+DRIPGGAEMIRGELAKLGPMTTPERRIALIFATAIFFWVAVPFIADIPAVADVAPWLGTI
+DDTQVAIAAAIACFIVPARRRGEDASQTALLQWSASKEIPWGLLLLFGVVVGLALTELTS
+NTATEAAFFPIFGAVALGLGMDPIFMTIAVTLAVCSAYMLPVATPSNAVAFGSGEVSIKQ
+MVRAGVGLNVVSIGLIMLVMYTLVPAVFG
+>2_1240
+MASRPVPPPSNVNEHVSRFAPQAAAQEFEHETSPGMRDQPLTGGEHTKRIIGLVAGPLLA
+IGLFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAAESDGGV
+TFDSIGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKLMGAKTVNLVLGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTEDALAADAVPAAEQSAPGEAPTQAEIRSL
+TKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMATEHGIEIGFGQWMLVGVPIAV
+VLLLACWLLLTRVMFRPEIDEVPGGRDLIAAELARLGRMSAPEAKVLVIFVLAALAWITV
+PLLSEYVLGLDSPLLSDAAIAMVVGLVLFLLPAGGGAGRGVRLLDWEAAKELPWGVLLLF
+GGGLALSGQFSKSGLSTWLGEQVRSLGEIPVWVLVVIAAIGILLLTEMTSNTATAATFLP
+VASGVALGTGVEPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKGGVWLNI
+TAAVLISVASMTLLVWVFGL
+>4_1506
+MESRPLPPPSNVNEHVSRFDPRAAAQEFEHELSPGMRDEPLPGGENVKRIIGLVVGPLLA
+VALFLLMPGDLGVWPRLVAATAVLMAVWWMTEALPIPATALLPLVVFPLGVPAEESDGGI
+TFDAVGASYGNNIIFLFMGGFMLALAMQRWNLHRRIALGVLKFMGARTVNLILGFMIATG
+FISMWVSNTATAVMMLPIGVSILVLVQRYGTDGALTADEGADQVDRPAAPASAAGEAPTQ
+AEIRSLTKSNFGTALMLGIAYAASIGSLGTIIGTPPNTLLAGHMAAEHGVEIGFGQWMLV
+GVPIAVVLLFACWFLLTRVLFRPEIDVVPGGRDLIATELARLGRMSAPEAKVLAVFILAA
+LAWITVPLISEYVLDLTSPLLSDAAIAMVVGLILFLLPAGGGAGRGVRLLDWEAAKELPW
+GVLLLFGGGLALSGQFSKSGLSTWLGEQVKGLGDIPVWVLVVIAAVGILLLTEMTSNTAT
+AATFLPVASGVALGTGVAPLMLAAPVALAATCAFMLPVATPPNAIAYGSGYVTIGQMVKG
+GVWLNIIAAVLISLASMTLLVWVFGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001316.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001316.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6d5cea5f842cad5c661f7affc97920eae0851bd8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001316.fa
@@ -0,0 +1,45 @@
+>0_1580
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPRRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
+>1_1295
+MDQPVTEGASAASDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVATTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFETREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDIRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVRDADQVAPDDRLDILVAVGRIAADVV
+ATHRPTPTPSHERTRQA
+>2_1236
+MDPSSTAHVEADALLDAGVPATASQTSAERPWPLRRLSENLKLHIERAPATWIEGQLIEY
+KTNRGNVYMTMRDLEEEYSLPVTAWRNVAVTFEGTVQQGSRVVARVKPNFWTKAGRLSMV
+VQEMRPVGLGDLLARVELLRRRLGEEGLLDPARKRPLPLLPGLVGLITGRDSDAKKDVLR
+NAQLRWPAVRFEVREVAVQGPEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADVRASTPTDAAKRIVPDAAQEAAGIAEA
+RRRLAAAVERRVQREGEGLAQLRSRPVLADPVVMVDGREQDLHAWRERARRATAHRLTRE
+RDAVEHLVARVRALSPQQTLDRGYAVVQQEGRLIRDAAQVAPGEDVDILVASGRISAEVT
+AVRPGRVGGVGTVQDEDEQAGTKEQA
+>3_1146
+MEESAAREEGTVVVPATASETSPERPWPLHRLSENLKLHIERAPATWIEGQLIEHKNNRG
+NLYMTMRDLEEEVSLPLTAWRAVAAGIDPSVQQGSRVVARVKPNFWVKGGRLSMVVQEMR
+PVGLGDLLARVELLRRRLAEEGLTSPARKRQLPVLPGVIGLITGRDSDALKDVVRNTHLR
+WPAAVFEVREVAVQGPDAPRQVAAALAELDARPEVEVIVIARGGGALEEVVLPFSDEALV
+RAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQESVGIREARLRLA
+GAVERRVRGEADALAALRSRPVLAHPHVMVDTRTEDLGRWQERGRVALGHRLAREADAVS
+ALRAQVRALSPQQTLDRGYAVVQHAGHVVRRAEDVTPGDDLDVLVAAGRIEAYVTDVTPV
+ETPSPTQEDA
+>4_1509
+MDQPVTEGASAAPDVPVSAPARAGETSAERPWPLRRLSENLKAHIERAPATWIEGQLIEF
+KNNRGNVYMTMRDLEEEVSLPLTAWRNVAMTLDGTVQQGSRVVARVKPNFWLKAGRLSMN
+VQEMRPVGLGDLLARVELLRRALAEEGLTSPARKRPLPLLPHRIGLITGRDSDAKKDVLR
+NTLLRWPAAEFEIREVAVQGAEAPRQVAAALAELDADPAVDVIVIARGGGALEEVVLPFS
+DEALVRAVAAARTPVVSAIGHEADRPVLDDVADLRASTPTDAAKRIVPDAAQEAAGLADA
+RLRLAAAVERRVRAEAEGLAALRSRPVLARPHVMVDTRQEETDRWRERGRSALGHRLVRE
+EDALTQLRARVRALSPQRTLDRGYAVVQHAGQVVREADQVATDDRLDILVAAGRIAADVV
+ATHRTTPTPSHERTRQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001324.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001324.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eede4bb67f8ef5cc5e4529e3432a0dd9d23b13d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001324.fa
@@ -0,0 +1,33 @@
+>0_1589
+MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLSAAADAARAARGRTGLHIRWGRTALFLAALVALLVFLVA
+GLAAAFGAGTLALAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPAAPAAEERQ
+APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRVVTIPAVPR
+PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR
+RAC
+>1_1304
+MDETTPPTTAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLGAAADAARAARGQTGLHIRWGRTALFLAALAALFVFLVA
+GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAADVVPARPAAPAAEERQ
+APPADPERDRRVLETVLAFETEAPRPAAAPAASRVEPVVVTASAAAPAADRAVTIPAVPR
+PTYLDAPEMARPLPAPLETPAPTGADTRLQDAASTADDRISAAAEQDIAALDLDNVLARR
+RAC
+>2_1225
+MEDTTAPASAGRAALDALADARVSASFVILALVAYFAWRLVVRRRRVESAPARPTMLRST
+MHRLQSSPAVRALTERLSGRVSGLADSARAAGRRTAGLQVRWGRTALFLAALAALAVALV
+AGVAAAFGAGTAGLAGACLLFAVAAVAGLRALAVRDRARRAPAAVVEAPAEAAPHAAPEA
+PRVDPERDRRVFETVLGLEDEAARVSAAAPAAPAAAPTVVAASAVRAPEATDTVTLPVVP
+RPTYLDAPEMLRPAPAPLTAPEAAGSDVRLKDAARAAEHEEALSATAEQDVAALDLDHVL
+ARRRAS
+>3_1137
+MTETPSPREDARLDAEPGHADSGFHVHWDRASLFLVGVGALAVALVTALCALAGLPTAGL
+AGWSLLVTVGAVVGLRVLAARDQREHHDDLADDADEPNLAEEDLDTHELPVVPDPERDRR
+VLAAALSLTDEAEDEEPAAEPVPVVVDALQRRRAPRIPLGGIVIPEVPRPTYLDAPEAPA
+AEAQAEYPAEDDAVATRPEAEEQAASAEVVEIPEPAARAVVLDLDGVLARRRAS
+>4_1519
+MDETTAPTRAVQAALDALADARVSASLVIVALVAFLAWRLVLRRHRLASAPARPSMPRSF
+MHRLQSSPAVRALTARFSGRLSAAADAARTARGRTGLHIRWGRTALFLAALVALLVFLVA
+GLAAAFGAGTLSLAGWSLLFAVAGLAGLRALAVRDRTRRARPAAVVVPERPTAPAAEERQ
+APPADPERDRRVLETVLAFETEAPRPAAAPAAPRVEPVVVTASAAAPAADRAVTIPTVPR
+PTYLDAPEMARPLPAPLETPAPTGADTRLTDAARTADDQISAAAEQDIAALDLDNVLARR
+RAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001325.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001325.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02818f37619781cc45c83fca00298e5b710eadf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001325.fa
@@ -0,0 +1,25 @@
+>0_1590
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMALDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLAGWLATRPRP
+>1_1305
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGAGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREA
+GRGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGA
+WRDHRTFAVTAEEVPDGLLARWLASRPRA
+>2_1224
+MSWQRSPWPVTLRHGTLSLRPLRRRDRDAWEAQRAHNHAWLTPWDATSPVPGAGPSSFGQ
+MVRWHGRQGREGSSFTWGVALDDDAPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMAADWAFRSAGLHRVEVNIRPENAASLRVVEKLGLRDEGVRRSYLHVDGDW
+RDHRTFAITAEEVPEGLLARWLASRPRA
+>3_1136
+MDVSGSLWPVALRHGTLTLRPLRRGDRRAWEEQRAANRDWLTPWDATSPVPGAAPASFAQ
+MVRWQHRQARAGTSYTWGMALDDDAPGRDRLIGLLSLGGVQHGSVMSGAVGYWIDRRQAG
+RGLTPTAVAMATDWAFHGLGLHRVEVNIRPENTASLRVAEKLGLREEGLRRAYLHVDGAW
+RDHLSFAVTAEEVPEGLLPRWLARREAAAGTAEPRDTAHTPGVAGDVPGPSGR
+>4_1520
+MSWQRSPWPVTLRHGTLALRPLRRRDREAWEEQRAHNREWLTPWDATSPVPGVGPASFGQ
+MVRWHGRQGRDGSAYTWGMVLDDDRPDRDRLVGLLSLGGIQYGSVLSGSIGYWIDRREAG
+RGLTPTAVAMATDWAFRSAGLHRVEVNIRPENAASLRVVAKLGLRDEGLRRAYLHVDGAW
+RDHRTFAVTAEEVPDGLLARWLATRPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3f60922a0a929509da2a3edc468efb3f1f426aac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001346.fa
@@ -0,0 +1,35 @@
+>0_1614
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAFVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAILVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>1_1329
+MTRQDTRETGPSGRRFGATELPPEIERVVQQAKRLEWVTLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLIALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLTLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRATTIDGARPHPLIDRAERVAWAEPWVRHAGARVRDEGHVFHVEMFVVPHEGADVTVAR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
+>2_1201
+MTHHASTTHRSPGGRRFGATELPPEIERALRRAVRLEWATLAVLAVTIALVAVVMGSSQA
+MRAAWIEDLLSLVPPIAFLVAVRVTRRHPTRARPYGSHRSVGVGHLVAAVALSVMGVILV
+ADSALGLVTGEHPPIGTLDLFGHTVWQGWFMMAVMALSIPGPVLLGRAKLKLAEQLHDRV
+LYADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWRNLREAVGNLA
+DRRATTIDGDRPHPLIDRAERVAWAQPWVRHAGTRVRDEGHVLHVEMFVVPHEGAGATVG
+RCAQLREEIVALDWKLEDVVVVPVAELPAEVHGGASGDEQSGEE
+>3_1113
+MSEKRTIGRAELPDDVARAAHQAVVLEWVSLGWLVLTVSLVAVVMGSSQAMRAAWIEDLL
+SLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVGDSLLGLLTA
+EHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVLYADADMNKA
+DWQTGVATIVGVAGIGLGWWWADAAAAIFVGVSIVLDGWKNLKEAVTNLADRRATTIDGA
+RPHPIIDRAERVAWAQPWVRHAGARVRDEGHVFHLEMFVVPRHGADVTVGRCADLRERIE
+ELDWKLEDVVVVPVAELPEEVHGGRSGDEQSKGSE
+>4_1544
+MTRRDTRETGPSGRRFGATELPPEIERVVQQAKRLEWATLGVIVVTIVLVAIVMGSSQAM
+RAAWIEDLLSLIPPIAFLVALRVARMAPTRARPYGSHRSVGVGHLVAAVALSVMGVVLVG
+DSLLGLVTAEHPPIGTFDLFGHTVWQGWFMMAVMALSVPGPMILGHKKLKLAEQLHDRVL
+YADADMNKADWQTGVATIVGVAGIGLGWWWADSAAAIFVGVSIVLDGWKNLKEAVTNLAD
+RRAATIDGARPHPLIDRVERVAWAEPWVRQAGARVRDEGHVFHVEMFVVPHEGADVTVGR
+CCALRDAIAALDWKLQDVVVAPVDELPAEVHGGRSGEHQTGEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001349.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001349.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3813fe1f478d8b34aefdd9cf98e1401f94c5e53f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001349.fa
@@ -0,0 +1,25 @@
+>0_1618
+MALLLAIDSSAAASVAVLRDGEELARWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWESATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>1_1333
+MALLLAIDSSAAASVAVLRDGEELAHWATDDTHAHAEVLAPAVQTVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHAAGVDAFRHGIEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>2_1181
+MALLLALDSSAAASVAVLRDGEALARWATEDTHAHAEVLAPAVRAVLAEAGVAGAGLDAV
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVRGVRSLDALAHDAAVDAFRHGAEEFVVATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPAYGAGAGLYPEALRAVPGWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
+>3_1110
+MPLLLALDSSSAASVALLRDGEPLAAWSTADTTSHAEVLAPAVRQVLAEAGVAGGDLDGI
+AAGVGPGPFTGLRAGLATAEALGFAWDVPVHGIRSLDALAHRAGTDAFAHAVEEFVVVTD
+ARRREVYWAHYAQVGGQPTLLHGPFVTPAAEVTPLPAYGAGAGLYPEALHAVDGWEGAVP
+DAVSLGRVDELALRRGRGVLPPTPLYLRESDATVPAPRTPARPAGA
+>4_1548
+MALLIAIDSSAAASVAVLQDGEELARWATDDTHAHAEVLAPAVQAVLGEAGVTGTALDAL
+AVGVGPGPFTGLRAGLATAAALGLAWDVPVHGVRSLDALAHEAGVDAFRHGIEEFVIATD
+ARRREVYWAHYAQVGGQPTLLHGPFVSPADEVTPLPVYGAGAGLYPEALRAVPDWETATP
+SAVGVGQVAELALRRGRGLVPAEPLYLRESDAKVPGPRKRAGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001355.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001355.fa
new file mode 100644
index 0000000000000000000000000000000000000000..81f2aa73621f7491024aaa66e8de50bd4c0d5293
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001355.fa
@@ -0,0 +1,65 @@
+>0_1624
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>1_1339
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDAVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRGPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+EAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHMLTRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
+>2_1175
+MHTVDIGQPYPLGATVDETGTNFAVALAREAESVELCLVDEDGVETRLPVVERHGTTWHV
+HVAGVGHGQRYGYRVTGPWDPSRGLWHNPAKILVDPYARAFAGEHEWGQQHHSYDFDEPD
+RMDTSDNLGTTMLGVVTDDDFDWGEDAPPNIEMTDTVVYETHVKGMTMRHPAVPEELRGT
+YAGMAHPEVVRHLTDLGVTAVELMPVHQFVDDATLQEKGLSNYWGYNTLGFFAPHAAYAA
+SQEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSMRGLDNAGYYHLVEA
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRHWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSAFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNAANGEDNNDG
+ESHNRSWNCGVEGETDDPEVLTLRARQQRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAVDDSLVAFTRDLIALRHDHAVFRRRHHFDGRPAARDVEAPLPDIVW
+LEPDATAKTEDDWGAEARSIGFYLNGHTLTRGDEDEEGPYRDFYVLMNAWWEPVPYTLPG
+PLFPETWEVVVDTSSHVAPSGSRPRVRAGEVLEVPARSTVILRQVPEGA
+>3_1104
+MHTVDIGQPYPLGATVDEAGTNFAVAVGREVEAVELCLIAEDGSEERIPVTERHDTTWHV
+HVAGIGGGQRYGWRVHGPWDPARGLWHNPHKLLADPYARAFTGDYAWGQQHFSYAFDEPD
+RMDTADSRGTSMVGVVVDDDFDWGDDAPPQRLLTDTVVYETHVKGLTALHPDVPEELRGT
+YAGVAHPSVLEHLTSLGVTAVELMPVHQFVNDSILQEKGLSNYWGYNSLGYLAPHAAYSS
+ADTVGGQVHEFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPLLSFRGFDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGIWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRNPGASVNFVTAHDGFTLRDLVSYNEKHNHANGEDNNDG
+DSHNRSWNCGVEGETDDPEVLTLRARQQRNFLTTLMVSEGVPMLSHGDELGRTQKGNNNV
+YCQDNELSWIDWSTRDDALIAFTRDVIALRRDHAVFRRRQHFDGRPAERDVEAPLPDIVW
+LEPDATAKTEADWGAEARSIAFYLNGHDLQRREGEPDEAFRDFYVLMNAWWEPVPYTLPG
+PLFPGEWEIVVDTSSHVAPAGTRPHVVAGEVIEVPGRSTMILREVVRQEQG
+>4_1554
+MHTVEIGQPYPLGATVDETGTNFALAVSREVEAVELCLVADDGTETRIPLEERHGTTWHA
+HVAGIGHGQRYGYRVHGPWDPARGLWHNPAKILVDPYARAFTGDYEWGQQHHSYDFDEPD
+RIDTSDNLGTSMLGVVVAEDFDWGDDAPPAVELTDTVIYETHVKGMTKLHPAVPEELRGT
+YAGMAHPEVVRHLTELGVTAVELMPVHQFVNDATLQEKGLSNYWGYNTLGFFAPHAAYAS
+SSEVGGQVREFKQMVKDLHAAGLEVILDVVYNHTAEGNDKGPMLSLRGLDNAGYYHLVEG
+DERHYMDYTGTGNSVDLSSPKALQLVMDSLRYWVTEMHVDGFRFDLATTLTRVEGEQGPD
+MFSGFFDVVRQDPVLRTVKLIAEPWDVGWGGYQVGNFPGLWSEWNGMYRDTVRDFWRGEP
+GTLGEFATRLTGSADLYEGDGRSPGASVNFVTAHDGFTLRDLVSYNEKHNEANGEDNNDG
+DAHNRSWNCGVEGETDDPEVVTLRARQRRNFLATLLISQGVPMISHGDELGRTQGGNNNV
+YCQDNEISWIDWSAMDDSLVAFTRDLIALRRDHAVFRRRHHFDGRPAARDIEAPLPDIVW
+LEPDATAKTEDDWGAEARSLGFYLNGHTLPRGDEEGEEPYRDFYVLMNAWWEPVPYTLPG
+PTFPAEWEVVVDTSSHVAPDGTRPRVRAGDVLELPARSTVVLRQVPEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3b363e3975e366b72ada5e6f97156e127a3bbe6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001359.fa
@@ -0,0 +1,14 @@
+>0_1631
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>1_1345
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
+>2_1168
+MSSEAVPRPPRWSPFGALLAGLAVLWGAAFLAVDAPVCERHGAPVEWLPCLDRDRGDPDV
+APQR
+>3_1099
+MSPRRDPGRLRPLAGPAALLAALWVAAWLAVSVPVCDRGGPADWLPCVDPGRSVPAPGAP
+>4_1560
+MTSDAAPRPRRWTLFAGLLAGLAVLWSAAFLAVDAPVCARQSAPVEWLPCLDPDRQDSEV
+APDAGSSADRTTSRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001360.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001360.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e91b2c576b7ec71c6e220f95b077f71a6222c0a9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001360.fa
@@ -0,0 +1,45 @@
+>0_1632
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>1_1346
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+TAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDEHGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
+>2_1167
+MSRLFGTDGVRGLANETLTVELSVQLAQAAAPVLGAEALEAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLGADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVEPRRPQGADVGRVKVFSDAEDRYVVHLLQALPHRLEGLKVVL
+DCAHGAAAGCSPEAFRDAGAEVVVIGASPDGLNINEGYGSTHLEKLQAAVLEHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVAMKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLAARVAETGRP
+LSALAAVMDRLPQVLVNVRGVDKSRAAEDVAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAEALADVVQRELRLHV
+>3_1098
+MSRLFGTDGVRGLANDVLTVELSVQLAQAAAPVLGADALAAGRRPVAVVARDPRISGQFI
+AAAVIAGLASSGVDVHDAGVVPTPAAAFLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDEQEDEIIQHLESEHPLRPTGAEVGRVRTFSDAEDRYVVHLLQTLPHRLDGLTVVL
+DCAHGAASGCSPDAFRDAGAQVIVIGAEPDGLNINEGVGSTHLEKLQAAVKEHGADLGIA
+HDGDADRCLAVDELGEVVDGDQIMGIMALALKDRGQLKEDTLVVTVMSNLGLKLAMRGAG
+IELVETQVGDRYVLAGMRLGEYSLGGEQSGHVIFADHATTGDGVLTGLQIAARVAETGTP
+LSQLAAVMTRLPQVLVNVRGVDKSRAAEDAAVQSAVREAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETARREAEALAEVVQRELRLHD
+>4_1561
+MSRLFGTDGVRGLANETLTVELSVQLAQAASPVLGAEAFDAGRRPVAVVARDPRISGEFI
+AAAVQAGLASSGVDVWDAGVLPTPAAAYLVGDLDADFGVMISASHNPAPDNGIKFLARGG
+EKLTDAQEDEIIRHLEGVTPRRPQGADVGRVRVFADAEDRYVLHLLQTLPHRLDGLKVVL
+DCAHGAAAGCSPEAFRAAGAEVVVIGASPDGLNINDGYGSTHLEKLQAAVREHGADLGIA
+HDGDADRCLAVDERGEVVDGDQIMGVMAVALKDRGVLRDDTLVVTVMSNLGLKLAMGREG
+VQLVETQVGDRYVLAGMKLGDYSLGGEQSGHVIFSDHATTGDGVLTGLQLASRVAETGTP
+LSELAAVMDRLPQVLVNVRGVDKSRAAEDEAVQAAVAEAEARLGETGRVLLRPSGTEPVV
+RVMVEAPDEETAGREAQVLADVVQRELRLHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001367.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001367.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8dba7c831cacfed6a5fc5b2db153ca845445c39b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001367.fa
@@ -0,0 +1,20 @@
+>0_1640
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>1_1357
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>2_1159
+MPPKTRASAARKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
+>3_1090
+MPPKTRSAVRKPRRKDKKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGSR
+KSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTPQ
+AHNGARPAKRRRV
+>4_1569
+MPPKTRASAARKPRRKANKNITVGQAHIKSTFNNTIVSITDTTGAVISWASSGEVGFKGS
+RKSTPYAAQMAAEQAAKRAQEHGMKKVDVFVKGPGSGRETAIRSLQAAGLEVGSIQDVTP
+MAHNGARPAKRRRV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001370.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001370.fa
new file mode 100644
index 0000000000000000000000000000000000000000..57e33d5e4ea0f77730b0f5148cfbf794966fd1b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001370.fa
@@ -0,0 +1,15 @@
+>0_1643
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>1_1360
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>2_1156
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
+>3_1087
+MAKKEGVIEVEGTVTEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRVVVELSP
+YDLNRGRIVYRYK
+>4_1572
+MTIVEDMAKKEGVIEVEGTVSEALPNAMFRVRLQNEHVVLATISGKMRQHYIRILPEDRV
+VVELSPYDLNRGRIVYRYK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001372.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001372.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ad24f6e0aefba970bf761b38fdfd61e4e8eeb7b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001372.fa
@@ -0,0 +1,25 @@
+>0_1645
+MTRMLLMGPPGSGKGTQATRIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGLSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
+>1_1362
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAESGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
+>2_1154
+MTRMLLMGPPGSGKGTQATRIADKLGIVAISTGDIFRHNVKSMTPLGVEAKKYIDNGDFV
+PDDVTNRMVADRIAQPDAEHGFLLDGYPRTKGQVEALDAMLTEAGLALSAVVELEVPDAE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETEAVIQEYVERGIVARVDGTGQIDDVTE
+RLLQSVYAVRAATGSLPVIAPDTES
+>3_1085
+MTRMLLMGPPGSGKGTQATRIADKLGIVAVSTGDIFRHNVKNMTELGKEAKRYMDAGDFV
+PDEVTNRMVADRLSQSDAETGFLLDGYPRTAGQVDALDAMLKDTGQALSAVVELEVPDAE
+LVARLLKRAEIEGRADDTEEVIQHRLDLYHRETESVIESYAERGIVARVDGTGQIDDVTE
+RVLQSVYSVRAATGTLPIITPDTQA
+>4_1574
+MTRMLLMGPPGSGKGTQAARIADKLGIVPISTGDIFRHNVKSMTPLGVEAKRYIDNGDFV
+PDEVTNRMVADRIAQADAEHGFLLDGYPRTKGQVEALDAMLAEAGQSLSAVVELEVPDEE
+LVERLLKRAEIEGRADDTQEVIEHRLDLYHRETESVIQEYVERGIVARVDGTGQIDDVTE
+RLLQAVYSVRAATGSLPVIQPGAES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001380.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001380.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e6f2ea78567183a4eec07e454e706d8d75f3f23c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001380.fa
@@ -0,0 +1,25 @@
+>0_1653
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>1_1370
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>2_1146
+MTEVQQTEKVAPRLKTKYREEIRATLQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVTDLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
+>3_1077
+MTEVQQTEKVTPRLKTKYREEIRASLQEQFEYANVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAIADLTAITGQKPMVTKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDK
+>4_1582
+MTEVQQTEKVTPRLKTKYRDEIRGALQEQFQYGNVMQVPGLVKVVVNMGVGEAAKDSKII
+DGAVADLTAITGQKPMITKARKSIAQFKLREGMPIGTHATLRGDRMWEFLDRLVTLALPR
+IRDFRGLSDRQFDGNGNYTFGLSEQTVFHEIDQDKIDRVRGMDITVVTTAKNDDEGRALL
+KALGFPFKTDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001381.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001381.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a213c259ab3b80b0bac37930cc108f787ad3ff2a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001381.fa
@@ -0,0 +1,15 @@
+>0_1654
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>1_1371
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
+>2_1145
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGR
+QVAEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGESKTVKVRFAKASGKEL
+>3_1076
+MAKIKKDDLVQVLSGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQNNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKNGEQVTVKVRFAKASGKEL
+>4_1583
+MAKIKKDDLVQVISGKDKGKQGKVLRVFPADERVLVEGVNRVTKHLRAGQDNNGSTEGGL
+QVVEAPIHISNVAVVDPETKKPTRVGYRFETVEKDGVSKTVKVRFAKASGKEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001383.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001383.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6f68db84900e6c34077580d5a1f665e5acfef2e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001383.fa
@@ -0,0 +1,15 @@
+>0_1656
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>1_1373
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
+>2_1143
+MTEQTPAVSEERGYRKALRGVVVSDKMDKTIVVEVEDRKKHSLYGKVMKTSKRVKAHDED
+NTAGIGDRVRIAETRPLSASKRWRLVEIVERAK
+>3_1074
+MTEQTAAPVEERNYRKSLRGVVVSDKMDKTIVVEVEDRKKHALYGKVMKTSKRVKAHDED
+NTAGVGDRVLIVETRPLSADKHFRLVEIVERAK
+>4_1585
+MTEQTPAVSEERGYRKALRGIVVSDKMDKTIVVEVEDRKKHSLYGKVLKTSKRVKAHDED
+NTAGVGDRVRLAETRPLSASKRWRLVEIVERAK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001390.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001390.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ba0835dcf0fa2a39e137b61d3e53a3d5cec858e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001390.fa
@@ -0,0 +1,15 @@
+>0_1663
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>1_1380
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>2_1136
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
+>3_1067
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKTEIKQAIERIFDVSVASVN
+TLNRPGKRRRTRFGWGQRKSTKRAIVSLKDGATIDIFGGPLAS
+>4_1592
+MSGSINKDPRDVIIAPVVSEKSYGLIDEGKYTFLVDPRSNKSEIKQAVERIFNVDVASVN
+TLNRSGKRRRTRFGWGQRKSTKRAIVTLKDGTIDIFGGPLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e049aa8e83b419ed9b0495353382a97c5f97272f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001391.fa
@@ -0,0 +1,25 @@
+>0_1664
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>1_1381
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>2_1135
+MAENSVKTVQVDLPAEIFDVQSNVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
+>3_1066
+MAENTVKTVQVELPAEIFDVQANVPLMHQVVVAQLAAARQGTHKVKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGIVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLESLNTGRKNVLLVIDRADDLTALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTKVAYEAYVAQASGAKKEDAQ
+>4_1593
+MAENSVKTVQVDLPAELFDVQSNVPLMHQVVVAQLAAARQGTHKTKRRGEVSGAGRKPFK
+QKGTGRARQGSIRAPHMTGGGVVHGPTPRDYSQRTPKKMKAAALRGALSDRARNGRVHVI
+EALVSGTTPSTKAAKAGLASLNTGRKNVLLVIDRADDVAALSARNLPAVHTLYADQLNTY
+DVLVSDDVVFTQAAYEAYVAQASGAKKEDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abebd2eefcd79e60764091958cd82b256218d0d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001395.fa
@@ -0,0 +1,10 @@
+>0_1668
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>1_1385
+MSDDGAAAAARLGSMPELLILIVVLAVAVVAVRWALRTFRPEIDRARRIRRANRGGELER
+>2_1131
+MPELLITLLVLAAAVVAVVWALRTFRPEIDRARRIRRANRNGELRR
+>3_1062
+MEWLIALVVIAAVVAGGLWARRAFAPEIERARRIRRAERGGRLER
+>4_1597
+MSDDGAAAAARLGSMPELILLIAVLAVVVVAVRWALRTFRPEIDRARRIRRANRGGELER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3db434288d7531ca52678531f77b57fb05d8d4cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001396.fa
@@ -0,0 +1,40 @@
+>0_1669
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>1_1386
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDPQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>2_1130
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDDAPVIRTSGLKA
+LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVAPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MTVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
+>3_1061
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEKRDFASIDSAPEERQ
+RGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQEFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMDAVDEYIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLA
+INSEVEIVGIRPVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVQPGS
+ITPHTDFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKINK
+>4_1598
+MAKAKFERTKPHVNIGTIGHVDHGKTTLTAAISKVLYDKYPDLNEARDFATIDSAPEERQ
+RGITINISHVEYQTEKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVAATDGPMAQTRE
+HVLLARQVGVPALLVALNKSDMVEDEELLELVEMEVRELLSSQDFDGDEAPVIRTSGLKA
+LEGDAQWVKSVEDLMEAVDEFIPDPVRDKDKPFLMPIEDVFTITGRGTVVTGRAERGTLK
+INSEVEIVGIRDVQKTTVTGIEMFHKQLDEAWAGENCGLLLRGLKRDDVERGQVVVEPGS
+ITPHTNFEANVYILSKDEGGRHNPFYSNYRPQFYFRTTDVTGVITLPEGTEMVMPGDTTE
+MSVELIQPIAMEEGLGFAIREGGRTVGSGRVTKITK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..245432c636b14b0c7c90f3cb58b63bbb9fe9a793
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001415.fa
@@ -0,0 +1,25 @@
+>0_1688
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>1_1405
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
+>2_1110
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSDGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRERRDGDVGPGMRPADIVPAFRSAEDVESLRAGDEGFG
+ITATITHPGSLAELYYGRIKGPQLQLVTDAVLRGSAAGDYHRATRMAGLVNGQLFWRWDS
+SGSEGAELEAHASAILDRMPSESEGRLAPGAPRPRGAGGAEPGERP
+>3_1040
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSEGTDIFYQRVDFVEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARQDGDVGPGMVPADIVPAYRSAEDVEALRSEDGAFR
+ITATITHPGSLAELYYGRIKGPQVQIVMDSLLRGAAAGEYARATRMAGLVNGQLFWRWDS
+SPAVEGPMEVHASAILDRMPDPSEGRLAPGAPRPRGERGRAPEQGA
+>4_1617
+MATELPYDLTPELAPLSWLIGSWEGQGRLGDGSAGTEIFYQRVDFTEHGLPFVEYRAESW
+LCEADGTLLRPLTVESGFWQVDRARRDGDVGPGMRPADIVPAFRSAEDVERLRAGDEGFG
+LTATITHPGSLSELYYGRIKGPQLQLATDAVLRGSAAGPYHRATRMAGLVNGQLFWRWDV
+ADAAGAELEAHASAILDRMPSAAEGRLAPGAERPRGARGEQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001427.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001427.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b38bd5d2dc0e77dd129b44bd5ff1187c906bccf3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001427.fa
@@ -0,0 +1,20 @@
+>0_1700
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>1_1417
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAAVSTVTSTLLVRGEES
+>2_1098
+MSVNPDVAGRSYPPAPPFQVGREAVRAFASAVQAQHPAHHDVEAARALGHADLLAPPTFA
+VVIAQRAEAAAVNDPEVGIDFSRVVHADERFVHHRPLVAGDEVVATVRIASVKSLGGNDM
+VTTVTEIADADGAPVSTVTSTLLVRGEES
+>3_1024
+MSETESLVGRTYPPAPPYQVGREAVRAFADAVQAAHPAHTDVDAARALGYADVVAPPTFA
+VVVAQRAEAAVVADPEAGIDFSRVVHADERFTHHRPIVAGDELTATVLIEAVKELGGNRM
+VTTVTEIVDAAGAPVSDVASTLLVRGEES
+>4_1629
+MSVNPDVAGRSYPPAPPFQVGREAVRGFAEAVQAQHPAHHDVAAARALGHADLVAPPTFA
+VVIAQRAEAAVVADPELGIDFSRVVHADERFVHHRPLVAGDEVVATVRVEAVKSLGGNRM
+VTTVTEIADLDGAPVSTVTSTLLVRGEES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001435.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001435.fa
new file mode 100644
index 0000000000000000000000000000000000000000..817a83432498c783fb3b83c696d8956263cb7ea2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001435.fa
@@ -0,0 +1,20 @@
+>0_1708
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLADGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA
+>1_1425
+MTTAFEPRPHAAAAPREPDPHGPGTAGSLRPGARGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPRAWSTTYRATILGAAPEAVCTIWDVFPLPAA
+>2_1090
+MTTAFEPRPHTGLAPREPEPHGPGTPGPLRPGVRGSVLIVSEHADPDTAMRHAMAWITAF
+EDDCGLVLDADGTELYAVGLAGELGASLRRSPGVAEDGTPTDTSEFVDAILTGGVWRLRE
+PDARAWSTAYRAAILGAAPHAVCTVWDVLPLPAA
+>3_1016
+MTAQHAEPTRTDRAEPHGPGTPATLRPGERGSVLVLSPAGPPEAAMGHAVAWITAFEDDC
+GLVLDRDATSLYAVSPADGLRREGDVPSDGGIAEHLDFVLAGDVWHHRGTCPPAPAGSDV
+DGWALLVHRLQREAPRGALGTVWDVFPLPAAG
+>4_1637
+MTTAFEPRPHTAAAPREPDPHGPGTPGSLRPGERGSVLIVTRHPDPDEAMRHAMAWITAF
+EEDCGLVLDTDETALYAVGRAGDLGEALRRGPLVHEDGSPADTSAFVDAVLTDGTWRLRD
+ADPREWSTTYRAAILGAAPEAVCTIWDVFPLPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001438.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001438.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6b1a213f07a324609352e5c045c5289f5105cf18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001438.fa
@@ -0,0 +1,45 @@
+>0_1712
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGFESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQQAEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGGAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELITGGASVVLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
+>1_1429
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAETATASGTRWGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVTALMRWQPG
+FLRYDARNPTP
+>2_1086
+MARLLVDLTPLKVSPAYRRLWVGNTLSFVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAVADRHDRRTVALASSAVMWLTTVGIAAHAWAGIESVPLLYALVALHSG
+ASGINQPTRGAIIPALVGMKLVPAANALNMMTFSVAMMAGPVLGGVLVASVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRAEGEAAPTGRVGVRSVVEGLRFLGSRPNLRMTFLADIVA
+MATAFPRALLPAVGGVVLGGGEAAVGVLLAAMAAGAFLAGLFSGPFTRLHAQGWGVYVSI
+LVWGASVAAFGGVVWWAQGLPDGDPRLTGAFVAAALCLAVGGAADSISGVFRTTILQSAT
+PDHLRGRLQGVFVVVVAGGPRVGELLTGGASVAVGEGLTLLLGGLACVLGVSLLMRRQPE
+FLKYDARSPTP
+>3_1013
+MPRLLVDLAPLEASPAYRRLWLGNALAFVGTQLTLVAVSLEVFALTGSSFAVGMLGLAAL
+IPLVVAGLYGGAVADRHDRRTVALASGAVMWAATALIAAHAWAGVESVGVLYGLVALHSA
+ASGINQPTRGAIIPALVGPALLPAANALNMLTFSTAMMAGPLLGGVLVASVGYAWTYTVD
+VVTFLAALWAVWRLPSLPPDRSAAPDDAGRGGLSSVLDGFRFLGTRRNVRMTFVADIVAM
+ATAFPRALLPAVGGTILGGGEAAVGVLLASMAAGTFLAGLFSGTFTRVHRQGRGVAVAIA
+AWGLSVAAFGAVVLWAAPLPDGDPRLGPALAACAACLVVAGAADSVSAVFRTTILQSATP
+DHLRGRLQGVFVVVVAGGPRVGEMIQGTASAALGEGATLVLGGVLCVAGIALLMRVQPGF
+LHYDARRPTP
+>4_1641
+MARLLVDITPLRVSPAYRRLWLGNTLAYVGTQLTLVAVSLEVFALTGSSFAVGLLGLAAL
+VPLVVAGLYGGAIADRHDRRRVALTSSAVMWLTTVGIAAQAWAGLESVPVLYALVALHSG
+ASGINQPTRGAIIPALVGLPLVPAANALNMMTFSVALMVGPVLGGVLVAAVGYAWTYSID
+VVTFLAALYAVWRLPSLPPQRGEAAAASGTRGGLASVVEGLRFLGSRPNLRMTFLADIVA
+MTTAFPRALLPAIGAVVLGGGEAAVGVLLAAMAAGAFLAGLFSAPFTRLHAQGWGVYVSI
+LVWGAAVAAFGGVVWWAQSLPDGDPRLTLAFALAALCMAVGGAADSLSGVFRGSILQSAT
+PDHLRGRLQGVFVVVVAGGPRLGELLTGGASVGLGEGPTLLAGGVLCMLGVSALMRWQPG
+FLRYDARNPTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001439.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001439.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b999ca19e5852a3d582f652bc3c3c88bc69795b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001439.fa
@@ -0,0 +1,35 @@
+>0_1714
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>1_1431
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAV
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVLTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTLDQLNASRLQRRAVRAGQGAHA
+>2_1084
+MARVSPSPASRRPGVPPDAAAPDTGALPAVSPAPANDPRGLALGFTAYFLWGLLPLYMAR
+LAPAGAVEIVVVRVGFALVFCLVLLALMRRLRELRTSLATPARWGATALAAGFIGTNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWAAVGIAVAAVVVMSVAMGQ
+VPWIALGLAFSFGLYGFVKKRFPTPVHAVTTMTAETVVLLPAFAVGMVWLGQAGLLTTFT
+EGPAHFWLMAGLGVLTAVPLILFSAAAKALTLTTLGMLQYTAPILQFIVAVTVLGEQMPV
+ARWAGFGLIWVSLLVFTLDQVRVSRLHRRAARAGHGARA
+>3_1011
+MAQVSHSPSPSGPDAPRDGVPVEAAAPDTGALPTITPAPANDPRGLALGFAAYVIWGLLP
+LYMAATAPAGAVEIVVVRVVFALIFCLLLLAVMRRLPELRTALATRARWGSITLAAAFIA
+VNWLLYAHSVTSGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWIAVGIAVVAVVVMS
+VAMGQVPWIALGLAFTFGMYGFVKKRFPVPVHAVTTMTAETVVLLPAFAVGMVFLVQAGL
+LTTVSEGPGHFWMMAGLGVLTAVPLILFSAATQSLTLTTLGMLQYIAPIMQFLVAVAVLG
+EHMPAARWAGFALIWLSLVVFTLDQANASRVQRRAARAAGRART
+>4_1643
+MVRVSPSSPAVRPGVTPDGAAPDTGALPTVSPAPADDPRGLALGFTAYFVWGLLPLYMAM
+LAPAGALEIVVVRIGFALIFCLLLLTVMRRLRELGTALATPGRWGTTGLAAGIIAVNWLL
+YAVSVTTGNVLQASLGYFMNPLVNVLLGVLFLGERLRRGQWVAVGIAVAAVVVMSAAMGQ
+VPWIALGLATSFGLYGFVKKRFPSPVHAVTAMTAETVVLIPVFVVGSVLLAQAGLLTTVT
+EGPGHFWLMAGLGVFTAVPLILFSAAARSLTLTTLGMLQYTAPILQFLVAVTVLGEQMPA
+ARWAGFGLIWLSLAVFTVDQLNASRLQRRPVRVRRGAHA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0b70bf4309ee9472d0ede76b652fbc8e2a366cd0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001446.fa
@@ -0,0 +1,50 @@
+>0_1724
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRASLKAKDSENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>1_1441
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPAAGTEALAVPPATGAAAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGAARPTPAP
+TAGAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPL
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGQDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAINDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
+>2_1075
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVVVDQPIVEVETAKALVEVPSPYAGTVLTLH
+GAEGQTMEVGRPLITVGAAGESGEGSAPVAGTEAQAVPPATGEDAAEADRPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDEEASGAVLIGYGTSGHSATSRTRPSKRGRRGAGTTTAG
+GSGAASGQGEQAGQARAPRVTSPIVRKLAREQGVDVAALTGTGPDGLITRADVLSAAQGG
+DAPQAAAAPAAQPAATAGAASTVGAGSADARTGLAVVARTPISGVRKVIADQLSRSRREV
+PEVTAWLDVDVTALLELRAALKAKDAENAPSLLGLIARFTLAGLRRYPVMNARIEAGADG
+KDEIVEVDGVHLGLAVQTDRGLMVPSVEHAERLSADELTAAINETVTRAREGKAAPAELT
+RGTFTLNNYGPLGTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHR
+VTDGATASAFLTFVADCLNDPQSALARI
+>3_999
+MSNTFLLPDLGEGLTEADIVRWLVAEGDEVAVDQPMVEVETAKALVEVPSPFAGTVLTLH
+GAEGETMEVGAPLITVGAVGESAGDAPPPSSAADAGTAPAADGAVPGALSYREEERAGVQ
+PKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHTATSRSRPSKRARGGAGTTQAAAGAAP
+AASGRAPRVTSPIVRKLARERGVDVATLTGTGPDGLITRADVLGAAGGASAPQDAQAPAP
+VQTAPSAAAQAPAVAAGATDARTGLAVVARTPISGVRKVIADQLSRSRREVPDVTAWLDV
+DVTALLELRAQLKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDG
+VHLGLAVQTDRGLMVPSVEHAEKMSADELTRAINDTVSRAREGRAAPAELTRGTFTLNNY
+GPLGTDGATPILNIPEVGMLGIGRIIDRPWVVDGEIVVRKVTEMTVTFDHRVTDGATASA
+FLTFVADCLNDPQAALARI
+>4_1653
+MSNTFLLPDLGEGLTEADIVRWLVAEGDTVAVDQPMVEVETAKALVEVPSPYAGTVLTLH
+GAEGETMDVGSPLITIGAAGESGEGSAPVAGTEALAVPPSTGADAAEAARPGALSYREEE
+MAGVQPKPDKARGGDGDVAGSDDEASGAVLIGYGTSGHRATSRSRPSKRGRGATRPTPAP
+TAWAGAPRVTSPIVRKLAREKGVDVAALTGTGPDGLITRADVLAAAEGSAPQAAPAQAPS
+VAAVPAAEAAAQPGAVDGRTGLAVVARTPISGVRKVIADQLSRSRREVPEVTAWLDVDVT
+ALLELRAALKAKDPENAPSLLGLIARFTLAGLRRYPVMNARIEAGADGKDEIVEVDGVHL
+GLAVQTDRGLMVPSVEHAEKLSADELTAAVNDTVSRARAGRAAPAELTRGTFTLNNYGPL
+GTDGATPIINVPEVGMLGIGRIIDRPWVVDGEIMVRKVTEMTVTFDHRVTDGATASAFLT
+FVADCLHDPTAALARI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001448.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001448.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8f92d06a7ae1582b6ec920e89352695304f49ab2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001448.fa
@@ -0,0 +1,40 @@
+>0_1726
+MSDPTPAVPGAARTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>1_1443
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+EHDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQITRDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
+>2_1073
+MSDPTPAVSGSARTDQAEARPNAGAAFGISLEEYLLPATRRIQLIGEDGTLLSPEEQGAE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLG
+KQDWLFPTYRDTVAVIARGVPPLEVMVSYQGTWHQGYDPNEHHVSVQSTPLTTQLLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVDLCRQGQGPFLVEADTYRMQAHTN
+TDDPTRYREDAEVQEWEARDPLRRMTAYLESTGALTEEVSAEIAQAAEDVAKDLRDAMNA
+EAELDPLELFDHVYSVQTPQLAAQRAQLTEELSRSENQEA
+>3_997
+MTSTRPGPATPDTRTEAAAAFGITLEEYLLPAARRIQLISPEGELLPAEEQGTAPGHEYP
+LPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVCLGQDDWLF
+PTYRDTVAVIARGVAPLDVMVSFQGTWHQGYDPKEHRVSVQSTPLTTQLLHAVGMAKAAR
+LRGEDVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFLVQNNKFAISVPFAKQSAAPSL
+AHKAVGYGLAGERVDGNDLAALLAVLGRAVDLCREGKGPFLVEADTYRMQAHTNTDDPTR
+YREDSEVKEWEVRDPLRRMTAYLESTGALTAEVSTSIAKDAEDVAQQLRDAMNADVELDP
+LELFDHVYSVQTPQLAAQRAQLAEELSRSENKEA
+>4_1655
+MSDPTPAVPGAVRTDEAETRPNAGAAFGISLEEYLLPAARRIQLIGEDGTLLAPEEQGTE
+PGHEYPLPSDEELLAAYRHLVIGRRVNDQAYALVRQGRMAVYPSSHGQEASEVAAAVSLG
+EDDWLFPTYRDTVAVIARGVPPLEVMVAYQGTWHQGYDPQKHHVSIQSTPLTTQMLHAVG
+MAKAARLRGEEVVCLAMVGDGGTSEGDFHEALNFAAVFKLPVIFFVQNNKFAISVPFAKQ
+SAAPSLAHKAVGYGLAGERVDGNDLGALLAVLGRAVELCRQGQGPFLVEADTYRMQAHTN
+TDDPSRYRDDAEVKEWEARDPLRRMTAYLESTGALTEEVSAQIARDAEDVAQQLRDAMNA
+ETELDPLELFDHVYSVQTPQLAAQRAQLAEELSRSENQEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001461.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001461.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac2a5ed94e383357e60a468825379dd6ebc0a8b6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001461.fa
@@ -0,0 +1,10 @@
+>0_1753
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>1_1461
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>2_1041
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
+>3_977
+MGSVIKKRRKRMAKKKHRKLLRKTRHQRRNKK
+>4_1675
+MGSVIKKRRKRMSKKKHRKLLRKTRHQRRNKK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001462.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001462.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acf780b9b3f0d8406ab45d10efc0e45f912cd762
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001462.fa
@@ -0,0 +1,40 @@
+>0_1754
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHLTDPLADLRLSVDGQRQLAFDVGDWADRFAY
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVRSEIPAAWIEHVRALTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>1_1462
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLV
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANEIGGSAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLQAFAPDVLVSQHGCDGHRTDPLADLRLSVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRTLTADELTGDMS
+VHEGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
+>2_1040
+MSTTSQRPAPTPAAVVWDPSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVSIIEP
+PVATDAQLALVHDPDYIAAVRRASEAASDEDAPFGLGTEDCPVFPDLHEASARIAGGTLA
+AAEAVWSGQVRRAVNFAGGMHHAARAKASGFCIYNDCALAIQRLLDLGAERVVYLDVDAH
+HGDGTQAIFYDDPRVMTISVHETGISLFPGTGFANEIGGPDAQGTAVNVAVPPRTGDAGF
+LRAVHAVVPQLLQGFDPDVIVSQHGCDGHHADPLADLRLSVDGQRQLAFDIGDWAEKFAD
+GRWVATGGGGYNPLRVVPRVWTHLTAAVLQTPIPVKAEIPQSWIEHARTLTAEELTGDMS
+LHEGDESERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRRELFPLHGLDPWFD
+>3_976
+MTSATSDCSQPAPSAVVWDPSLLKYRFSAQHPMAPLRLDLTHRLASSLGLLDAEHVRILQ
+PPVATDEQLATVHDPAFIAAVRAASREDAEADEPHGLGSEDCPTFPDLHESAARIAGGSL
+VAAEAVWSGEVSRAVNVAGGMHHAARAKASGFCIYNDCAVAIQRLLDLGAERVAYVDVDA
+HHGDGTQSIFYDDPRVLTISLHETGISLFPGTGFANETGGPGAEGTAVNVALPPGTGDAG
+FLRAVHAVVPQLLGAFQPDVLVTQHGADAHRGDPLADLRLSVDGQRQLAFDLGDWADRYA
+HGRWLATGGGGYNHVRVVPRAWTHLIGAVTGQPVPSSTPVPESWLEHVRSLTPDDLEGDM
+SLFEGAEEDRYPLTMTEDADVWWRSWEVGYDPADPVDQTIMATRREVFPIHGLDPWFD
+>4_1676
+MSTTSTPPAPTPAAVVWDSSLLRYRFSAEHPMAPLRLDLTHRLVEAFGLLDAPHVRIVEP
+PVATDEQLALVHDPEYVAAVRRAAATSSAEDGRFGLGTEDCPVFPDLHESAARIAGGSLA
+AAEAIWSGEVDRAVNFAGGMHHAARSSASGFCIYNDCAVAIQRLLDLGAERVAYVDVDAH
+HGDGTQSVFYDDPRVLTISLHETGISLFPGTGFANEIGGAAAQGTAVNVALPPRTGDAGF
+LRAAHAVVPPLLEAFAPDVLVSQHGCDGHRTDPLADLRLTVDGQRQLAFDVGDWADRFAH
+GRWLATGGGGYNPLRVVPRAWAHLTAAVLQTPIPVKSEIPAAWIEHVRALTADELTGDMS
+VHVGDDAERIPTVMGEDADVWWRSWEVGYDPADPVDQSIMATRREVFPLHGLDPWFD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001465.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001465.fa
new file mode 100644
index 0000000000000000000000000000000000000000..712b905036658fa09e57610e240c0e781065d1e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001465.fa
@@ -0,0 +1,30 @@
+>0_1757
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLASSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAGALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDREMAEEFGA
+>1_1465
+MKLTILGLGTMTGAILAGALEAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKGMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQTTAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
+>2_1033
+MKLTILGLGTMTGAILTGAIEAGAVRAEDVRATTRSAASAERARGRHPGVEVLAAEEDAH
+ANKRAVEGADVVLLGVKPKDIAATAAEVAQALGTDTTVVSVAAGVRAETIAAALREGQPL
+VRTMPNTPLTVGSGVVGVAPARGVTDAQTQAVEALFAGSGLVVRVAEEQLAAVVAAAGSA
+PAYVFLLAESIAKHAEQLGLDRANAEAMAAATVKGAGLMLQNGIREGDQTAEDLRRGVMS
+PGGTTEQAIRTFQEGGFERLVADAMDAAARRDEEMGRELAG
+>3_972
+MTAQPRIAILGLGSMTGAILTGLLAASVTTPERVVATTRTAASAQAKGNRFPGVRVLSGE
+QDVDANLTAVAEADVVLLGVKPKDIVVTARQIAPALRPEAVVVSVAAGVRAETLAGALPE
+GQPLVRTMPNTPLTVGSGVVGVAPAAGVTADQRALVESLFSGSGVVVPVSEEQLPAVVAA
+SGSAPAYVFLLAEAIAAHAVELGLSAEAAEAMAAATVKGAGAMLVDAVTSGEQTAEGLRR
+AVMSPNGTTERAIAAFEDGGFAGLVADAMDAAARRDEEMGREFGA
+>4_1679
+MKLTILGLGTMTGAILAGALDAGAVRAEDVTATTRSAASAEKAAAQHGVTVTSQERDERA
+NHAAVAEADIVLVGVKPKDMVATLTDLAPSLRPETVVVSVAAGVTAATMAAVLPAGQPIV
+RTMPNTPLTVGSGVVGVAPGPGVTEEQATAVRALFEGSGLVVPVAEEQLSAVVATAGSAP
+AYVFLLAELIAAHGAEMGLDAASAEAMAAATVKGAGIMLQQEGARAEALRKAVMSPNGTT
+EKAVEAFLDGGMGDLVNRAMDAAAQRDKEMAEEFGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001469.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001469.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30a5a3fe657e9bbd3aaaad909188f5e6239d8395
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001469.fa
@@ -0,0 +1,55 @@
+>0_1761
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVASGMQAWFIQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQAVDEALGTAWAAAVARRDRLTAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>1_1469
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATRALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRHGTRGLAAAVGAWLLGDSVPAADLDAALPRLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRDR
+LEDRVRLAAGDLLAPVTGERFDLVVSNPPFVITPRTDPGAPVLIYRDGGREGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTANADTAPWDARPRSWVAPGMQAWFLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRGWVVA
+EELTQPVDEALGAAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
+>2_1028
+MKPPAPSPSSPSLPAPRLTPATAAALDADLAALPYTTAAVEELLGPVATAALDREHAEPA
+RRVVARVLTAAPGDHTQALYDDGALGSGARPLEAGIGSPAARRALAALVSVWMLGDAADA
+ADVAAALPALGLDGAREAGLVAEEGGGTVRGTVDLSPYEADEPGRMWVASDQTALQRRGP
+LPEDHVLGIGRASLTLAGATQRRPVACALDVGVGCGIQTLHLLAHAEHVTATDLSERALE
+FTRFNLLLNADVLGLDRERLEDRVRLAAGDMLAPVAGERFDLVVSNPPFVITPRTDPDAP
+VLTYRDGGREGDRIVAELVAALPAHLTEGGTAQLLANWEIPAGAAAIPAAAAASADGDLA
+DTAGPAPWDARPRSWIAPGMQGWIIQRDAQDPAGYAETWLQDSSLELDPHRYEAAYRGYL
+EDFAARGVAGVGFGHVWLRRPVDDGAQGRAWTVAEELTQPVDEALGAAWAAAVARRDRLA
+AGAPDGAGDPALAALRGLHLRVAEDVSEERHGRFGAEHPEVILARQGAGFRRTARLDTAT
+AGVLSASDGELSVGQLVGAVAALLELDDAGRAGLLAAIRELYEDGFLVERAED
+>3_968
+MSLPAPHLSPAAAAALAADLTALPYTTDVVETLLGPVATAALDREHAVAARRVVAGVLAA
+PAARDAAAASRPLAAVVGAFMLGEPVPAADLAAALPALGLDGAVEAGLVVLDGADTGAER
+ARATVDLSPYAADEPGPMWVASDQTALQRRGPLPEDHVLGIGRASLTLAGATQRRPVARA
+LDLGVGCGVQTLHLLAHAEHVTATDLSERALDFTRFNLLLNADVLRLDRERLEDRVRLAA
+GDLLGPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGREGDRLVAELIAALPEHLVE
+GGTAQLLANWEIPAGAAEIPAGAAEVPAGDDAPPAWDARPRSWVGPGMQAWFVQRDRQDP
+AGYAETWLQDSSLELDPAAYEAAYRGYLDDFAARGVTGVGFGHVWLRRPAADRSQGRAWT
+VAEELTQPLDEALGTAWAAAVARRDRLAAGPEAGATDAVVTGDPALAALRGLHLRVAEDV
+TEERHSRFGAEHPEVILARQGAGFRRTARLDTATAGVLSASDGELSVGQLVGAVAALLEL
+DDAGRAGLLAAVRELHEDGFLLEA
+>4_1683
+MSPVPTPPSPPAPRLTPATAVALAADLAALPFTTAAVEGLLGPVATLALDREHAEAARRV
+VAGHLAGPGRHDDAAGPGDRPGTRGLAAAVGAWLLGDPVPAADLDAALPSLGLAGAVAAG
+LVVEGPDGRVRGAVDLSPYEADEPGRMWIASDLTALQRRGPLPPEHVLGVGRASLTLAGA
+TQRRPVARALDVGVGCGIQTLHLLAHADHVTATDLSERALAFTRFNLLLNADVLGLDRER
+LEDRVRLAAGDLLAPVAGERFDLVVSNPPFVITPRTDPDAPVLTYRDGGGEGDRIVAELI
+AALPDVLAEGGTAQLLANWEIPAGDTADADTAPWDARPRSWVAPGMQAWLLQRDRQDPAG
+YAETWLQDSSLELDPPAYEAAYRGYLDDFAARGVAGVGFGHVWLRRPAADGSQGRAWVVA
+EELTQPVDEALGTAWAAAVARRDRLAAGAGAGDAVGDPALAALRGLHLRVAADVTEERHQ
+RFGAEHPEVILARQGSGFRRVARLDTATAGVLSASDGELSVGQLVGAVAALLELDDVGRA
+GLLAALRELYEDGFLVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001472.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001472.fa
new file mode 100644
index 0000000000000000000000000000000000000000..534b8019942fed04f517c9514cb74882bf1ff5c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001472.fa
@@ -0,0 +1,79 @@
+>0_1764
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLCPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRIWAREHASVLMTNPDMLHVGILPHHERW
+ATFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPAAAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVDQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEVEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALASGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSSGGATDAAPGA
+>1_1472
+MTGHLPEHDPWADPAGGWGPPGTADSAPPVDDAAPDFSGPEPQPVGAVLADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRAAPYDGDTAPQDRIWAREHATVLMTNPDMLHVGILPHHERW
+AAFFRNLTFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPATAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDAREGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECTEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASTDGSGGGASGGSADPAPGA
+>2_1025
+MSTPPPEPAAAGVAFDPWADPAAGWGAPDDGPSDRRDAPADVDETDHPGDEAHPWDEPAP
+LADAVADVVAGLSVSRPGDPVAGGEAADVLRGALGRHGLPEQIRHVVTLPAREARHADWP
+SEAPEALVGAFAGRGIERPWAHQVRAATVAGAGTHTVVATGTASGKSLAYQLAAGIRLSG
+DPHATVLHLSPTKALAADQLLAWRALERDGATWLRAAPYDGDTAPPDRIWAREHANVLMT
+NPDMLHVGILPHHERWARFFRHLAFVVVDESHSYRGVFGSQVGILLRRLRRVAAHWRGDR
+PEPVFIGASATSADPAGHFSRLIGAPATAVAEDASPHGAVTVAFWEPELTDRRGENGAPV
+RRSAMAASADLLTDLALQQVRTLAFIRSRRGAEAIASAARRQLEELEAGLGSRIAAYRSG
+YLPEERRALEADLRSGRLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGR
+GGQDALAFFVASDDPLDTYVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPLTP
+EAFERFGDPERVRALLDVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAE
+SGTLLGTMDSPQTHYQAHPGAVYVHQDRTYLVEELDEDAHAVIVTRAWPDFTTQARDVTE
+IEIVDVHRRLDAREGTLRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLELPARDLFTSA
+VWFQASSEELIAAGLTMDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSP
+AVFVYDGRPGGAGFAERGFAQARRWVEATAGAIAACECEAGCPSCVQSPKCGNRNSPLDK
+AGALTVLRFLLGQADHLVPVVAEGSGETDGGTDDGVGVDGEDASGSGSSGTA
+>3_965
+MTGGPVPWPDDDPWAARGPAEDRSARDVPTPAPGGPGWEPPQELATGDPEARAAFAAALG
+RRSLPAQIRHVTTIPARTPRSAPWPAGTPAGLVRAFAARGVQAPWEHQARGTAAALAGRH
+TVLATGTASGKSLAYQLAVGATLAADPRATVLYLAPTKALAADQLASWRALERDGAAWLR
+AAPYDGDTAPQDRIWAREHANVLLTNPDMLHVGILPHHERWAVFFRNLAYVVLDESHTYR
+GVFGSQVGILLRRLRRVVAHYRGERPETVFIGASATSAAPAEHLATLIGAAPGEVEAVTE
+DASPHGAVHVAFWEPELTDRRGENGAPVRRSATATAADLLTDLALQQVRTLAFIKSRRGA
+ETIAGAAKRQLEEVEAGLGSRIAAYRSGYLPEERRALEEALRSGRLLGMASTPALEMGID
+VAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPLDTFVVEHPGAVFDLGV
+EDTVLDPANPHLLGPQLCAAAAELPLRPEDLPWFGGPERVRELLDVLVEQGLLRRRPAGW
+FWTHTEHAASLVSLRDDGGGPMDIIDVESGALLGTMDSPQTHYQAHPGAVYVHQDRTFLV
+EDLDEDAHAVLVQRAWPDFTTQARDVTEIEIVAVHRRLDAAGSSLRWCLGDVQVTTQVIS
+FQRKALLSGEVLGEEPLDLPARDLFTSAVWFQAASEELVAAGLTMDRLPGALHAAEHAMI
+GMMPLVASNDRWDIGGVSMVLHPDTGVPTVFVYDGRPGGAGFAERGFAQARRWVEATAGA
+IAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLAERFDGLIEVPAHLPDVTA
+>4_1686
+MTGHLPEHDPWADPAGGWGPPGTADAAPPVDDAAPDSSGPEPQPVGEVVADVVAGLSVTA
+PGDLRPDTPAGAGLRAALGRTGLPEQIRHVTELPARQARHTDWPADAPEGLVRAFAARGV
+ERPWLHQVRAAALAGAGTHTVLATGTASGKSLGYQLAVGTRLAADPRATALYLAPTKALA
+ADQLTSWRALERDGAPGLRSAPYDGDTAPQDRVWAREHASVLMTNPDMLHVGILPHHERW
+AAFFRNLAFVVVDESHTYRGVFGSQVGILLRRLRRIAAHYRGDRPETVFIGASATSADPA
+GHFARLIGAPARAVTEDASPHGAVTVAFWEPELTDRRGENGAPVRRSAMAAAADLVTDLA
+LQQVRTLAFIRSRRGAEAIASAAKRQLEEVEPGLGTRIAAYRSGYLPEERRELEADLRSG
+RLLGMASTPALEMGIDVAGLDAVVVAGWPGTRASFFQQIGRAGRGGQDALAFFVASDDPL
+DTFVVDHPEAVFDLGVEDTVVDPENPHLLGPQLCAAAAELPITPEAFGWFGEPERVRALL
+DVLVEQGLLRRRPAGWFWTHPEHAAGMVSLRDDGGGPMDIIDAESGALLGTMDSPQTHYQ
+AHPGAVYVHQDRTYLVEELDEDAHAVVVTRAWPDFTTQARDVTEIEIVAVHRRLDARAGT
+LRWCLGDVQVRTQVVSFQRKALVSGEVLGEEPLDLPARDLFTSAVWFQAASDELIAAGLT
+TDRLPGALHAAEHAMIGMMPLVASNDRWDIGGVSMVLHPDTGSPAVFVYDGRPGGAGFAE
+RGFEQARRWVEATAGAIAACECAEGCPSCVQSPKCGNRNSPLDKAGALTVLRFLMDHADH
+LVPADASSDGSGGASGGATDAAPGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001476.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001476.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d949c0413448aa23f3f0894cdb6f6762a5161e7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001476.fa
@@ -0,0 +1,37 @@
+>0_1768
+MLVGALRRWAALVAAGLTEEQAWRETACTLPACGSGPGEAGAACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATA
+ALLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
+>1_1476
+MSPTTATGPARRSHAGRAVALLPWRAGRVPPEEETEVLIGVLRRWAALVAAGLTEEQAWR
+ETACTLPACGSEPSEAGTACCAHHHARRRAEALAWDVPAAHAPTGEAARRGGTLPWRTPA
+RDPGWALVDAALAAGARAGAAPAAVARRLAHSLEADVDAARARRSAAAGPGATSRLLQWL
+PLGGLGLAWLLGTSPGDLVRSPFGAVVAAVGLLFWLAGRSWTRLLLRAAAREPAAVGAAV
+VLDVLAALLSAGRSLPAALDDLGRTLPGARGLRATAALLLWGRDWDEAWVGLDTDPVWAE
+TAARLRPLHRSGMAGARTLAETAAAVRQQTRRADERAAEELAVRLVMPLGLCLLPAFVCW
+GVVPVVMALLGAGPG
+>2_1021
+MSTAAPEDATEELVVVLRRWAALVSAGLTEEAAWRETVRMLPDDDGHARHAARLRAERLA
+WDAAGDLSTGRDAPDVRGLRRDEHPPGDTHDASPDRSRRRWCPPWRTPPPDPGWALVDAA
+LAAGARAGAAPAVVVRRLAESLEADVDAARARRSAAAGPAATARLLQWLPLGGVGLAWLL
+GSSPWETVSTPFGAVVAAVGLLFWLAGRSWTRLLLRSAAREPAALTAPVVLDVLAALLGA
+GRSLPAALDDLARTLPGARGLRVTSALLLWGRGWDEAWAGIGEETVWAEAAARLRPLHRS
+GMAGARTLAESAAAARQQGRRADERAAEELAVRLVMPLGLCLLPAFVCWGVIPVVMALLG
+AGA
+>3_961
+MIALPGRAEERAEERAQEVVEALRRWAGLTAAGMTPAEAWTAVAQASSPCGRPTPGCCPR
+HEALRRAALARWGGPGRGAEGGQPRPGERSPWDLADAALAAAARAGASFSRTAARLADAL
+EADVDASRARRTAAAGPRATARLLSWLPVGGLGLAWLLGMGPADLLATGFGWVLLVLGGV
+LTAAGRAWTRLALRRGARPLGEASPGVVVDVAAVLLGAGRSLPAALDDVSAHLPGAADLR
+VVAVLLRWGADWDEAWAPVTEEPRWAALGERLRPLHRTGMAGEAVLHQTAAALRQETRRA
+DERGAEELAVRLVVPLGLCQLPAFVCWGVAPMALALLGAR
+>4_1690
+MLVGVLRRWAALVSAGLTEEQAWRETACTLPACGPGPSEAGTACCAHHRARRRAEALAWD
+VPASHAPTGEAARGGGTLPWRTPARDPGWALVDAALAAGARAGAAPAAVARRLAHSLEAD
+VDAARARRSAAAGPGATSRLLQWLPLGGLGLAWLLGTSPWDLARSPFGAVVAAVGLLFWL
+AGRSWTRLLLRAAAREPAAVGAAVVLDVLAALLSAGRSLPAALDDLGRTLPGARGLRTTA
+TLLLWGRDWDEAWAGLDTDPVWIETAARLRPLHRSGMAGARTLAETAAAVRQQTRRADER
+AAEELAVRLVMPLGLCLLPAFVCWGVVPVVMALLGAGPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001478.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001478.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e568e07e0171cc04ee822ad9cf12858018229d4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001478.fa
@@ -0,0 +1,30 @@
+>0_1770
+MPETPASPRPTSRDAVGTSDASLAGARDQLADLVARWGAAPADAPGHHDPVSLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLGLLGWDVPWDDSRVRDARTHEILRD
+>1_1478
+MPETPASPHPTSRDAAGTSDASLAGAREQLADLVARWGAPPAEAPGHHDPASLTTVPPEA
+VPMWGFDWPRSGDPRPSAVLILFGALDDVPARHDAGRVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDGDVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHRILRD
+>2_1019
+MAAVRDRLAALVERHGVPADQAPRDALTEIPASAVSTWGFDWPRAQRARPSAVLILFGSL
+DDVPAHHADDRVHPDVDVLLTQRAATLRTHAGQIAFPGGRVDPEDADVVATALREAEEET
+DLDPDGVEVLGVLPPVPVVVSGHVVHPVIGWWRDPSRVAVVDQAEAAAVFRMPVGDLVDP
+ANRCRVARPGGRRGETPGFLVGERLVWGFTAALLDRILTLLDWDTPWDSGRVIDAHTHAP
+LRG
+>3_959
+MSIPPLPPSSPSSARADLQRIVAEHGVAPVAGDDEAGLTTIPASSVRVWGFDWPQAARPR
+ASAVLILVGELDDVPAAHDGRACGVSPAVDVLLTQRAAGLRTHAGQVAFPGGGVEAQDAD
+VVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGYVVHPVIGWWRDPSRVAVVDHNEAT
+AVFRVPVADLAAPANRVRVRRPGGRRGETPGFLAGDRLVWGFTAALLSRVLELAGWDEPW
+AGAPLIDAGSRAVLEG
+>4_1692
+MPETPASPRPTSRDAAGTSEASLTGARDQLADLVARWGTAPADAPGHHDPASLTTIPPEA
+VPMWGFEWPRSGDPRPSAVLILFGALDDVPARHDAERVHPHVDVLLTQRAATLRQHAGQI
+AFPGGRVDPEDADVVATALREAQEETGLDPAGVEVLGVLPAVPVVVSGHVVHPVLGWWRD
+PSRVAVVDQAEAAAVFRMPVADLVDPANRCRVARPGGRRGETPGFLVGERLVWGFTAALL
+DRVLALLGWDVPWDDSRVRDARTHEILRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001499.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001499.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3e769e026f0efa5df53c9dce92479d7379f1a8e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001499.fa
@@ -0,0 +1,50 @@
+>0_1797
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVEADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVESTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRTPL
+>1_1504
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDERTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDAAIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEKGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDEDGETTTVTATGCEPGPDADDEKLLTETDRIPL
+>2_987
+MIASRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAASDGKRIGVYKDIGLVSQVFDESTLATFTGHIAVGHCRYSTTGANKWANAQPTLGATA
+GGDTVALAHNGNLVNSGELLRMVQARDGLQLRGEMKQGNTTDTALVTALLHGEEGRKLEE
+TALELLPKVRGAYCFVFMDEHTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDASIAGRSVYESRVDMGRRL
+ALEGPVDADVVIPVPESGTPAAVGYAEASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFASRAELIANGAGVAEIASSIGADSLGYISEEAMIAATGQPRERLCTACFTGTYPIELA
+DESERGKSVLETDAGSAAVTVMAPDGDATTVASTGCEPGPDADDEKLLTETDRTPL
+>3_932
+MISARTRRGDGRLTAALDPQEAGPQDECGVFGVWAPGEEVAKLTYYGLYALQHRGQESAG
+IAASDGKRIAVYKDMGLVSQVFDEPTLAALTGHVAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVESKEGAHTLGEIKQGNTTDTALVTALLHGEKGVSVEE
+TALELLPKVRGAYCFVFMTERTLYAARDPHGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAEATPAGCVFEYVYLARPDAAINGRSVYESRVEMGRRL
+AQEHPVDADVVIPVPESGTPAAVGYADASGIPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQPSVVAGKRVVVVDDSIVRGNTQRAIVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAGVQEIASSIGADSLAYISEEGMIAATEQPRERLCTACFTGTYPIELA
+DEKERGKAVLENGTPTAEATDVVSEDGTVTTVASTGCEPGPDSEDEKLLTQTDRTPL
+>4_1718
+MIAPRTRRGDGRLTAALDPQDQGPQDECGVFGVWAPGEEVAKLAYYGLYALQHRGQESAG
+IAVSDGGRIAVYKDIGLVSQVFDEATLTALSGHIAVGHCRYSTTGVNKWANAQPTLGATA
+DDGTVALAHNGNLVNSAELLRMVHAADGRHTHGEMKQGNTTDTALVTALLHGAPGDRLEE
+TALELLPKIRGAYCFVFMDEHTLYAARDPQGVRPLVLGRLERGWVVASEQSALATVGASF
+IREVEPGEMIAIDEEGIRSTRFAESKPAGCVFEYVYLARPDATIAGRSVYESRVEMGRRL
+ALEQPVDADVVIPVPESGTPAAVGYADASGLPFRQGFVKNAYVGRTFIQPSQTLRQLGIR
+LKLNVQSTVVAGKRVVVVDDSIVRGNTQRAVVRMLKEAGAAEVHVKISSPPVKWPCFYGI
+DFATRAELIANGAAVDQIAASIGADSLAYISEEGMIEATGQPRERLCTACFTGDYPIPLA
+DEGERGKGLLEPVAVSPASTVVLDVDGETTTVTATGCEPGPDADDEKLLTETDRTPL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001501.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001501.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90e06dd2370a74f5b906f1be77d3f36cd4a979b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001501.fa
@@ -0,0 +1,35 @@
+>0_1799
+MATSSLPLSDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRVFAS
+>1_1506
+MVTSSLPLSDIAEAGRPFTRGDLRAAGVSERLVRGADVRRVTHGVHRLRSDHLGSWADLG
+YVEAPAPFAPEETAAIVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
+>2_985
+MSMSTSTSTSLPCPQDRRPPVPARPLDVVAAGGPLFTRADLSAAGLPADRLRAADVRRVT
+HGVHRRADDVPGDWGALGYAEPPVAFAPEETAAIVTASRGVASHLSALLLHGIPVPPFLV
+DDGRVHVSRPHSRGASERPEVRSHARSVPEADAVVLHGIRVTSVERTWADLAALVRPGHL
+DPVVAAGDAVVTGIWTPQGRLPPRATILRLRAGLARSGRFKGARTARAALELIRAGADSP
+PETALRLALLHAGLPEPELQLVLHRGRRRSPDADLGWRAWRLVVHYDGDPHLDPAQQAVD
+AWRNGGWARAGWSQIVATVDDARDDFRRVVAEVLAHRARLGGRAYVA
+>3_930
+MALESLADVLGSAPLPIRAEGPPPLGLFTRSDLRAAGLGGHRVHGRDVRRVTHGVHRLAT
+DPAGDWAVLGHRCPPAPFAPEETAAIVEAAGGVASHLTALLLHGVPLPPFLAEDGTVHVS
+RPHARGASGRLEVTSHARSVPAADVTSLHGIRVTSLERTWADLASLVPPGLVDPVVAAGD
+AVVRHPWTPQGRSAPRTTPARLAAALDRAGRFKGVRTARRALEAVRVGSDSPQETALRLA
+LVHAGIPEPELQLVLHPGRERSPDADLGWRMWRLVVHYDGASHLEPAQRAVDARRHEGWE
+RAGWAQIVATVDDARDDFRRVVAEVQAHRRRLGGRVYVC
+>4_1720
+MATSSLPLPDIVETGRPFTRGDLRAAGVSERLVRGGDVRRVTHGVHRLRTDHLGSWADLG
+YAEAPAPFAPEETAAVVEASGGVASHLTALLLHRVPLPPFLAEDGTVHVSRPHPRGASVR
+PEITSHARLVPAADVTALHGIRLTSLERSWADLAALLRPGMLEPVVAAGDALIHRPWSPE
+GRRSPRTTTAALRSALLRAGRFKGVRTARAALELVRVGADSPQETALRLALLHAGLPEPE
+LQLVLHPGRARSPDADLGWRQWRLVVHYDGGHHLDPAQLAVDSWRDEGWARAGWTQIWAT
+VDDARDDFRRVVAEVQTHRARLGGRIFAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001512.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001512.fa
new file mode 100644
index 0000000000000000000000000000000000000000..563b9f3725a819cb7902274b7a9405c93864c9eb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001512.fa
@@ -0,0 +1,30 @@
+>0_1810
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>1_1517
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSIVGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
+>2_970
+MLPAVTPLTLAASTVTADTDYGWLGNVVVDIMEAVGPVGVALAVFAENIFPPIPSELILP
+LAGFTAAGGAFSPLAALLWATVGSVTGALALYGIGALLGRRRMYRIADRMPLVDVEDVAK
+TERWFARYGYWTVFLGRMVPVFRSLISIPAGIERMHLGMFTLFTTLGSLIWNAIFVYGGY
+ALGERFHLVSDYADVFSNVVVVLVLAFLVVWVVLRLRRNARRAKDPDWHQPTADEMAARV
+DALLESSDHRK
+>3_909
+MIRRGRTTSDAAAVVVVENGGMSALSTLPLLAAAGTPDYGWLGNTIVAIMEAIGPVGVGL
+AVFAENIFPPIPSEVILPLAGFTAAGGAFSPHAALIWATVGSVVGALALYGLGAWLGRRR
+LYRIAAWMPLVDVSDVERTEKWFARYGYWTVFVGRMVPVFRSLISIPAGIERMNVAKFTL
+FTALGSLLWNAIFVYGGYALGENFHVISDYADMFSNIVMVLILVFLAVWVVLRLRRNRGR
+AADPAVDHEDPEAAAARVEAEIKALQHRK
+>4_1731
+MLPLVAPLTVAAAAPTDYGWLGNIVVDIMEAVGPIGVGLAVFAENIFPPIPSEVILPLAG
+FTAAGGAFSPHAALVWATVGSILGALALYGLGAWLGRHRMYRLADRMPLVDMEDVAKTER
+WFIRYGYWTVFLGRMVPVFRSLISIPAGIERMNLAKFTLFTALGSLIWNAIFVYGGYALG
+ERFHVVSEYADVFSNIVLVLILAFLAIWVVLRLRRDARRRNDPDWRPPTADEMAARVEAI
+LESSDHRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001525.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001525.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8ea240f29a19877ea2676c4aaffdd55ec0ed788f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001525.fa
@@ -0,0 +1,15 @@
+>0_1826
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>1_1533
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAAHRH
+THHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
+>2_952
+MTDPFHLAAWIAGTLLFVGALGALYRIVRGPSLLDRAIATDVLLVVLSSGLILDMAVRRH
+TDNVVLVVLAATVGFVGSVTVARFVEDRRPDHSMEDQARVPGTSDVPGGEEGR
+>3_891
+MSLPLTLAAWIGGAMLFVGAVGALYRIARGPSLLDRAAATDVLLVVLSGALLLDMGVHRR
+TDTVVLVLLAAAVGFMGSVMVSRFVEDRRPEHPQEHEALVPGTSDVPAPREDA
+>4_1747
+MDPMDLATWAGGALLVVGAVGALYRIVRGPSLLDRAVATDVLLVVFSGMLVLEMAVHRHT
+HHVVLVVLAATVGFVGSVTVARFAEDRRPDHSLEDQARVPGTTDVPGGEEGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001526.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001526.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5bfac68b57ac1e48b8d0dedc62934b9089219d2c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001526.fa
@@ -0,0 +1,26 @@
+>0_1827
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
+>1_1534
+MPGSDSARRDVVRPDRVRGIVAQWPLILVMVAVWCALWQDFAPHVALAGLAFALLILGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVTGVVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALVLVPGSIVLDVDRVRSVLYLHVLDATTDEDVEGFRAKALDVEAGIIRAVGT
+REDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>2_951
+MPGTDPARDAAGAERPARPHRVRDMVGQWPLIAVLVLLWCAVWEDYSLHVALAGLAFSLL
+VMVLFPMPRIPFSGRLNPWWFLVFTAQFLGDVVRSSVEVSKVVLLRGRAARSSIVGVRLR
+SHDDLVITLVSHALALVPGSIVLDVDRARSILYLHVLDATTDEDIEDFRAKALRVEAGII
+KAVGTREDLELVHRYPDTAPPEEESAERRRPAAPRPGGTAPIGSTADHAKEGT
+>3_890
+MPAAETTSPASAPTRPAPGGVRSVLRQWPLLLALVLMWCAVWQDFSAHVALTGLLFSLLV
+VVLFPMPPIPFGGRFHPGHALVFTGRFLADVVASSLSVTRVILTRGRTVRSSVVRVPLRS
+HDDIVLTLVSHALALVPGSIVLDMDRANGVLYLHVLDATTDADVADYRAKALRVEADIIR
+AVGTRADVAVLRDHPDSAPDPEGVEERRRHPAYRAELLPDTPGPVAPAPVDARPEPDAPG
+GDR
+>4_1748
+MPGSDSARRGVVRPDRIRGIVAQWPLILVMVAVWCALWQDFAPHVALTGLAFALLIIGLF
+PMPSIPFSGRLNPWWSLVFTVRFLVDVVRASVNVAGTVLLRGRRARGSIVGVPLRSHDDL
+IITLVSHALALVPGSIVLDVDRVRSVLYLHVLDATTDEDVAGFRAKALDVEAGIIRAVGT
+REDLELVRRFPSSAPPAARPPKEEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001530.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001530.fa
new file mode 100644
index 0000000000000000000000000000000000000000..29f2b5470b475e4d57325434c1f091ae78f5256e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001530.fa
@@ -0,0 +1,45 @@
+>0_1831
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRLWLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>1_1538
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLGLTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGAVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDEGLNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPSPGGGPRRESLAASYRAL
+GSTLARMWREDRNTLWFLLSSAVFRDGVGAVFVYGAILGTTVYGLAASDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
+>2_947
+MPGMDPAASAVPDAALPRLATAAPRRQVVAWALWDWGSAAFNAVMVTFVFGTYLASDAFG
+PDERGTAWLSTALAVAGVVIALTAPVMGRRADGAGRRRLWLGVMTAAVIACTTACFLVTP
+QESSLLLGVTMIALGTVFFEFAEVQVNAILVQISTPATIGRISGIGWGAGYLGGILLLLI
+VFVGFVSGDAHWFGITGDEALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPTPGGGPRR
+ESLAASYRALGSTLARMWRQDRNTLWFLVSSAVFRDGVGAVFVYGAILGTTVYGLAASDV
+ILFAIVANVVAAAGAFAGGRLDDAIGPRRVILGSLAAMVLVAAGLALASGTLAFWIGGLA
+LCLFVGPVQSASRAFLGRLTTERTAGEVFGLYATTGRAVGFITPMLVTLALAAVPDNRVV
+IPVIVLVLIVGGVLFARVTDPVTRSAEPAP
+>3_886
+MPRMSSPAPHAAPQPCPAPHGGAGPAPARVPRGRVVAWAAWDWGSAAFNAVMVTFVFGTY
+LASDAFGPDDRGTQWLSAANALAGVVIALTAPALGRLADGTGRRRLWIALTTGAVIACTA
+ACFLVTPEESMLGLGVTLIALGTVFFEIASVHINAILLQISTPATIGRVSGFGWGAGYLG
+GIVLLLIVFVGFVSGDDHWFGVGEERALNIRVVALVAAAWFLVFALPVLAASPEPPAARG
+ADGSPRRESLVESYRGLGRTLARMWRQDRLTLRFLAASAVFRDGVGAVFVYGAILGTTLY
+GLAAQDVVLFAIVANVVAALGAFAGGRLDDALGPRRVILGSLAAMVVVAAALVLAEGTAA
+FWAGGLALCLFVGPVQSASRAFLGRLTVPETAGEAYGLYATTGRAIGFITPALVSAALAV
+WGDSRVIIPVIALVLLAGGALLLGVREPEGPTVAGARPGTGPRAAR
+>4_1752
+MTDVALPPVASAAPRRQVAAWALWDWGSAAFNAVMVTFVFGTYLASDAFGPDERGTAWLS
+TAMAVAGVVIAVTAPVLGRRADGAGRRRRGLALTTGAVIACTAACFWVTPEESSLLLGVT
+LIALGTVFFEFAEVQVNAILVHISTPATIGRISGIGWGAGYLGGILLLLIVFVGFVSGDA
+HWFGVTEDAALNIRVVALVAAAWFLVFAIPVLVAVPDPAPAPAADGGPRRESVLGSYREL
+GATLARMWREDRNTLWFLVASAVFRDGVGAVFVYGAILGTTVYGLATSDVILFAIAANVV
+AALGAFVGGRLDDAVGPRRVILGSLAAMVLVAGALFFASGTLAFWVGGLALCLFVGPVQS
+ASRAFLGRLTTPRTAGEVFGLYATTGRAVGFITPALVTLALALHPDNRVVIPVIAVVLVA
+GGLLFARVTEPITRSAESVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..52c7e5b8fa267446b8154f525482d87a31686756
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001532.fa
@@ -0,0 +1,35 @@
+>0_1836
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
+>1_1543
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREVRRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLPGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
+>2_942
+MTQVLSGFVVVWVIIAVGFLVGRSGVLGEDARTVLSRTAFYIGSPALLFVTLSGADVAAV
+LGPQLWVATLSALAAAALFLAISIPVFKQRPASERIMAALSASMVNSANLGIPIAAYVLG
+DAALAAPVLIFQLAIYTPLYVAAMDVATTSEARARAAGGRPAVRRSRGQALAAQLRQTGT
+NPMILGSAAGLLFSLNDWTLPGPLMQSVELIGGLSIPAMLLAFGMSLVGSRPLERAGGRR
+ADVLLASGVKLLVHPLIAWVLAQFVLGLDAREVFVAVVLASLPTAQNVFVSAVRYDAGLR
+VAKDTILITTIVAIPAMIAVALLLA
+>3_882
+MIEVLSGFSVVWVIILVGLLLGRTGVLGDEAREVLSRTAFFVGNPALLFVTLSRADVGAV
+LGPQLWVACLSAFAAAVVFLGLSIPLLKGRPASERVMSGLSASLVNSANLGIPIATYVLG
+DAALAAPALIFQLAIYTPVYVAVMDWATTHEAAARASSAGAAHDAGAPAPRTVRPRNPVL
+AQLRQTATNPMILGAFGGLLLSFTGWTLPGPLMTSVELIGGLSIPAMLIAFGMSLAGSRP
+LARDSGRRADVLLASAVKLVVHPLVAWMIAQFVFGLDARRVFVAVVLASLPTAQNVYVSA
+VRYRAGETVSKDTILVTTIVAIPAMIAVALLLA
+>4_1757
+MTQVLSGFAVVWVIILVGVLVGRTGVLGEHGRTVLSRAAFFIGNPALLFVTLSRADVGAV
+LGPQLWVATLSAFTAAALYLAVTVPLLKGRSASERIMSALSASLVNSANLGIPIAAYVLG
+DAALAAPALIFQLAIYTPLYVAAMDAATAREARRRTTAGRRRAVRRSPGRAVADQVRHTV
+TNPLILGSVAGLVFSLTGWSLQGPLMESVELIGGLSIPAMLLAFGMSLVGSRPLERAGGR
+RADVLLASAVKLVVHPLLAWLLAQFVFGLDARHVFVAVVLASLPTAQNVFVTAVRYDTGL
+RVSKDTILVTTIVAIPAMIAVALLLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001535.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001535.fa
new file mode 100644
index 0000000000000000000000000000000000000000..700f5d20a5651e6c8bfc10b30e4f9cac5246218d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001535.fa
@@ -0,0 +1,30 @@
+>0_1841
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>1_1548
+MSADRLPPLGRPAAPRRGRLRLAAAVAAGLLALTGCGAGDGDPAAASASADGVHGDAGTA
+APTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDEAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
+>2_937
+MLALTGCGAGDEPAPEQPSAPADALHGDVGGAAPAPEEGAEGLGLGDRQDERMAAAAAER
+AVGFGFVRQRAAAPEEIDAAREDSRARRSDADRTTVQPAACKAPLTALDFSPISLDEGEA
+TRVDVGADTFTGTGTVEVARLTGSGRQEVERHLQTVNGLLADCREMTMTVQDGDASVDYR
+LAVSEAPLSEGTPAQSALVWERSLASADGPQLTAQVLTAVTADAVVMVSFVGQPEAGRKE
+FTLIAEEMLAAALAAG
+>3_878
+MSADRTRPRPAVRRLAVASSGAALAAVLLAGCASGGDAAASSGAQAAGPSSSAATGGLDL
+GDRVDQRRAEAAAARAASFGFTRQDAVGADQIAAARGDAADRAADDGRTTVEPARCQAPL
+AALDFSPILLDQEEVSRVDVGTDSFAGTGTVEVATLDGPGRQRVEEHLQTVNTLLADCRD
+MTVTTRDADGARTYRLQMSAAGLSDGSPAQSGLVWTQTPAGRDEPATAAQILTAVGPEDV
+VMVSFTGQPQAAERQFTVMAEEMLAAAGTVTR
+>4_1762
+MSADRVRPLRRPAAPRRGRLRLVAAVAAGLLALTGCGAGDNDPAAASVPADGVHDDAGTA
+VHTESAAPEGLGLGDRQDERMAEAAAERAATFGFVRQRAATAEEIDAAREDSRDRRADAD
+RTTVQPAQCKAPLTALDFSPIALDGAEATRVDVGADTFTGTGTVEVARLTGQGRQDVERH
+IQTVNALRADCREMTMTVQEGDATVDYRLEVSDAPLSDGTPAQSALVWERTVASESEPQL
+TAQVLTAVTSDAVVMVSFVGRPEAGRKEFTLIAEEMLAAALAAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001542.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001542.fa
new file mode 100644
index 0000000000000000000000000000000000000000..387d8c73b091d1f10012f104e3aa392c89e1518e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001542.fa
@@ -0,0 +1,15 @@
+>0_1848
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>1_1555
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>2_930
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
+>3_871
+MAKKSKIAKNEQRKVMVARNAEKRLELKKTLIDPNASDEAREAARVGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFREMAHRGELPGVTKSSW
+>4_1769
+MAKKSKIAKNEQRKAIVARYAEKRLELRKTLVDPNASDEAREAARLGLQKLPRDASPVRV
+RNRDAIDGRPRGTFQRFGISRVRFRDMAHRGELPGVTKSSW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fe3d174611600b89092737b923011239a3a2183d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001543.fa
@@ -0,0 +1,10 @@
+>0_1849
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>1_1556
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>2_929
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>3_870
+MAKDKDVRPIIKLKSTAGTGYTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
+>4_1770
+MAKDKDVRPIIKLKSTAGTGFTYVTRKNRRNNPDRITLKKYDPVVRKHVDFREER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001546.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001546.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51d38acfa6d09132c16b6dde6092ea099250c72b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001546.fa
@@ -0,0 +1,40 @@
+>0_1858
+MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEEGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMSALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
+>1_1565
+MENQQTGQAADRGTIDTREGFTGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLSTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
+>2_922
+MENQQTGQAADRGTIDTREGLKGNYVQSGAEFTRDTNYITDRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRAIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERLQENYFARFPDYPRGITVPAVVDVPTGDVVTNDYPQMTLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIKRVFTEVNNGVYRCGFAGSQEAYDAAYDR
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNRLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGEEVEPAHTPLR
+>3_858
+MEDQQTGQAADRGTIDTREALTGNYVQSGAEFTRDTDYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDAGGKDPVLGTERLQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWAAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG
+YARDLFQTPGFGDTIDFAQIKEHYYVVHEDINPTGIVPAGPDLSGWTTEHGRADLGGDPW
+GGGTAPGPVRDDERVDPEHTPLR
+>4_1779
+MENQQTGQAADRGTIDSREGLKGNYVQSGAEFTRDTNYIADRIVADPEAVRALPVAEPST
+VGRVGGGLTEGAEAWPVEAGRYRLVAARACPWANRTIIVRRLLGLEDAISLGTPGPTHDE
+RSWTFDLDEGGKDPVLGTERIQENYFTRFPDYPRGITVPAIVDVPTGGVVTNDYPQITLD
+LSTEWTAFHRDGAPQLIPDAGPERDEMFEVIERVFTEVNNGVYRCGFAGSQEAYDAAYER
+LWTAMDWLEERLTTRRFLMGERITEADVRLFTTLVRFDPVYHGHFKCNRNKLTEMPALWG
+YARDLFQTPGFGDTIDFVQIKEHYYVVHEDINPTGIVPAGPELASWLSEHGREAFGGDPW
+GGGTAPGPVREGERVDPEHTPLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001556.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001556.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25ecbed6519cb8e8653052cf797a043d3aa2fe11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001556.fa
@@ -0,0 +1,25 @@
+>0_1870
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG
+>1_1577
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRGWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG
+>2_908
+MHLIPRTLWVLARARRRPPLSIWDSASLPMRALPTDVDIAGHVNNGQYFGLFDLGRFDLM
+ARSGLMRAVRRRGWLPVVQAEQIAFRRSVTLGTAFTLETRIIGLDERAVWFEQRVVVAGD
+VAVRGYVCTRLRGRDGTPVGNDEVRALAVELGHDPAAEPELPGWLHDWREQVALPSARTP
+LPHAWGR
+>3_843
+MLHLLPRTALVVVRARRRPRLGIWEASTLPLRALPTDVDFAGHINNGQYFGLFDLGRFDL
+MVRAGVWDGAKRRGWLPVVQAEQIAFRRSVTLGTRFTVESRIIGLDERAVWFEQRAVVDG
+DVAVRAFICTRLRAKDGTPVSNEDVRDLARELGHDLAAEPVLPEWLHGWRSDIALPSART
+PLPHAWGTPAPAGV
+>4_1790
+MHLIPRTIWVVARARRRPRAGLWEPTTLPMRALPTDVDMALHVNNGQYFGLFDLGRFDAM
+VRTGLWDEIRRRHWTPVVQAEQIAFRRSVTLGQRFDVETRMIGLDERAVWFEQRVVVDGD
+VAVRAYICTRLRKKDGRPVENDEVRAIAAAAGHDLAGEPTLPEWLHEWRRSVALPSARTP
+LPHTWDLDTVRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001557.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001557.fa
new file mode 100644
index 0000000000000000000000000000000000000000..72cfe6c6d9fcbcc7ce60a174a13f262eee518871
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001557.fa
@@ -0,0 +1,36 @@
+>0_1872
+MAAVDPAPTDARERRDLVVPVPGPEDPPERAWLVLPHRHPVPTLLEETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFVRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPDTGPWGGPGHLASWVRLQGDGEAAVHWRGDRFNP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGRPQLSFPAPPLLRLAGALNDLVLLQPRP
+>1_1579
+MAAVDPAPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVSDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAAQPAAYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLPQLSFPAPPLLRLAGALNDLVLLQPRP
+>2_907
+MPAAETVPADAAGRPDARPRVPGPREQPERAWLALPRRHPVPALLDEARDAVAGLAETLA
+EVLPVTVLTDPADHAVRSLIPPEVDLLAAPVDSPLLGRTGPGFVRRPEGLAAIAWRPAAG
+AGGPGPRDAGVAAAVAAAAGLPLLTPMLRAPRDAWVADGEGTAVVAADPVLDGRTNPAWT
+PEQVEAEFAALLGITRVAWLPPVPRIPTGPWGGAGHLGAWVRLLGGGEAAVHWRADRFHP
+EHLHGAAALRILQDAPDAAGRPLRVRTVPGGALPPEHDPAEIGPRSLVDTVPLGSAVLRP
+AFEDAATEEAAAAACAALHPGLRPVPFPGPPLLRLAGSLSDLVLVQPHP
+>3_842
+MSTPAVPEPPRAPAPWEVPERLWLALPAVHPVPGLLAEARDAVAGLAETLGAHAPVAVLT
+DPDDADAARLLPGVVERVPVRGASPLPGREGPTFVHAAGTRGSVEAVHWRLPSDAAGTAG
+RAAATADAVARSAGLPLRTPLFSAPAGTWAADGDGTAVVSAALLDPAVNEGWTRAQAEDA
+LAGLLGAERVLWLPPVAGHAAGPWDGGGAAQPHPHPWLRFVAPGEVAVHWQPGRLHPDHA
+ASAAALHALTGARDARGRALSVRTVRALPPGPDADLEARGPLSALDLLPLAPGVVLRPAH
+ADPEADAATAEAAAALFPGAEQVPFPGPPLLRLLGTLSDLVLPQPPGARTRRPSPAPAHP
+EGPRAAP
+>4_1792
+MAAADPVPTDARERRDVVVPVPGPEDPPERAWLVLPHRHPVPTLLDETRDAVVGLAETLA
+AVLPVTVLAHPRDAGAARLVPPEVDLLRAPVGSPLLGRTGPSFIRRPEGLAAVAWRSAAG
+LTGTGPLDGAAATAVAEAAGLPLLTPLLCAPRGAWVTDGEGTAVVAADPVLDGRINGAWT
+PGQVAAEFAALLGITRVLWVPPAPRPGTGPWGGPGHLASWVRLRGDGEAAVHWRGDRFHP
+EHPYAAAALRFLQGADDAAGRPLRVRTVTGAVQPAEYDPAERGPRSLLDTLPLGAAVLRP
+AFEDAAGEEAAAAACAALHPGLAQLSFPAPPLLRLAGALNDLVLLQPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33381492feee6841df13044a143228e6c3886dfd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001558.fa
@@ -0,0 +1,45 @@
+>0_1873
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGKDEDRAPTDGGDDDGPATDEVTG
+GAGAAPGR
+>1_1580
+MSAAQPAGVTPPSASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSAVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAILGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDDGPATDEVTG
+EAGAAPGR
+>2_906
+MSAAQPVGAAPTPSAAGPVSDWDIRRPHRMWPRMLVIVLTLAGLVLLVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGVHPVLGAAASVVVVVAVLGAFVGMIVWSGLELVAELPK
+YSGQFQQIVLDVSNWLNARGVTPDMVSQQLASIDVSAVTSAAVSALTKIATNLYAVLGLL
+VTVVMGMFFLAMDSMDVERRVRLLSTARLELGEALIDFAHGVRRYWVVTTVFGLIVAALD
+VIALVLIGVPLALVWGVLSFLTNYIPNVGFIIGLIPPAILGLAAGGWTSFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+SRWVNSLIASDLKGMERRQHSLLERLRVGRRGEGRAGKADAEAVAGADVAAAGVEAALDV
+DDAAAGARRPEAAPTGSTLTEPARTEPGPAAPADAADGPGLTGGAAPAPGR
+>3_841
+MSASAPPAVTGTSTPATEWDNRRPHRMWPRMLVIVLTLAGLVVLVQFFQGIASIAAPVFL
+GLNLVIVAYPLQAWLIRRGLHPVLGAATTVVVVCAVIAAFLGMIAWSGMELLTELPKYAG
+QFQQIMHDASQWLSDHGVTPDMVNQQLASVDMSAVTGAAVSALTTIASNLYAVLGLLITV
+IMGMFFLAMDSMAVERRVRLLSTARHELGQALIDFADGVRRYWIVTTVFGLIVAVLDMVA
+LVIIGVPLALVWGVLSFLTNYIPNVGFIIGLVPPAILGLAAGGWPAFLWVVVSYSVLNFV
+LQSIIQPKVAGDAVGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLVKAVLIDADPNSRW
+VNSLIASDLKGMERRQSSMLERLRLPRELIRHGGSTASHATAADVQGDDDVAPERTAEDA
+APAQDRRRVRAAAQEARLEGPPPSTLRAPRVDLPGEPEPATADGSAPPEAGAAPGR
+>4_1793
+MSAAQPAGVTPPPASSSPASDWDIRRPHRMWPRMLVIVLTLAGLVLVVQFFQGIASIAAP
+VFLGLNLVIVAYPLQAWLIRRGLHPVLGAATTVLLVVAVMAVFGGMMVWSGLELVAELPK
+YADRFQQIVLDVSHWLNERGVTPDMVSQQLASIDMSTVTGTAVSAITKIATNVYAVFGLL
+VTVIMGMFFLAMDSMDVERRVRLLSTARHEFGHALVEFAQGVRRYWVVTTVFGLIVAVLD
+VIALMLIGVPLALVWGVLSFLTNYIPNIGFIIGLLPPAVLGLAAGGWSDFLWVVVSYSVL
+NFVLQSVIQPKVAGDAIGVIPTVSFLSLLFWAWVLGPLGAILALPCTLLAKAVLIDADPN
+ARWINALIASDLKGMERRQSSLLERLRPAAWRSDAHGGDEDRASADGGDDEGPAADEVTG
+EAGAAPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a4e2964aa7935edcf61ac525dd9caa158fb505bc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001559.fa
@@ -0,0 +1,36 @@
+>0_1874
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWRGLKENGGKVADSWSDAYNSDFSGGEGKGRFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>1_1581
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSASGAGGGEPTTVTIMTHDSFNLPQE
+LVQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEY
+TPQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVA
+TSPVASSPGLALLAATTEKYGDDGWQDWWRGLMENGGKVADSWSDAYNSDFSGGEGKGRF
+PVVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFMLTEEVQSALPE
+SMYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
+>2_905
+MTTAPHRVRTRPRRHGALAALSVAALALTGCSVADRGGSGDQGSSSAEARTVTIMTHDSF
+SLPDELIARFEQESGHTLVTTAPGDAGSVVNQLLLAKDAPTVDGVYGIEDHSAHRLVSEG
+VIAEHVPADLPDSARDLVVDGRMTPVDQGQVCLNVDTPWFQEQGLAAPTTLEQVAAPEYA
+ELTVVTSPVSSSPGLALLAATVAEFGEDGWQDWWRTALQGGMQVDASWSDAYNTSFSGGE
+GTGTRPIVLSYSSSPAFAPDTDVVAASCTPQVEYAGVVEGAENPEGARAFVDFLLTEDVQ
+AAIPDAMYMYPVDSSVPLPEAWAEHAPLVEDPIVPDAGLLDSRREDLLKEWTALHEEAAS
+>3_840
+MSVHRTATTRRGVLAAACLSALALTGCSVSAPSTGSSSSAASSSAAPSSASGSSSTSASG
+TAAAGSKGTVTIMTHDSFALPKELIAQFEAESGYRLVTTAPGDAGAVVSQVLLSKDAPVA
+DGVYGVENHSAHRLVDQGAVQDVAPADLPASAEDLVVDGKMIPVDQGQVCFNTDPAWFTE
+HGVAEPTSIDQLRDPEYAKLTAVTSPVTSSPGLALLAATTEKYGDDGWQGWWEDLLKGGA
+KVDSTWSDAYSTDFSGGEGKGEFPVVLSYSSSPAFAPQTAVIEDSCTPQVEYAGVLTGAE
+NPEGAKAFVEFLLSKDVQAAIPENMYMYPVDDTVELPAEWAANGPLVEDPITPDPAEIDT
+EREGLLKEWTALSESAGSR
+>4_1794
+MSRTPHRALAALSVAALALTGCSVSGSSGDGASSSAAGAGGEPTTVTIMTHDSFNLPQEL
+VQKFEQESGYTLKTTAPGDAGSVVNQLLLAKDEPTVDGVYGVEDHSAHRLVREGVVAEYT
+PQDLPASAQDRMVEDRMTPVDQGQVCFNTDPAWFEAHDVEAPTSIDQLDDPEYAKLTVAT
+SPVASSPGLALLAATTEKYGDDGWQDWWQGLMENGGKIADSWSDAYNSDFSGGEGKGQFP
+VVLSYSSSPAFAPETEVIEDSCTPQVEYAGVLEGAKNPEGAQAFVDFLLTEEVQSALPES
+MYMYPIDESVQLPEEWAQNAPLVEDAITPDPARIDERREDLLKEWTALAEASRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001563.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001563.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a30154e205b9a3b451d6f0871a521ecf5490deba
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001563.fa
@@ -0,0 +1,45 @@
+>0_1878
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
+>1_1585
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWEFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSAFWSTVTVDLPPERPVIVRLGSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIRLRVEDDAAAG
+>2_901
+MRVVAAPLAMLPGVDHGPALRMDLHPVPGGIVYVARDLVLRELGDDVRGHVHAGMVGTAQ
+LHAFWSTVTVDLPPDRPVIVRLRSDRDAELLSLLEVLAPVEMRVVSYRLDESPVGTQRSS
+YLLPDVDPEIVARAESPRVPLEAIEATQEEEDALRRSSGVFLSRRRTDRFLRRTLPTVTH
+SLSFSDEADVADVYVDGSVLRSSRIGGAAAVGGPSMWAVQAVNGATTPLEVELEALVLGH
+VVSAWAGVPGERVTIHSDSRAALALLNAARRERLTLGGARGERVRRTLRRLLAAVDLAQA
+ADVRVETTWVKGHVGVQGNELADDLARAAARHAGVGTSEEDLRRRLDRLIDLHEEAEAEA
+GQTPARAVAAEGHRPMPPGRRPGPRL
+>3_836
+MDNSSTHPREGQVRSLHFDTDASSPDALLDPMWAFTGPRASRAGAPAPDGADVLARRARP
+AHPGAALVRAATSLFTLPGPPGMPHRSRSAALEAARAPAGYLSPVPHRLALPRPARPRPA
+PPRMRVRQDGVRVVARPLAMLPGVDHGRALRLDLHPVRDGIVFVSRHLELRELGDDVKGL
+VLTGVVPAARLGYFWDTVAGDLPEGRPVIVRLRSNDDAELLTLLRAIAPPWLRVVSYRLD
+ESPVGSQRSSYLLPDVDGEAVAASGAERVPLETLREAHQASAEVERASRVFLARRRVDRF
+VRRSVPDLMHSLSYTDPAEVRHVYVDGSVLRGTRTGGAAAVTRSGPWAAHALPGATIPLE
+AELEALTLGHLMAAWSGTPDERVLIHSDSRAALALLREAHRERLTLGDARGERIRRALRR
+LLAAVDLAGSAGVEVSTLWVKGHAGTHGNELADDLARSAARNTAAGVSADEMRRRMRHVV
+QLWDATTHPQA
+>4_1798
+MGARINHPRTVVDRTLHHDVEPAHPAALVDVGWDFRGPGAKAEEQHRPLRVVRARRPRGT
+PRDRNGVDLTRTGPVVPRPSPPRTRIRRDGVRVVASPLAMLPGVDHGPALRLDLHPTTGG
+IVYVARELELRELGDDVRGHVYTGMVGTAHLSVFWSTVTVDLPPERPVIVRLRSDRDAEL
+LSLLEVLAPVDTRVVSYRLDESPVGTQRSSYLLPDVDPETVAQTGAARIPLEAIEAAQEE
+EDALRRSSGVFLSRRRTDRFLRRNLPGVTHSLTFADEADVTDVYVDGSVLRGSRIGGAAA
+VAGPSMWAVQAVAGATMPLEVELEALVLGHVICAWAGTPGGRVTIHSDSRAALALLNAAR
+RERLTLGGARGERIRRTLRRLLAAVDLAQAADVQVDTTWVKGHVGVHGNELADDLARAAA
+RHASVGTPEGDLPERMGQLIQLRVEDDAAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001570.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001570.fa
new file mode 100644
index 0000000000000000000000000000000000000000..072a9a904427b2713224a798b6e8d14983ee266d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001570.fa
@@ -0,0 +1,68 @@
+>0_1891
+MINSAEPRHVHELFSSQTKAHYVVPPYQREYSWHRAQWEALFADLVESEDEHFLGTIITL
+SRTKDSLSGPVLEVIDGQQRLTTLTILLAAVHSHLQDAEDLDEDARFERMTLRRELVRDE
+AKAPRLTPQVQGANRADYQAMLADAGLPVKSEKKAYYPSRKVAKAFWFFRAAITELAEER
+GESLSTTALSVLAAARRALIVNIEVASAADAFVLFESLNNRGVPLTPVDLIKNSFLARAE
+HRAGMEVEEAFELWSDTLAHLGDSYATHERFLRHFYNAFRGDLPPVKLAPVATRKNLIRI
+YETLLDQDLEGTVRSLERAAQVYGRIAGGGDVDEPTSLDQELTALRRAQAAPSYVLVMWL
+LVRQEKAGWSEEDLAAVARLLVSFFVRRNLTGFPATYALPRLFMDVIDQVAAGEPDRLLT
+IVRGSLVAASASDATFRERLEGPVYEENRDVTRFLLATLAEDAMTKETRVDLWAQSGKTF
+VWTIEHILPQGENLPQEWVDALGGPEAAAETQNRFVHTLGNLTITGFNSTLGNQTFLRKR
+DRIDHQGRAIGYRNGLALNAELAEKEAWSSADIEARTVRLVERALERFAL
+>2_886
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLFGLSQPSADGEE
+EQLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVITAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEIST
+VPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRKDDPHDVLAAEGVRF
+SEDGRAYGGQRLVAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRASARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGVEFGPEALRRRPSIRPQILQPAAAQEAFLDALEWFLHTIQ
+EDDRSA
+>3_278
+MSHERVYRIGSPGAEPLVPVSFAEAGLRERQDLQEWVIAHPEILGEDIRIVAFEFDRWED
+ADGGRQRDRLDVLGLDQSGCLVLAELKRDAAPDTVEMQAIKYAAMASRFTEEKLVAWHAA
+MLGRLENRPVSEEEAREALTDHAGELDVEQLRRPRIVLVAGAFTRSTTAAVVWLTEMGLD
+ITLQRVQAYRMGGDDVVITVSQLFPVPDVEEFTVSPMRMESTARRTSSTRSPSTVRRLVK
+AGTLPDGTVLTLVPTTEVNAETREAIADWISDDPRRGRATWWNDPTKPMEWELDGNRYRP
+SRIVQQALREATGITRSPRGPAWWVTESGMSLTELAGDVENGAFDWTQLHRLLCELPAGR
+WTTYGEVARLIGTAPQPLGGHFRTCTLCRNAYRVLDANGAVSSGFTWGDPQETRTQQEVL
+EAEGISFDGGRAAPSQRLQPSELESVWKVAQAALGE
+>3_826
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRAAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSAAGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKVRQTEIYAGQQRRMRDLQDESQVRA
+EVGRFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARAFLYLESYLVRRLVFGRYSDGLNTTLLAATADVQGQDDPADALQRFLSTGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVMPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVDIWPGPSAEAASGVAHTAWQTLTDAVEAIPAGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWTDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLVAEQLAELIDVDVDLIDPRSLAAPGNDPALRDRWVDRLHDHNDPESAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWP
+PFTDEALLDDFRGRLNLIPGLEFGPEALRRRPSIRPQTLQPAAAQEAFLDALEWFLHTVQ
+EDDRSA
+>4_1813
+MVAAREVTLQELLGGSYQYTVPLYQRTYSWGRPQWQRLWEDVVDVADHRRDNPSATHFIG
+SLVLAGFRDNGPGGVQRWLVVDGQQRLTTLTLLLAAVRDHRAEHEGPMHADRVNEKYLVN
+KWEDGDLRYKVLPTQADRGAYRGRIEHAPDAAEGSRISEAHQFFLTKLLGLSQPSADGEE
+EPLTLAEVESAVVAGLSIVSVTTGENDNAHRIFESLNNTGLKLTQGDLLRNYLFMQLPTR
+ADEVYTTLWLPLQNLLSNEELETLFWLDLVQQDPKIRQTEIYAGQQRRMRGLQDESQVRA
+EVERFLALGRLYDVMLRPEKEKDAAVRFRLARLRAWRTTTTFPITLHLMERRSLGDIDSD
+ELARALLYLESYLVRRLVFGRYSDGLNTTLLAATADIQGQDDPADALQRFLSSGRKHFAS
+DDQIRQAVMTAPFYTTGRAAHRKLILRWIEESYGSKEPVDLDSATIEHVLPQTLTEEWER
+ALAGQLEAHQDLREVHTELLHTLGNLTLTGYNSELSNGPFAVKRAELAKSGIRMNQEISA
+EPVWGPAQIRARAERLADRIVGIWPGPSAEAASGVAHTAWQTLTDAVEAIPDGSWTSYGE
+LARLIGSHPVPVGTYLARTALPHAHRVLQAGGTVSPSFRWSDVHRTDDPHDVLAAEGVRF
+SEDGRADGGQRLLAEQLAELIDVDVDLTDPRSLAAPGNDPALRDRWVDRLHDHNDPETAR
+ALIEVQRGWVERGGRAEFADNAAGGCFLVVPRTSARAIWPVILYPTYGVEVVFYHLAKWA
+PFTDETLLDEFRGRLNLIPEVEFGPESLRRRPSIKPQTLQPAAAQEAFLDALEWFLRTVQ
+EDDRTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001581.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001581.fa
new file mode 100644
index 0000000000000000000000000000000000000000..26a1440369bf51625f1f8f5b62ec8b1f78a6ad84
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001581.fa
@@ -0,0 +1,30 @@
+>0_1919
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
+>1_1624
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPTSAGVRRGPSARVEEARR
+>2_859
+MRVALFATCIVDAMYPKVALATVRILERLGHEVVFPRGQGCCAQMHVNSGYLDDALPVVK
+NHVRTFQGADYDVAVAPSGSCVASLGHQQPMVARAAGDEALARDAEEVAANTYELAALLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGDRQERLLRSVADIDYRALPDAEECC
+GFGGTFSLKNPDVSGAMAEEKIGNIERTQARLCTGGDASCLLHLGGVMSRRGTTAPDGSP
+VTTLHFAEILAATRENPLDVSGPVDLSIPAQGPARRRRQKEATR
+>3_795
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYVEDALPVVR
+NHVRTFMKADYDLAVAPSGSCVASLGHQQPDVARSCGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAAAQLGSWFPHTVTYHPSCHGMRLLRLGTRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASICTGGDASCLLHLGGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEAHR
+>4_1846
+MRIALFATCIVDAMYPKVALATVRILERLGHEVVFPPGQVCCSQMHVNSGYMEDALPVVR
+NHVRTFMKADYDLAVAPSASCVASLGHQQPDVARSGGDEGLARDAEVVASRTLELSQLLT
+DVLGVTDAGAQLGSWFPHTVTYHPSCHGMRLLRLGSRQEDLLRTVADIDLRPLPDAEECC
+GFGGTFSLKNPDVSAAIAEEKIEKVTASGASLCTGGDASCLLHLDGAMHRREARGQDGRP
+LRTVHLAEILAATRENPLEVDGPVELSIPASAGARRGPSARVEEARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001583.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001583.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb9657b240a2d70461d73d866d4adc75d6f16dd7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001583.fa
@@ -0,0 +1,30 @@
+>0_1921
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
+>1_1626
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
+>2_857
+MTARPPTPPAEPEPGRRRAPGHAVILDWLEGELRSGRIQVGDKLPSERTLAERFGMSRSS
+VREAGRVMDAMGLVRSATGSGPRAGAIVVSEPSAALAWALRMHVATRALPVADLVTTRVL
+LETEAALEAAEHDVPGRGAILATAHAHLDRMDVPDFPAREFHRLDAEFHVLLSTLSGNVV
+LETILRSLREATIGYVEEAMAGVEDWGAVRDELQRQHRDILAAAVERDGPRAAQAVREHI
+HWFSRFTTAGPDAAGG
+>3_793
+MTAAPAYTIVLDWLEAELRSGAVAVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQTGRVPA
+AG
+>4_1848
+MTAAPAYTIVLDWLEAELRSGAVVVGDKLPGERTLAERFGISRASVREATRMLEAMGLIR
+ASAGSGPNSGAVVVSEPSAALGWALRLHIATRSLPMADVVAARVLLETDAAQAAAATSGD
+PESVAVLAEVETLLDRMDDPALPEEDFHLLDTEFHVRLATLGGNVVTAMMLDSLRQATIG
+YVTETVAGLSDWPAVRAGLQADHRRILAASAAGDGRAAAQELREHVLGFAALAQAGRVPA
+GG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001588.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001588.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0d23f5bf28fff201893a1541bf287f7bba5fbed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001588.fa
@@ -0,0 +1,40 @@
+>0_1929
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAATVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFATWQLEAVATGTDDQGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
+>1_1634
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLISLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEAMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAAALVDAVREHWDPAVEFITPQGGFFLWATLPVGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVAAEKLVEGVRRLAPAVNESIARAR
+>2_848
+MRHLRDHLSHRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAAAAVMAADGIPDADPELVVITPGSQAAIDTACRAFGNPGD
+VVVVEDPTFVGALTTFNTWELDAVATGTDEHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPADRRAEVAAICERHGVLIVEDNPYGQIAFDGDPVAPIAAEHRDGVVYLGT
+MSKIFSPGVRIGWALVPAELKREFYLSAESAFIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGVLVDAVREHWDPGVEFITPRGGFFLWATLPGGVDTIELMHRGIEAGAVFVPG
+GAFTPVEGVHSTLRLAYPFVEAERLVEGVRRLAPVVNDAVARAR
+>3_1720
+MSTLDPAGARAHLARRATTVQQSAVRDVFDIAMDPDLVSLAGGNPWLAGLPLEELGATAA
+RLVAEQGTASLQYGPGQGLECMRVAACAVMAADGIPDADPELVVITPGSQAAIDTACRAF
+ADPGDVVVVEDPTFVGALTSFQTWELEAVATPTDEHGLVPADLDATLARLEAEGRRVAFL
+YTIPSFANPSGLLLPADRRDDVAAVCERHGVLIVEDNPYGQIAFDGAPVAPIAAAHRERT
+VYLGTMSKIFSPGVRVGWALVPEALHREFYLCAESAFIHASTTSQMLSTAFVTEYDWQDH
+VRGVTGLYRSRAQALQAAIAEHWDPGFTFTPPAGGFFLWGSLPAGVDAVELMHRGIAAGA
+VFVPGAAFTPVPGTHSTLRLAYSFVDEETLAEGVRRLAPVVNTAVEGAR
+>4_1856
+MRNLRDHLSQRAVGVKQSAVRDVFDIAMDPNLVSLAGGNPWLADLPLDELGRIASDLMTR
+FGTESLQYGPGQGTEEMRAAATAVMAADGIPDADPDLVVITPGSQAAIDTACRAFANPGD
+VVVVEDPTFVGALTTFTTWQLEAVATGTDDHGLVPAALDETLTRLAAEGRRVAFLYTIPS
+FANPSGALLPPGRRAEVGAICEKHGVLIVEDNPYGQIAFDGEPVAPIAADHRDNVVHLGT
+MSKIFSPGVRIGWALVPAALKREFYLCAESAYIHASTYSQMLSTAFVTQLDWQGHVRHVT
+GLYRERAGALVDAVREHWDPGVEFITPQGGFFLWATLPAGVDTLEVMHRGIEAGAVFVPG
+AAFTPVEGTHSTLRLAYSFVDAEKLVEGVRRLAPAVNESIARAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001589.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001589.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c937d3bc5bf6e785b882232c471409a18007d582
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001589.fa
@@ -0,0 +1,46 @@
+>0_1930
+MTQSTPEPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRPPQAPGYFLKAGTSLAR
+SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGRLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAEAASSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPVHRGRRVLGYAKTLRYVPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>1_1635
+MTQSTPDPTPTVTEHDFTVRENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAG
+SGDTIERPAGTELLAYEGEIALIIGRTARRVSPEEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVDSEHSLAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPIHRGRRVLGYAKTLRYIPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLQEVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
+>2_847
+MDENGHWVASAPQPDRSLLTPELRAKIDAVAVATLTAQLQKRGIQNATIDGPRPIHQGRR
+VLGYAKTLRYVPKREDLFKEFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLAL
+RAQVNGANAVITDGGIRDSAAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQ
+PGDVIVGDDDGVVVIPPSLLQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAT
+FDEYRKTLPDAPAPEGDA
+>3_786
+MTQNTSPATPSVTEHDFTVRQNRPGKVLALHLNYPSRIAQRGRSPQFPGYFIKAGTSIAR
+SGDAVERPAGTELLAYEGEIALIIGRTARRVRPEEGWSYVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVIAAANLDPAALRVRTWVNGALVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPTAPGAPSTGRLITHVTDSDIPMADY
+GHGPRVDDLQREEAWGSREAAGLAPVEDAPAQDDAAPASTAVDENGHWVASAPQPDRSLL
+TPELRAKIDAIAVATLTAQLQKRGIQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLFK
+EFGGGFNAQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDS
+AAVAEVGLQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVVPPSL
+LQEVVDDAYEQELQDAWAYEQVKAGHPVDGMFPPNAEWKAKFDEYRKTLPDAPAPEGDA
+>4_1857
+MTQSTPDPTPTVTEHDFTARENRPGKVLAVHLNYPSRIAQRGRSPQAPGYFLKAGTSLAR
+TGDTIERPAGTELLAYEGEIALIIGRTARRVSPKEGWSHVSGITAANDWGLYDLRHADKG
+SNVKNKSGDGYTPLGPAVISAAGLDPAALRVRTWVNGEIVQDDTTEGLVFPFGQLVADLS
+QLMTLEEGDVILTGTPAGSSVAQPGDVVEVEVDAPSAPGAPTTGRLVTTVVESEHALAPF
+GAQPQVDDVQREEAWGSREAAGLAPQAAAPSSSAVDENGHWVASAPQPDRSLLTPELRAK
+IDAIAVATLTAQLQKRGVQNATIDGPRPIHQGRRVLGYAKTLRYIPKREDLAKEFGGGFN
+AQKRAIDSVQPDDVVVMEARGEHGTGTLGDVLALRAQVNGANAVITDGGIRDSAAVAEVG
+LQVYAGATHPAVLGRRHIPWEVGGTIACGGTTVQPGDIIVGDDDGVVVIPPSLLREVVDD
+AYEQELQDAWAYEQVKAGYPVDGMFPPNAEWKAKFAEYRKTLPDAPAPEGDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6071f730549fb876a70332eee7fc690a754b8375
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001591.fa
@@ -0,0 +1,50 @@
+>0_1932
+MTEKTSIEARKPAGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHAIADIMETRGNQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>1_1637
+MTEKTSIEARKPEGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPQGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>2_845
+MTEINDRKPEGLPDLIRHYIDGQSVDSVDGDTFDVLDPVTNQPYIKAASGKTADVDKAVA
+AAKAAFESGVWSQALPRERSRVLHKIADIMETRGDQLAAMECFDTGLPIKQAKGQAARAA
+ENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAIATG
+NSVVLKPAEFTPLSASLWPGIFEEAGLPKGVFNMVHGFGEEGFAGDPLVKHPDVPLISFT
+GESRTGQIIFGNAAPHLKGLSMELGGKSPAVVFADADLDAAIDATIFGVFSLNGERCTAG
+SRILVAREVYDEFVERYAAQASRVKVGMPNDETTEVGAIVHPEHFEKVMSYVEIGKSEAH
+LVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDSDEEALELANNTK
+YGLAAYIWTNDLKRAHNFAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRSIDF
+YTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
+>3_784
+MTEKTSIAARTPEGMPDVIRHYIDGEFVDSIDGDTFDVLDPVTNEPYIKAASGKSADVDA
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQAKGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPTGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKA
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALQLAN
+NTKYGLAAYIWTNDLKRAHNFAQDVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQESKETGDA
+>4_1859
+MTEKTSIEARKPQGLPDVLRHYIDGEFVDSIDGDTFEVLDPVTNEPYLTAASGKAADIDR
+AVAAAKRAFESGEWSQALPRQRSRVLHRIADIMETRGDQLAEMECFDTGLPIKQARGQAA
+RAAENFRFFADLIVAQHDDTFKVPGRQINYVNRKPIGVAGLITPWNTPFMLESWKLAPAI
+ATGNSVVLKPAEFTPLSASLWGGIFEEAGLPKGVFNMVHGFGEEGYAGDPLVKHPDVPLI
+SFTGESRTGQIIFANAAPHLKGLSMELGGKSPAVVFEDADLDAAIDATIFGVFSLNGERC
+TAGSRILVQRSVYDEFVERYAAQASRVKVGLPDDETTEVGAIVHPEHFEKVMSYVEIGKT
+EARLVAGGGRPEGFPEGNFVQPTVFADVAPDARIFQEEIFGPVVAITPFDTEEEALELAN
+NTKYGLAAYIWTNDLKRAHNVAQNVEAGMVWLNSNNVRDLRTPFGGVKASGLGHEGGYRS
+IDFYTDQQAVHINLGEVHNPVFGKQEQAAAKIDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001600.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001600.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb842d85bb1d016fe345d5fdd0891dc3232f35f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001600.fa
@@ -0,0 +1,20 @@
+>0_1946
+MPPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRAALGG
+LVSAATDVRSAIQTGWRGEAAGAYGEAVRRAAALAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>1_1667
+MSPLIGPQQIATALRAVGLDDDAARLAAWADPARREREAAEQALADLAAAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RNAEARQRAAEETALAVLRSLAVAA
+>2_816
+MLQLIGPQHLAAALQAAGLDDDAARLLAWADPARRDRDAAQAALDELAVAQESLRGALAG
+LVAAARDVRAGAAVAWRGPAAGEYADAVAEAVGAAEGLEREAGEWLALRATAEREAEDAR
+QDAEARLRAAEETARAALRALAVAA
+>3_754
+MLLPPTAQALLRTLVAAGLDDDAARLAVGLTDAHADLQAARAAQDALADAAEDLRDLLAL
+LEELTRGVAAALDVDWRSEAGAEYGERTDGLHRTATDRQDEAREWAGLLGRARSEAEQAE
+RDAELRVRRAEEGASALLRAMAAA
+>4_1885
+MSPLIGPQQIATALRAVGLDDDAARLVAWADPARREREAAEQALADLAVAQTQLRTALGG
+LVSAATDVRSAMHTAWRGEAAGAYGEAVRRAATLAAELEREAGEWLALRATAERDAEDAR
+RDAEARQRAAEETALAVLRSLAVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001618.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001618.fa
new file mode 100644
index 0000000000000000000000000000000000000000..abbd52cf0d5b7fc139f394dcef01141a1e160824
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001618.fa
@@ -0,0 +1,19 @@
+>0_1967
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>1_1687
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
+>2_773
+MTLTEDHHNGFGMAHGGAVFAFADSCFALTCNDPGGDGSTITVASGVDVNFLAGTRAGQT
+LVAEGRLVAAAGRSAVYDITVTTDDGTPVAAFRGRSRTIPAPGR
+>3_734
+MTETPHHPALVGDRVARWLGVTLEAAEKDHARIRMTLGEEHHNAFGMAHGGVVFAFADCC
+FALTCNDPASDGSTLTVASGVDVNFLSGTRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TLVAAFRGRSRTVAVKGA
+>4_1905
+MTETAHHPMLAEDRVARWLGVTLEAAEKDHARIRMTLTEDQHNGFGLAHGGAVFAFADTC
+FALTCNDPASDGSTLTVASGVDVNFLAATRAGQTLVAEGRLVAAAGRSAVYDITVTTDDG
+TPVAAFRGRSRTIPAPGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001622.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001622.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5edb505daa8e6d8625efbaa0ebdf6cf5e31da589
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001622.fa
@@ -0,0 +1,36 @@
+>0_1975
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLARLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDADGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDEKG
+>1_1693
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD
+>2_762
+MDVQQFFADLSDVPWLLTTLDLIGIFFFATSGALLASRKEFDLVGSMALALLAGLGGGFT
+RDILLDRGLPASLENPIYLAPPVLVSLLVYVKALHPNRLNLTITLFDAGGLALFTVSGVL
+IAHSMDVHPVSTVVVAMVAALGGGVLRDIVANEVPSIFDPRGVYVMPTFVGATVATIAAM
+NGVLNAFTGFLIAFLIFAVRMLAYRYQWRLFGADISQDKESLDRLRRLATQAQDAAARRV
+ERARERRLRSASGPGGMDVGEAEAIADRAVHHPPAPAGYHYDAVEDAYTRDHAFDDDGEP
+GSASYGPRQEYEDQVRVDEYDPETQTITVIDPASRQQVRLDPATGVMDVTDLRTGRTRSY
+DDPEHDWIADDAEDDARG
+>3_729
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPVLVSLLVYVKLIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNAFTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRAPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPEDSRD
+>4_1911
+MDVQQFFATLTDVPWLLTTLDLIGIFFFATSGALLAARKQFDLVGSMALSLLAGLGGGFT
+RDILLDRGLPASLENPVYLAPPLLVSLLVYVKVIHPNRLNLTITLFDAAGLALFTVSGVL
+LAHSMGVHPVSTVVIAMVTALGGGVLRDIVANEVPSIFDPRGVYVLPTFLGAVLATVVAM
+NGALNGYTGFLIAFLIFAVRMIAYRYQWRFFGAEISQDKESLERLRRLATQAQEAAARRV
+ERTLERRLRSPGAPAFPDDDTHGSYGPRQEYEDQVRVDDYDPQTQTITVVDPASHQQVRL
+DRGTGVMDVTDLRTGRTRSFDDPEHDWIADDPADPRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fa9d3e99a2d27525a7cf2d058b4732dd4d9fe30b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001624.fa
@@ -0,0 +1,50 @@
+>0_1984
+MTTSETTSETTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRE
+LDQVTAATAGWLRHRGVGPGDRVAVMLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELG
+YFLEDSGARMLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPD
+DDAVLLYTSGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVV
+LNGAVFAGSTLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGAEPAD
+FSRLRMPLSGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRP
+VDGFEFRIVAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDI
+ARRDEAGYVMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAA
+FVSLAPGSTATGEELQAFAAERLARYKQPREVTIMDGLPKNATGKILRRELRQG
+>1_1701
+MTTSETPDTSATTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RVLWAMPGLPAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITLRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGVTFLPGVPTMHGAFLSVARARREAGAEPEDFSRLRMPL
+SGGASLPVETLRAAEKLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTAAAFDQDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEQLQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRQG
+>3_717
+MTTSETPDTSTTTHGRPTERRGHVAELLSATVARQPDAVALRIGEARMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAVLLPNVPAFVAVYEALMRLGAVMVPLNPLFTARELGYFLADSGA
+RMLWAMPGLQAVDEVAGNVDVEVVTLDLEAVGRECAAEGIAPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFSG
+STLSLMPRFEPEAAYDQLQDHGVTFLPGVPTMHGAFLTVARARREAGAEPADFSRLRMPL
+SGGASLPVDTLHAAEKLYGVPVFEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGHPEDTVAAFDADGWFRTGDIARRDEAGY
+VLIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+TVTGEELQAFAAERLARYKQPREVTVLDGLPKNATGKILRRELRG
+>3_723
+MNSALPATDPHRGDVCALLEAGHDRDPRAVAWREDGVDTTYAELLELVQATAGVLRRQGV
+GPGDRVALLMPNTLAFPAVYYGALWLGAVVVPLNPLSTDRELEYFLTDSQAVLLWSMRGT
+SAAAEAAQAVGVPHLQSSPADLRDVVAGAEPVRERTPRTSEEADAVVIYTSGTTGQSKGA
+RLSHRTVASSAVLTSEALDWLQAGHTVLGVLPFFHVFGMSAALNMPLYTGCRNSVVTRFA
+PHTALEQVVRDEVRALPAVPTMIGALLRALRSARAKGDDVDLSALRYILSGGAPLPVETL
+HEAEEEFGVPVREGYGLTESCGPVSFNPMLRPSRAGTVGQPLPGVEFRLVTTDGVEVPAG
+DTETPGELRIHGPVLMTGYLGEPQADAASFDDEGWLRTGDVATRDEEDYYRIVGRLKDII
+IHGGYNVYPREVEEAFYEHPAVSEAAVLGVPDERFGEKVVAYVALQDGPEVEVAELNAFV
+RERLASYKWPSQVTVMDALPKNTTGKIVKDLLR
+>4_1919
+MTNSETPDTSATTVGRPTERRGHVAELLSATVARQPDAVALRIGEASMTYRELDQVTAAT
+AGWLRHRGVGPGDRVAMMLPNIPAFVAVYEALMRLGAVMVPLNPLFTARELEYFLEDSGA
+RMLWAMPGLPAVDGVAGNVDVEVVTLDLEAVGRECDAEGITPVTEITPRDPDDDAVLLYT
+SGTTGRPKGARLTHTNLRSNAMATATGLGRLGPDDVVFAALPMFHVFGLSVVLNGAVFAG
+STLSLMPRFVPEAAYDQLQDHGITFLPGVPTMHGAFLSVARARREAGTEPADFSRLRMPL
+SGGASLPVETLRAAETLFGVPVLEGYGLSENAGACFFNPVDAPTRPGTVGRPVDGFEFRI
+VAMDGTEVPEEDLETSGELRIRGEGIMAGYWGRPEDTEAAFDEDGWFRTGDIARRDEAGY
+VMIVDRLKDVIIRGGMNVYPREVEEVLYEHPDVVEAAVVGVPDERLGEEIAAFVSLAPGS
+AVTGEELQAFAAERLARYKQPREVTILDGLPKNATGKILRRELRQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001629.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001629.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ee236f639157bf6a4750c48e68af1b531d08b20
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001629.fa
@@ -0,0 +1,29 @@
+>0_1996
+MSPDRSVTLTGVRVEADGPEGAVVLLDGVDLTLAAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWIHSGRVERTGPAEEVVEAY
+ERFLDHAVAAELR
+>1_1713
+MSPDRSVTLTGVRVEADGPEGVVVLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLAD
+VVAGEVTVHGVDAVRDVKALRRTVGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLT
+KDDVAARVAAALQEHRLTALADRACLSLSSGQAQRLAMCSVMTTGPSLVIADEPTSLLDG
+RHRRIVADRLLAADPSAPDGFQLLLVTHDLELARACDEAVWVHGGRVERTGPAEDVVEAY
+EHFLDHAVAAELR
+>2_745
+MEQTTGVRLRGARVEADGPEGVVALLQDVDLDLTAPRVAVVGENGSGKSTLARAVAGLVD
+VVAGEVTVHGVDAVRDVKALRRVVGMVFANPAAQAVMPTVREDVELTVKSLRDDDGRRLS
+KDDVAARVAAALAEHRLTELAERPCLALSSGQAQRLAMCSVMAGRPRLVIADEPTSLLDG
+RHRRIIADRLLAADGFQLLLVTHDLELARACDDAVWVHEGRVRAVGPAGEVVDAYAAFLD
+EAVAAESAEAAAGDPAAVNPAGASAEARP
+>3_709
+MTGRTPPTRAPHDDDAAVRLAGVQVAAPGGPVLLDGVDLHLTAPRVAVVGENGSGKSTLA
+RAVAGLAEVTAGEVAVHGVDAVRDVKALRRTVGMVFANPAAQMVMPTVREDVELTVKALT
+DDAGRRLSRAEVAARVDAALAEHRLTDLAERPCLSLSSGQAQRLAMCSVLVGAPRLVIAD
+EPTSLLDGRHRRIVADRLLGGAERGEFQLLLVTHDLDLARACDAAVWVHSGRVERHGPAA
+ETVAAYEAFLDDAVARELA
+>4_1931
+MLLDGVDLTLTAPRVAVIGENGSGKSTLARAIAGLADVVAGEVSVHGVDAVRDVKALRRT
+VGFVFANPAAQMVMPTVREDVELTVKSLRDDAGRRLAKDDVAARVAAALEEHRLTALADR
+ACLSLSSGQAQRLAMCSVMTAGPSLVIADEPTSLLDGRHRRIVADRLLAADPSAPDGFQL
+LLVTHDLELARACDEAVWIHGGHVERTGPAEDVVEAYERFLDHAVAAELR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..02a60a652ee7db4c5f48187a80ae5016e5a67f9e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001630.fa
@@ -0,0 +1,25 @@
+>0_1997
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLDAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLIKLVVSVILIVGLWKAYPRAFR
+>1_1714
+MSTSVPSSHDGHVRPAATTTADRPTDAGRPRRGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFAGLVALGLPLLSGGRGGLGVFAGPTAG
+FILGWIPSALIVGLIFWALTSRARPGLGAGRVALGAAVAGLIGGVVMVYFFGVLGFVGIA
+GMEFGAAVLSMAPFVPGDLLKLVVSVILVVGLWKAYPRAFR
+>2_742
+MPTSDTLASGRPAHSTDDRRPRRSSAGSGLARVAVFAALMAVLGLVPPVPVAGIPAPIVL
+QNLAVTLAGVILGPWRGAAAILLFNVLVALGLPLLTGGRGGLGVFVGPSSGFILGYVVAA
+AAVGLVFWALTGRARPGLRPGRVLAAALVAGLVGMVVLYAAGAVGFIVAAHMEPGAAVLA
+MGAFVPGDTVKVVLAALLVTGLWKAYPRAFR
+>3_705
+MTSPSAPQTAVVDAPATHRPRRSPGADLARIAVMAALIAVLGAMPGIPVPGIPTPITLQT
+LGVMLAGLVLGAWRGAASVALFHLLVALGLPLLAGGRGGAAVFVGPSAGFLWGWIPGAFV
+VGLLFHLYLRGRRDGRNTGGLVAAALTACVVGGIAVIYLFGIPGMNLFGGVPLDKAAIGS
+LAFIPGDLLKAVVAALLAAGLWKAYPRAFA
+>4_1934
+MSTSVPSSHDGHVRPAATTTADRPADAGRPRHGSAGGSLARIAVMTALMAVLGLVPPIAV
+AGVPAPIVLQNIAVILAGVILGPWRGAASMALFNALVALGLPLLTGGRGGLGVFVGPSVG
+FILGWIPSAMIVGLIFWALTSRSRPGLSAGRIALAAAVAGLIGGVIMVYVFGAFGFVGVQ
+GMEFGAAMLSMAVFVPGDLTKLVIAVLLCAGLWKAYPRAFR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001631.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001631.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e9ce4edb7e94f4a5163dea1bb3652dd9165d59c9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001631.fa
@@ -0,0 +1,42 @@
+>0_2010
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLMGRFIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPGDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR
+>2_541
+MPSRAVAPSPATGPAARPAERPVLQEMSFLDRWLPVWILAAMAAGLLLGRLVPGLAEALD
+AFTVAGVSVPIALGLLVMMYPVLAKVRYDETHRIAADRRLMGTSLVLNWIVGPALMFALA
+WLFLADLPEYRTGLIIVGLARCIAMVLIWNDLACGDREAAVVLVAVNSVFQVVAFGALGW
+FYMQVLTGWLGLPTTTAGFSVGAIVLSVLVFLGVPLLAGFLTRVLGERARGRAWYEGRFL
+PRIGPWALYGLLFTIVLLFALQGEAITTSPGDVARIALPLLVYFTVMFLLGLVASRAVGL
+DYARSTTVAFTASGNNFELAIAVAIATFGVHSGQALAGVVGPLIEVPVLVGLVYVARWLA
+PRLFPGDPTVPPPRPRPHRQEHPVTEHAPTDRRPSVLFVCVHNAGRSQMAAGWLEHLSGG
+RVEVRSAGSAPKDRINPSAVAVMAEAGIDLSANTPKVLTTEAVRESDVVITMGCGDTCPV
+FPGKRYEDWAVEDPAGQGVNAVRPIRDEIRGRVEALLADLLPEG
+>2_724
+MSVSTTAPAPHQPVLKEMSFLDRWLPAWILLAMAAGLLLGRFVPGLNTALEAVKIGEVSL
+PIAIGLLVMMYPVLAKVRYDEAHRVAGDKWLMITSLVLNWIVGPALMFALAWMLLPDLPE
+YRTGLIIVGLARCIAMVFIWNDLACGDREAAAVLVAINSVFQVVAFGALGWFYLQVLPSW
+LGLPTTSADFSVWAIVLSVLVFLGVPLLAGFLTRLLGERAKGRTWYEERFLPRIGPWALY
+GLLFTIVLLFALQGEAITSNPWDVARIALPLLAYFVLMFGIALLASKAVGLNYAKSTTVA
+FTAAGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVGLVYVSLWAGRKLFPGDPT
+VPARPQAAAAHRA
+>3_470
+MSSTPRTTAEAAPVAARLSSLDRLLPVWIGAAMLVGLLLGRLVPGLGGVLAAVEVDGVSL
+PIALGLLVMMYPVLAKVRYDRLDSVTGDRRLLVASLVLNWVFGPLLMFALAWIFLADLPE
+YRTGLIIVGLARCIAMVIIWNDLACGDREAAAVLVALNSIFQVIAFAALGWFYLSVLPGW
+LGLPQTGLDVSPWDIARSVLIFLGIPLLAGFLSRVIGERRWGRAAYEGSFLPTIGPWALY
+GLLFTIVVLFALQGEQIAARPWDVARIALPLLVYFAVMWGLGYTVGRRLGLGYERTTTLA
+FTAAGNNFELAIAVAIATFGATSGQALAGVVGPLIEVPVLVGLVYVSLWLRRRFPPAADA
+GTPASAMTVPATTAQENR
+>4_1939
+MSTTTKDVEQPRVMKEMSFLDRWLPVWILAAMAVGLLLGRLIPGLNTALEAVKIGSVSLP
+IAIGLLVMMYPVLAKVRYDETRRIGADRRLLVTSLVLNWIVGPALMFALAWIFLADLPEY
+RTGLIIVGLARCIAMVLIWNDLACGDREAAAVLVAINSVFQVIAFGALGWFYLQALPSWL
+GLPTTSAEFSIGAIVLSVLIFLGIPLVAGFLTRILGERAKGRTWYEERFLPKIGPWALYG
+LLFTIVLLFALQGDAIISAPVDVARIALPLLVYFVVMFLGSFLLGRAIGLDYAKSTTVAF
+TASGNNFELAIAVAIGTFGVTSGQALAGVVGPLIEVPVLVALVYVALAMGRRLFPGDTTA
+PTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6d5d2fa3e22491a69dff4f6be15ee4e9c39a8c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001633.fa
@@ -0,0 +1,25 @@
+>0_2020
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>1_1735
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>2_685
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALHPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPTAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
+>3_596
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVIATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASILWFTALGYGARLLARVLADPKAWRV
+VDLVIAVVMAVLAVRLIAGSGVWG
+>4_1959
+MWTLAGTGLLTGLALIVAIGAQNAFVLRQGVRREHVGAVVLVCMASDAVLILAGTAGVGA
+LVQAVPWLLEVLRWGGALYLLWFAVSSLRAALRPQGLVAEQAPRTAGSVVATTLALTWLN
+PHVYLDTVVLLGSLANQHGPDARWVFAAGAVAASVLWFTALGYGARLLARVLADPKAWRV
+VDVVIAVVMAVLAVRLIAGSGVWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001642.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001642.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aaeb61196f5fa3160ee81da7ee64ae9c99a13d29
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001642.fa
@@ -0,0 +1,43 @@
+>0_2034
+MSPSAPQRRAARAATFAATLAAAAIALTACGADAAPFSPASAPASASDGAESPAGEATAA
+SSVSEEDRVDPTQTTEVSAVTPRILLSHEDGLTLLDAESGEVVKEQDVTGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFA
+DGTGAIRTFDSTHLDKATPDLMPVMTEAETEDPHHGVALELSDGALFTTQGTEDSRDALQ
+VIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEANVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGQPESVKPDEAADAASGHDEHTDHDH
+>1_1753
+MSHSAPQRRSARTAALSATLAAAAIALTACGADAAPSGPTSAPAPAADGAESPSGEARAA
+SSVSEGDRVDPTRTTEVSAVTPRILLSHEGGLTLLDAESGEVVREQDVPGFTRLSNAGNG
+KDVLVTTGNGWEVFSTGIQAKAHGDHVHHYESAPGMTGVTFPGEHPGHVVTHNGRTTLFG
+DGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQ
+VIDPKTSEVTAETDDCPGSHGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQ
+RSGNLFGLHDSPIVLGDHKVEEEPEEAVERPTAIALIDTRTDELTTVDLGSSYWFRSLGR
+AEDGSAVVLTYDGEVTVIDEETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAYVTDA
+EAQKLVAVDLETGETVLEKDLEFAPVEMAVVTGEPESVKPEEGADAESGHDEHADHDHGH
+ESDEHTDHDH
+>2_665
+MSHSAPQCRSTRTAASDGAESTSGETTAASSVSEEERVDPTRTTEVSAVTPRILLSHEDG
+LTLLDAESGEVVKEQDVPGFTRLSDAGNGKDVLVTTGNGWEVFSTGIQAKAHGDHVHNDE
+SAPGMTGVTFPGEDPGHVVTHNGRTTLFADGTGAIRTFDATHLDKATPDLMPVMTEAETE
+DPHHGVALELYDGTLFTTQGTEDSRDTLQVIDSTTGEVTAETDDCPGSHGEAAAQPTEAG
+DVVVTGCENGPVVYRDGEFHKVEVETEYQRSGNLFGLHDSPIVLGDHKVEEEPTEAVERP
+TAIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYAV
+IEPWKEKDEWQEPGPILKVAGNTAYVTDAEAQKLVVVDLETGETVLEKDLDFAPVEMAVV
+TGQPESVKPEEAADAESGHDEHTDHDH
+>3_581
+MTPRILLSHEDGLTLLDAESGEVVKEQDVAGFTRLSNAGNGKDVLVTTGNGWEVFSTGIQ
+AKAHGDHFHNYESAPGMTGVTFPGEHPGHVVTHNGRTTLFADGTGAIRTFDSAHLDKATP
+DLMPVMTEAETEDPHHGVALELSDGTLFTTQGTEDSRNTLQVIDPTAGEVKAETDDCPGS
+HGEAAAQPTEAGDVVVMGCENGPVVYRDGEFHKVDVETEYQRSGNLFGLHDSPIVLGDYK
+VEEEPKEAVERPTEIALIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVID
+EETGEVTAEYPVIEPWKEKDEWQEPGPILKVAGNTAHVTDAEAQKLVAVDLETGETVLEK
+DLEFAPVEMAVVTGQRESVKPEEAADAESGHDEHTDHDH
+>4_1974
+MTGVTFPGEHPGHVVTHNGKTTLFADGTGAIRTFDSAHLDKATPDLMPVMTEAETEDPHH
+GVALELSDGALFTTQGTEDSRNTLQVIDPKTGEVTAETDDCPGSHGEAAAQPTEAGDVVV
+MGCENGPVVYRDGEFHKVDVETEYQRSGKLFGLHDSPIVLGDHKVEEEPKEAVERPTEIA
+LIDTRTDELTTVDLGSSYWFRSLGRAEDGSAVVLTYDGEVNVIDEETGEVTAEYPVIEPW
+KEKDEWQEPGPILKVAGNTAYVTDAEAHKLVAVDLETGETVLEKDLEFAPVEMAVVTGQP
+ESVKPEEGAHGDEDHDDDGHEGHDHGAEPSEGHEGHDH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..66566f925fd03709a1294d1cbc8d5ad85f717837
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001643.fa
@@ -0,0 +1,54 @@
+>0_2038
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>1_1756
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQSFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
+>2_662
+MGGRLIPELLAAGFDVRAGARNPSDLADRPWSEGVEAVELDLTEADLVEAAMQDVHTVLY
+LVHSMGGGGDFVTQEQRIADIVGTAADTAGVAQLVYLSGLHPDTIPVAELSDHMRSRALV
+AERLEQAATPALTFEAGVIIGSGSTSFEMIRHLAERLPVMPGPSWLKNRVEPLAIRDVLY
+YLLQACALPEPVQLRAQIGNGHPQSFASVLVDYAKAAGLSRRIVIPTPFPLQTLAGFWIG
+TVTPIPVAVALPLAASLAEEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDV
+TFDADVHAAADPADPLPSDPAWSGTTVYTDERERESDLPPQDVWPVIESVGGANGWYSTP
+MLWKVRGLADKLVGGPGLIRGRRDQDRLRRGDAVDWWRVEDVEHGRRLTLRAEMKAGGRA
+WLQMSTEPRDGGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAQRRTT
+GGERRRPRSLARALVDRLPLRRNPLDRGASA
+>3_577
+MSTPSTSRGSGLTSAAASGDTPAGTGATTASLSPLGLALPDGHDRRVLVTGATGYVGGRL
+IPELLAAGFRVRAGARTPRDLEDRPWSDRVEVVELDLEKPDLVKAAMQDVHTALYLVHSM
+GAGGDFVEQEQKIADIVATAADEAGITQLVYLSGLHPAGKPVEELSDHMRSRALVAERLE
+AAATPALTFEAGVVIGSGSASFEMIRHLSERLPIMPGPSLLKNRVEPIAVRDVLHYLVQA
+CALEEPVQLHAQIGNGRPQSFASVLVDYAEVAGLSKRIVIPTPLPLSRLAGLWVGVVTPI
+PVKVALPLAASLAEDAVVEDHAIRDVIPAPEGGLTSYKEAVRRALAAEKNGPLDVTFEAD
+VYDSSDPAAPLPSDPEWAGHTVYTDDRERESDLAPEDVWPVIESIGGRNGWYSTPLLWKV
+RGYMDKVVGGPGLMRGRRDQDHLRRGDAVDWWRVEEVDPGHRLTLRAEMKAGGRAWLQLT
+TEPREQGGSVYRQRAIFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEAERRRTGGARR
+RTRGLVRALADRLPLRRSPLDRRAG
+>4_1979
+MASTQPSPVPAGATPASHTSPLGLSLPDGRGRRVLVTGATGYVGGRLIPELLAAGFDVRA
+GARNPSDLADRPWSDSIEAVELDLTEADLVEAAMQDVHTVLYLVHSMGGGGDFVAQEQRI
+ADIVGTAADTAGVAQLVYLSGLHPDTVPVAELSDHMRSRALVAERLERAATPALTFEAGV
+IIGSGSTSFEMIRHLAERLPVMPGPSWLRNRVEPLAIRDVLYYLLQACALPEPVQLRAQI
+GNGHPQPFASVLVDYAKAAGLSRRIVIPTPLPLKTLAGFWIGMVTPIPVAVALPLAASLA
+EEAVVEDRSVRDLIPDPPGGLTSYMDAVRLALKREKEGPLDVTFDADLQSSADPAASLPS
+DPEWAGTTVYTDERERESDLPAQEVWPVIESVGGANGWYSTPLLWKIRGLMDKLAGGPGL
+TRGRRDPNHLRRGDAVDWWRVEDVEPGRRLTLRAEMKAGGRAWLQLSTEPREGGGSVYRQ
+RAVFMPDGLLGRAYWTAILPFHAVVFPEMAANILAEARRRHDGGERPRTRGLLRPLVDRL
+PLRRNPLDRRARGAGGAQSRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001653.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001653.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb579021b2ac08997b3f57fd1c2ee0706533dcfa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001653.fa
@@ -0,0 +1,20 @@
+>0_2053
+MGTQDPRARLLEKLAKVNVCMLTTAEPDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVQTAQFWESPGAVATAVELVKAKVTGGEAHPGDSETVRF
+>1_1772
+MGTQDPRTHLLEKLAKVHVCMLTTAEADGTLVTRPMGLQQAEDGGTLWFMTRSTSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNSATEAFFGEGSSPEDPQIVLVRV
+DVNTAQFWESPGAVATAVEMVKAKVTGGTAEPGDSETVRF
+>2_648
+MGHKDPRTHLLEKLEKSNVCMLTTSETDGTLTTRPMGLQKAEETGTLWFMTRAASDVASD
+ASQRPVNVSVQDKDFWASVAGHGQVVRDDARKKEFWNPATEAFFGEGAKPEDPQIVLVRV
+DVESAQYWESPGAVGTVVELIKAKVTGGEAHPGESTTVQF
+>3_565
+MTEQDPRTALLEKIEKAGVVMLTTAEEDGTLASRPMAVQEVEQEPGVLWFITRATGDAAQ
+DSAGRPVNVAVQEKGFWASVAGHGEIVRDEARKTEYWNSATEAFFGEGARPEDPQIVLVR
+VQADSAEYWDGGGAASVVEIVKAKVTGGEARPGDHDTVEF
+>4_1992
+MGTQDPRARLLEKLAKVNVCMLTTAEQDGTLVTRPMGLQQAEDGGTLWFLTRATSDVAAD
+APQRPVNVAVQDKDFWASLAGHGQLVRDDARKKEFWNPATEAFFGEGSSPEDPQIVLVRV
+DVDTAQFWESPGAVATAVELVKAKVTGGTAEPGDSETVRF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001655.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001655.fa
new file mode 100644
index 0000000000000000000000000000000000000000..444a9f6ba9b937410f1491fbffdbcbaa6419db70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001655.fa
@@ -0,0 +1,15 @@
+>0_2056
+MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI
+TTFLPALAEREATRRLQAATPAHEAMAVAA
+>1_1775
+MSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREVVADLKRGARI
+TTFLPALAEREATRRLQATTPAHEAMAVAA
+>2_645
+MSINTVHHLPAAPSPLMQRHVLKRVEETLARRFEGVATAEAVRATVREVASELKRSARMT
+MFLPALTEREAARRLQAGAPAHEPLAAAA
+>3_563
+MTATLTTQHHMPVHPDTTMQQRVLERIAGTLIRRFDGSVPAADVRTTVAEVTAELEAEAR
+LTTYLPALTEREALNRLEAMAAAPAHMTITHARHAA
+>4_1995
+MVRQPKEVLTVSINTTSHHLPTAPSPLMQRHVLQRVEETLLRRFEGTVTAETVRSVVREV
+VADLKRGARITTFLPALAEREATRRLQAATPAHEAMAVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001662.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001662.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3b713d1e8cf94249d35239ee60905661163c7751
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001662.fa
@@ -0,0 +1,20 @@
+>0_2065
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLAAWFTGHSTSPRVHA
+>1_1784
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>2_636
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHG
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>3_553
+MTDTPQSSSGQSRDEILARLEEIYANDPAVREHDVTLGEVAEGRVVLHRDVTAGMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPAKLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRVHA
+>4_2004
+MTETPQSSSGQSRDEILARLEEIYANDPAVREHGVTLGEVAEGRVVLHRDVTADMVNSHE
+ICHGGFLFHLADSALAYCVATFGAAPVTRRAEITYVAPARLGAHLVATARQSVEFGRDRM
+IEVGIEADGQLVAWFTGHSTSPRARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001666.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001666.fa
new file mode 100644
index 0000000000000000000000000000000000000000..92ed96ef7a6e9ffa1d7231349b9664fcb2582c53
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001666.fa
@@ -0,0 +1,48 @@
+>0_2069
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSSTAPTGADQGLRAALQGLRREVRESWLR
+SLGALTPAGSALDAGASAAAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLLSTVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAGAPHRHDEAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAVGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVAT
+LERIERDLA
+>1_1788
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSTSPGVASIRAELGEALREA
+VAQDADVDQLWAYLGRPEARDDVELWGAALRLLPTDSPRRALAVATLERIERDLA
+>2_632
+MSSTLATGAYRRAVDRAHESLDSVRLSLAPSSPTAPTGADQGLRTALQGLRREVRESWLR
+SLGALTPAGSALDAEAAATAPAVPGQTDPATLADDDLAAARREQRLAVALPVVRRMLIHP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVH
+AAWRDLPAPSRGRPRGTVPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETAGPRSAPSDAPARAISLRAEVHRL
+RRALQDAGAPVELLSRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSVSPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGVALRLLPADSPRRALAVAT
+LERIERDLA
+>3_549
+MSSTLATGAYRRAVDRAHESLAAVRLSLAPSSPTAPTGADQGLRAALQGLRREVRESWLR
+SLGVLTPAGSALDAGASATAPAVPGQTDPATLSDDDLAAARREQRLAVALPVVRRMLIQP
+AAEAGMLAAIGNARGHLLWVEGDRTAVRHAEALGFVAGADWSEASMGTSAPGIVLATGAP
+TQVSRGEHLSPRVHPWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQTTVDAVH
+AAWRDLPAPSRGRSRGTVPTPGPSAPPSVSPGPSPAAAPHRHDAAAGLLRVTGHLPPTLD
+GVELTGRHAEILTLLAWHGPGLTGAELEVALYPEETVGPRSAPGDAPARAISLRAEVHRL
+RRALRDVGARVELLSRPYRLVGAVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGV
+ASIRAELGEALREAVAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVAT
+LERIERDLT
+>4_2008
+MSSTLATSAYRRAVDRAHESLAAVRLSLAPSSPTAPAGADQGLRAALQGLRREVRESWLR
+SLGALTPAVPGQTDPATLSDDDLAAARRDQRLAVALPVVRRMLIHPAAEAGMLAAIGNAR
+GHLLWVEGDRTAVRHAETMGFVAGADWSEASMGTSAPGIVLATGAPTQVSRGEHLSPRVH
+PWSCSAVPLTDPATGRLVGVLDLTGGEDAVSHLALPLLQATVDAVHAAWRDLPAPSRGRP
+RGTAPTPGPSAPPSASPGPSPAAAPHRHDAAAGLLRVTGHLPPTLDGVELTGRHAEILTL
+LAWHGPGLTGAELEVALYPEETAGPRPAPGDSPARAISLRAEVHRLRRALRDVGAPVALL
+SRPYRLVGEVHADLLCAREALRAGDLDRALHAAAGPVLPRSASPGVASIRAELGEALREA
+VAQDADVEQLWAYLGRPEARDDVELWGAALRLLPADSPRRALAVATLERIERDLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001673.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001673.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95fd23fb897bd6d1e4ba715cb3e5688a3ac42140
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001673.fa
@@ -0,0 +1,45 @@
+>0_2077
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNLAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTAWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVV
+>1_1796
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
+>2_616
+MAEPQGSTAAPAPQDGRALTRRILALAVPAFGALLAEPLFLLADTAIVGRLGTPELAGVG
+IGTTVLHTATGLMIFLAYATTPAVARLIGAGDHAAAMDRGRDGVWLGLLLGAALAVLGWI
+AAPWLTGALGATGEVQEHAVAYLRWSMPGIPALLAVLAATGVLRGLQDTVTPLVVAGAGF
+AVNIGLNFALVYGAGLGVAGSAIGTSAVQWGMLLTYLAVLAPRFRRAGTSLAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDMTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGASRPATARRLTDVMVRWGLGFGVVTGGLLALAAPWLPALFTTDPQVQAAATVG
+LWVLAAGQPIAGYVFVLDGVLIGAGDARYLALAGLVNLAVYAPVLWVLAQVAAGGLGWTV
+DWSDPAAHVPDAGEQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRVGAH
+>3_541
+MPSRPPHDDAAPAPEDRRALARQVLGLAVPAFGALIAEPLFLLADTAIVGHLGTAQLAGV
+GVGTTVLHTVTGLLVFLAYATTPAVARMVGAGNPAGALDRGRDGMWLGLMLGFVLGAAGW
+LAAPWLTGALGAAGEVHSHATEYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGGG
+FAVNIGLNWALVYGAGLGVAGSAIGTAAVQWAMLAVYLAVLAPRFRAAGTRPGPRADGLR
+ATAQVGSWLMLRTASLRAAILITVAAATGLGDVTLAAHQLVFTLYSTLAFALDALAIAAQ
+ALIGAELGASRPRTARRLTDLMVRWGLGFGVVTGAGLAAAAWALPPLFTPDPGVHAAATA
+GLLVLALSQPVAGYVFVLDGVLIGAGDARYLALAGVVNLAVYAPVLWGLARLAAGGADAG
+AQVALLWLGFAGVYLGMRAATLGLRARRDAWMRLG
+>4_2016
+MAGPSGSTAAPAPQDARALTRRILALAVPAFGALIAEPLFLLADTAIIGHLGTAQLAGVG
+IGTTILHTLTGLMIFLAYATTPAVARLIGAGNPAAAMDRGRDGIWLGLLLGAVLAVLGWL
+AAPALTAALGATGEVQAHAVAYLRWSMPGLPALLAVLAATGVLRGLQDTVTPLVVAGVGF
+GANIGLNVALVYGLGWGVAGSAVGTSVVQWAMLVTYLFVLAPRFRRSGTVWAPRASGMRA
+TAQVGSWLLLRTASLRAAILITVMAAAGAGDLTLAAHQLVFTLFSTLAFALDALAIAAQA
+LIGAELGAARPDAARRLTRTMVRWGLGFGVVTGAVLALAAPVLPGLFTTDPTVQAAATVG
+LWVLAAGQPVAGYVFVLDGVLIGAGDARYLALAGLVNLVVYAPALWVLAQLATGGFGWTA
+AWPGPNAAVPDAGVQLGLLWLGFAGVYMGMRALTLGWRARRDDWMRLGVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001674.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001674.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0e00fbe2242857f673a2f997db05d780a4142eff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001674.fa
@@ -0,0 +1,34 @@
+>0_2078
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>1_1797
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
+>2_615
+MPAGWPGRTPGPRTAPDWEPGRFHWGDAVVVLAYAGLMLFGLGLPLAMLLGLVPGDLAAF
+DLVRDGFTVNMVSYAILTALVLIVAWRPLVTSLRVFRTGTWWKILLLPAVWFTCILVNVL
+VLSLIGEAQTSANQAALEEMSAQAPPVLMILMTVVGAPLVEEYLFRHLLVGKLSRWVNVW
+VCAVVSMLAFTLLHFLGTGGQFDLVETVPYLTLAIAITVTYILMGRSFGYAVLLHMVNNG
+IAIAMLYLVAPLLPDVLPEPTAPAAALSPLLALLG
+>3_540
+MSVPPPGPHDAGALPPPGSTAPTSAAGEAPEGWPPAGWPGRASAGGAPQGWPPSGWPGRT
+ASARTAPSWEPGRLHWGDAAVVVLYVLMMVVGLGYLLAVLLGLAPRDPAAMDVMDGFRVN
+LVSYAVLVVAVLAVSWRPLVASLRVFATHTWLKILLLPALWLVTVLVNALLLSLIGQAQT
+SANQAALEEMTTQAPALGMVLMTVVGAPIVEEYLFRHLLVGKLSRWINVWVCAAISVAAF
+TLLHFLGTGGDFQWVETVPYLTLAVTITVTYVLIGRSFGYAVLLHMVNNGIAIAMLYLVA
+PLLPSAPAPVGPGALLSPLLALLG
+>4_2017
+MSVPPSGPPAGPPAGWPPSGRPSARRAAVAPSLHGHPGAPGGVPAGWPGRRPAARPAPDW
+TPGRFHWGDAVVVLVYVALMVLGLGLWLAVSLGLVPGDLEAFDLVRDGFTVNIVSYAILV
+VLVLAVAWRPLVTSLRVFRTGTWWKLLLLPATWLACIVVNVIVLSLIGEAQTSANQAALE
+EMTTQAPPVLMILMTVVAAPLVEEYLFRHLLIGKLSRWINVWVCAVVSVLAFTLLHFLGT
+GGDFRLVETVPYLTLAVAITVSYILMGRSFGYAVLLHMVNNGIAIAMLYLVAPLLPDTLP
+GPTAPTTALAPLLALLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001680.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001680.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0f250c1149f2878e153906fc871747a059e364e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001680.fa
@@ -0,0 +1,29 @@
+>0_2085
+MVGLVGALLLAGCASGADAGASAHAETGSTPSKVWDAATWKPTEVIEPVLATEPEKEAAY
+REQMDRLAESGGTPEILQVQRKDWSTTPLESDQKVASCMRADGFPVEVSPTGGLRYSTPP
+AAQARAWALAMNTCIAQHPVDPSYTQDWSEPQLRLVYDYWDQYLIPCLEAQGFTVDTSTR
+PSKESFVTAFFTPGRHDWWPLQATMRGVPEERQTQVVQTCPELPPQDVFWGTSG
+>1_1803
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
+>2_608
+MKTKFAAVTAAAVTAVLTLSGCATTAPSTSAAATGSPTEKVWDPETWTPTEKIERRMTEA
+DERERWYESQLARNAAFLGIRNPPAVTRRGWATSRQEQARWSAQCMTERGVPATYNEVMV
+GVTYDTPPPSQEAAVKLVSWTCDALFPIDPSLDQEFSDAQLRLLYDYWDQYAIPCLEDHG
+ITVDTSQRPSKETWLAAFNTPERISWWPVQDSIMGLTDARSAEVSEACPVQPPDSMLFGY
+SE
+>3_533
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKEAAQREQVERMAREAGTPELLQVRRMDWSSTTLESSQKIGECMAAAGFPV
+EVTPTGGLRYPTPPESQKRAWNLAENTCAVKHPVDPAYAHDWTEPQLRLVYDYWDQYLIP
+CLEAQGLHVDTSSRPSKESFVTSFFTQDRHDWWPFSTTMVGVSEERKAHIAQTCPELPPP
+DVFWGTAP
+>4_2023
+MTSLRIPATAALVAAVALTLTGCVGRESAGLGGSSTVAAPPTATAEKTWDASQWVPTERI
+EPLLTTEAEKERAYREQVARHAQGAGMPAPPQVERSGWYATSLESDRMVSTCLAEAGWPN
+SVGPTGGIQIDTPPESQRSAFEAAYVTCYAQHPVDPSYTQDWTDPQLRLVYDYWDQYLIP
+CLEAYGYTVDTSARPSKEAFVSAFYTPGRHQWWPFADSMRGVSAERQAEVAQTCPELPPQ
+DVFWGSSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001683.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001683.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea2d5b2eac744fcc749d32d52aa6dd9cc73cfddd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001683.fa
@@ -0,0 +1,43 @@
+>0_2088
+MRRPSLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPG
+VFDAHVEGSELRIFTSGEDLYKEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL
+>1_1812
+MAAGVGLVGLPLTVAAGLTGVDMVKRGGRVRRPAPNPGVFDAHVEGSELRIFTSGEDLYK
+EMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAARGVEVYVSYDGFGNLVVPPRFY
+RQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVDDEVGFAGGFNIGDDYARLWRDT
+HVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTWDPRVTVAANQPPLLVYPIRLSY
+LDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDVQVMVPEDSNHIVADWASRGFFG
+KMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDRLSLGFNYESNVVVVDRDFAARM
+EEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRPLL
+>2_595
+MSPLPASPLHRIPVRRIVRGAALAAGTGLVGVPMAVAAGLTGVDMVKRRGRRRRPAHNPG
+VFDAPVKDCHLRIFTSGEDLYEEMLAAIDSAERIVKFETYIWKADPTGQRFIEAFNRAAA
+RGVEVYVSYDGFGNLVVPRAFYRQLDPRIRVFRLPAFARPFWRGPVRNTGFNHSKIMVVD
+DEIGFVGGFNIGDDYATFWRDTHVCERGPAVWALDQSISIKWNAHHREGEQMSWRPPESW
+DPRVTVSANQPPLLVYPIRLTYLEAIQRAQHRILINTPYFIPDQQVLQALLHAARRGVDV
+QVMVPRDSNHIVADWASRGFYAGMLEAGITILLYEASMIHAKTATVDGIWSTVGTANIDR
+LSLGFNYESNVVVVDRDFAARMEEIFAIDAEQSERVESPRWQDRHGVARMVERLLVPLRP
+LL
+>3_520
+MGYALRRAAVAGTTAFVGVPLATAVAVSAYDAFKHRGRKLRPAERPGTFQAQVGPDALTI
+YTAGDDVYDAMIQAIDDARETVKFETFIWKDDATGQRFVDALNRAAARGVQVWASYDGFG
+NLLIPPSFYRQFDPRVRVFRLPAFARPLWRGVVRYSGFNHSKILTVDGRVGFVGGYNVGD
+LYAAHWRDTHLRVEGPAVWGLEHSLSVLWNEGYTDMAEMPWTRPEEWEERTVVAANLPTQ
+LVYPIRNTYLNAIARAQDHIYISTPYFVPDRQVLDALKEAARRGVDVQVLVPKDSNHVVA
+DWVSRGFYSEMLDAGITILLYAAGMIHAKTATIDGRWATVGTANIDRLSLSFNYETNVSV
+VDRDFAARMEDVFRADAARSERIQSPRWKDRHGLARVVEKLLVPLRPLM
+>4_2032
+MHRPPLPSLSRLPVRRLLRGAAVAAGVGLVGLPLTVAAGLTGVDMVKRRGRVRRPAPNPG
+VFDAHVKGSELRIFTSGEDLYEEMIAAIDGAQRIIKFETFIWKGDPTGQRFMDAFNRAAA
+RGVEVYVSYDGFGNLVVPPRFYRQLDPRIHVFRLPAFARPIWRGVVRHSGFNHSKIMVVD
+DEVGFAGGFNIGDDYARLWRDTHVRERGPAVWALGQSISIKWNAHHRAGEQMSWRPPDTW
+DPRVTVAANQPPLLVYPIRLSYLDAIQRAQHRILINTPYFIPDQQVLEALLHAARRGVDV
+QVMVPEDSNHIVADWASRGFFGKMLEAGITILLYRASMIHAKTATVDGIWSTVGSANVDR
+LSLGFNYESNVVVVDRDFAARMEEIFALDAQRAVRIDTPRWEDRHGLARVVEALLVPLRP
+LL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001684.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001684.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e365b2ab5ae9bb8611a510b25196185c80d0b8f4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001684.fa
@@ -0,0 +1,35 @@
+>0_2089
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>1_1813
+MRPPGALALEFRADSFDHPTGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEGGVPVT
+VPVWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEDQAQRVRQYIPESESARRLQETA
+IELVRMRSEVSAAWTEMRRSTDPR
+>2_594
+MKPAGALALEFRADSFDHPGGLVDAGTVISWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+SVPVDHRAVVQARVVHTDGADVHVQTRLLLPEVKDESGDPVVATSSLVVYSAEEDGARVT
+VPAWVPSTPGQIERDEQASRSTVARRAVERGMARLPFPSPGQAPEEMSTLAFLAPASEAT
+VGGTMNAGAILRWLDEAAAVCAARWTGHESVVAVFGGGVRFVRNILVGDLVRVDALLVNT
+TERSMQVALRVYAGRPTGVQPRLVAHSIAVMVDVSAEDKAQPVRQYVPESEGARSLQEAA
+VQLVRLRSEVGAAWTETRRSPESR
+>3_519
+MMRSGALSLDFRADSFDHPSGLVDAGTAIGWIDKVGYAVAASWSGTYVRARYMGTMQFRH
+PVPVDMRVTVQGRVVRTHGAAVHVQLRLLLPEVLDDDGRPVVSTSTLSVYYAEEDGQMLQ
+VPEWTPSTPDQIERDERARVSSVERRGIEQVMARLPFPEPGQEHEEMTTLAFIAPMAEAS
+VGGTVAAGAVMRWLDEAAGVCAARWTGHENVVAVFAGGVRFVRPVKVGDLVRVDALLVHT
+SERSMHVALRVHAGPRHQRDHRLVAHSIAVMVDVTREGRAESVRPYAPGSPAAHRLEESA
+VELVRLRSEAGAVWSDPS
+>4_2033
+MRPPGALALEFRADSFDHPTGLVDAGTVVSWIEKAGYAVAASWAGTFVRARYMGHTQFRH
+PVPVDRRAVVQARVVHTDGAEVHVQTRLLLPEIRDDDGDPVVATSSLVVYAAEEDGVPVT
+VPAWEPSTPGQIERDEQARRSTVARRAVERGMARLPFPAPGEAPEEMSTLAFLAPNAEAT
+VGGTINAGAILRWVDEAAAVCAARWTGHESVVAVFGGGVRFVRNIHVGDLVRVEALLVNT
+TERSMHVALRVYASRRTGAESRLVAHSIAVMVDVSAEGQAQPVRQYVPESESARRLQETA
+IELVRMRSEVSAAWTETRRSTDPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001685.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001685.fa
new file mode 100644
index 0000000000000000000000000000000000000000..41d8745bac9bf39615160d94c0ebf0361de9669a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001685.fa
@@ -0,0 +1,25 @@
+>0_2090
+MTAFDRFPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA
+AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
+>1_1814
+MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPDDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVLASRAGSLRRDA
+AVDRTLVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
+>2_593
+MTAFDRLPLPAEPQTPHDRLRRRVAAAVAERGEAAVAGLAVRLLTGSVTPADVTSGAARA
+LTGDDGDLTAGATGALALGHAWHRSALPALTSALSAPEPDVRSAAHLVLAARAGSLRADV
+AVDRALVDAVRAGCADPDPQVRASAASALGALAGPQDLEAALPVLTGMVMDVDADLATAA
+ELALDHLAERLDRPDLRVGAEG
+>3_518
+MTSRDLPLPVEPQTPHTRLARRVEAAVSARGEAAVAGLAVRLLTGAPTPEDVTSGAARDL
+IGDDGELTPGATGALALGVVWHRGAAGALAAALDAPEPEVRAAALLVLAARADRLRADAQ
+AGRALVEAVTARASDADPQVREAAASALGALARAEDLSAVEPVLSALVMDVDPELATAAE
+LALAHLAARLDRPELDPTPQA
+>4_2034
+MTAFDRLPLPAEPQTPHDRLRRRTEAAVAERGEAAVAGLAVRLMTGAATPEDVTSGAARA
+LTGDDGDLSPAATGALALMHAWHRSALPALTGALTAPEADVRSAAHLVIASRAGSLRRDA
+AVDRALVDAVRAGCADPDPEVRASAASALGALARPEDLESALPVLTGMVMDVDADLAAAA
+ELALEQLAIRLDRPGLRVSLEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001686.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001686.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9034ee18c555bd998dd2a2673638d4e9a73aee3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001686.fa
@@ -0,0 +1,41 @@
+>0_2091
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADALDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFEACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSFEKRRSRPDAVVVNPPRRGIGAELADALEDSGAPTVLYS
+SCNPTTLAQDLARMPSYRVARVQLFDMFPQTLHAEVLTLLTRR
+>1_1815
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLRMELNGIGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEGGVPASAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SDGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
+>2_592
+MQCHHYDAGRCRSCALMGVPYGVQLTDKDAAVCARLDAAVPAEAWLPPQASAESGFRNKA
+KLVATGTAAAPRLGILDPEQHPRHHDGTGHDLRDCGLYEDGMEAAFHAIAETIPAAGLEP
+YDVAARTGELKSVIVTLSPDRELMVRFVLRSAARLDALRAAVPGLRSALAGLGTPAAVVT
+ANLHPEHVALPEGPDEVHLAGDPTLRMELNGIGLRLRPQGFFQTNTDVTRRLYATAAAWL
+AEAAAADGTPVHSAWDLYCGVGGFAFHLARPVAEGGAGVAEVWGLETSEDAVAAARDTAA
+ELGLAGAVRFTAGDATRALSPGRREPSEALSSGKREAWDALSSGSREPSDAGAHPDDDAA
+PAAMPDAVVVNPPRRGIGPELAARLQDSGVPHVLYSSCNAASLAKDLAAMPAYRARRAQV
+FDMFPQTGHAETLVLLSRA
+>3_517
+MQCPHFDAGECRSCALMGVPYGAQLADKDAAVRARLAEATDARTRWEAPAASAESGFRNK
+AKLVVTGTAAAPRLGILDPRQHPRHHDGTGVDLRDCGLYEDGMEAAFHAIAGAVTAAGLE
+PYDVAARTGELKNVIVTRSPDRELMVRFVLRSADRLEALRPEVPALREALAALGTPAAVV
+TANLHPEHVALPEGPEEVHLAGDATLRMELNGIGLRLRPQGFFQTNTDITQRLYATAAAW
+LAEAAAEGGTPVERAWDLYCGVGGFAFHLARPVAEGGAGVAEAWGLEVSAEAIEAAREAA
+AELGVAERVRFTAGDATTALAAPGGTRPDAVVVNPPRRGIGAELAGRFEESGVPFVLYSS
+CNAATLATDLTAMPSYRVARAQVFDMFPQTGHAETLVLLARR
+>4_2035
+MQCPHFDVGECRSCPLMGVPYARQLADKQAAVLAALADAVDADTVVAEPFASAEAGFRNK
+AKLVVTGSAAAPRLGILDPRQHPRHHDGAGVDLRDCGLYEAGMEGVFDACAAAVTAAGLE
+PYDVAARTGELKNVIVTLSPDREAMVRFVLRSADRLDALRAAVPGLLDDLAARGTPAAVV
+SANLLPEHVALPEGDEEIVLAGGPTLTMRLNGVGLRLRPQGFFQTNTAVTEGLYATAAAW
+VAEAGLPAAAWDLYCGVGGFAFHLARAGVRDVWGMESSAEAVAAARETAAELGLADRARF
+SAGDATSALSFEKRRAPEALSSKKRRPRPDAVVVNPPRRGIGAELADALEDSGVPTVLYS
+SCNPATLAQDLARMPSYRVARVQVFDMFPQTRHAEVLTLLTRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6aeeb701db42636473b646470c3b7ef6558b3e70
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001688.fa
@@ -0,0 +1,50 @@
+>0_2096
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPHMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>1_1820
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTVFGVAPGDLGGAVGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
+>2_583
+MQVLLALTPILLTLALLLTRLPAWVAPAAGGVLAAALAPTVFGVDPGVLAAEVGRGVPTV
+VEILAIIAGGITLSRVMEHSGAHARLALWLSAGNGPTLATALLMVHGIIPFLETVTGFGV
+SLIVGVPLLLGLGFTAFRSALLAVLALTIGPWGSMAPGTLMGARLYDLDFQAVGVTAALF
+NLPASLVAGAATVLLLRGAQGMRGDGEPARTVPWLAVGLLSGAAQWALILGANLSVGTAP
+AGAVGTFVLTVAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVFGTTVEDALGLTGVLSVVG
+TPALWSFVAVGAGVALLGLGPHARRTVPGEAARLWVGTAIPNALYVAFGLTLSAGGVSQA
+LAGALSGMGPAYLAAIPVIGAFSGFVTASNTGAMALMGPLQMDTGAALGVPPTWTNGLHN
+AAAGWGIIAGPARIQVAHAMAVGAQTPEMPGWAVSRRALLAVLLPAMVVGIALMSLLGLA
+VLPRV
+>3_506
+MQVLLALAPILLTLGLLMTRLPAWAAPAAGSVAAVVLGLTVFGVDPAVLGAAVGHGVPTV
+LEILAIIAGGITLSRVMEHSGAHARLGGWLSAGNGPTLATALLMVHGVIPFLETVTGFGV
+SLVVGVPLLLGLGFTAYRAALLSVLSLTIGVWGSMAPGTLMGARLAGLDVQEVGVTAAVF
+NLPASLVAGVATVLAVRGARGLRDDSAPARLAPWLGVALASGTAQWALILGANLLVGTAP
+AGAVATFALTLAWLLVIRRGRLTPGPGRDVVPYVTLMAGTVLGTTAEDALGLTGPLSVVG
+TPALWSFVAVGVGLRLLDLDAAARRTVPRESLRLWRGTAVPNALYVAFGLVLSAGGASPA
+LAGALSGLGESYLAAMPFIGAFAGFVTASNTGAMALVGPLQMDTGAALGVPPAWSNGLHN
+AAAGWGIIAGPARIQVAHGMAAPAQTPDMPGRAVSPRGLVAALLPASLAGVAGMSLMGWL
+LLPR
+>4_2040
+MEVLLALSPILLTLVLLLTRLPAWVAPAAGTAVAVLLALTAFGVAPGDLGGAIGAGVPTL
+LEILAIIAGGITLSRVMEYSGGHARLAAWLSAGNGPTIATALLMVHGVIPFLETVTGFGV
+SLIVGVPLLLGLGYTAFRSALISVLALTIGPWGSMAPGTLMGARLFGLDFREIGVTAAVF
+NLPACLVAGVATVLLLRGARGMRVDVGPARTLPWLGVAVLSGVAQWALILGANLVVGTAP
+AGAVATFVLTVAWLLVIRGGRLLPGPGRDVVPYLTLMAGTVLGTTVKGAFGLEGAAALVG
+TPALWAFVAVGVGVQLLHLDAAARRRVPREAGKLWVGTAIPNALYVAFGLILSAGGVSQA
+LAGALSGMGESYLVAMPFLGAFAGFITASNTGAMALIGPLQMDTGAALGVPPPWSNGLHN
+AAAGWGIVAGPARIQVAHGMAAGAQSPQMPGWAVTRRNLFVVLLPAMLAGILGMAVMGWF
+LLPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69433afa4f06a0c2e8a9fece17611f92799d659f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001689.fa
@@ -0,0 +1,40 @@
+>0_2097
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAERPDRWGVNLFVPDAVNTAIPAAARTEAARSARAAAVAAYRAGLTADGA
+ADLPAVADVVPDPDAERADFEAMLVAAEEQAWPLVSFTFGLPAADVFARLAAAGVPAGAT
+VTDAAEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPTRAELPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTALTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAVGDLERVH
+LWAGTEAHRVREAPAADVLASLTP
+>1_1821
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARAAAVAAYRADLTADGA
+ADLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALEHGAAFLVVQGHRAGGHRGTSDPAAEPPRAELPAVLPAVRDVVGTGATS
+AVPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAVDVLASLTP
+>2_582
+MSAAQLPDDVVRARLIPPARVLAAPMAGGPSTPELVAAVVRAGGSGFLAGGMRTAAQVRE
+QVDALRGLLGGGDGSVDGSDAARRWGVNLFVPDAVNTAIPAADRTERARAERRAAVAAYR
+ERLAAEGERAAGGAAAEGAGGAPTLPSPDDVTPDPARERAEFAAMLTAAEEQAWPLVSFT
+FGLPEPAVFARLAAAGIPAGVTVTDADEARSARAHGAAFLVVQGHRAGGHRGTLDPAADP
+VERELPSVLAQVRAVVGTRVPVVAAGGVGAAAHVRSLLAAGADAVAAGTAFLLAAEAGTS
+VAHRAGIRRCAAGEGFVGPDGAARTVLTRAYTGRWARTLATDFAAAHPDAPAAYPELNAL
+TTGLRAAAATAGDLERVHLWAGTQAHTAREAGAADVVAGLTP
+>3_505
+MSSTTVPSVPAPVPAPLDPPVPVLAAPMAGGPSTPELAAAVIRAGGGAFLAGGMRSAAQV
+REQVDGLRALLTAPEEAGRFGVNLFVPDAVNTAVAASARGGAARIARAQAVASYRERLAP
+LAADLGAELPSVLTVTPDPDAERAAFEDMLAAAEEQSWPAVSFTFGLPAPDVFARLDAAG
+IPAGVTVTSPAEAMAAVASGARFLVVQGPKAGGHRATLDPQGRPGITDLRTLVFAVRHAL
+GPAAVPLVAAGGITDGAQVRPLLEAGAVAVAAGTAFLLTPEAGTSAAHRTALRQASAGVA
+FAHPDDGAASTALTRAYTGRWARGLVTPFMDEHHDAPAAYPEVNGLTGPLRRAAAEEGDL
+EHVHLWAGTGAHRVEEVGAAEVLASLAPRAEP
+>4_2041
+MTQPSHPDDVTRARLIPPVPVAVAPMAGGPSTPELVAAVVGAGGGGFLAGGMRTAAQMRA
+QVDALRALLGAEGPDRWGVNLFVPDAVNTAIPDAARTEAARSARTAAVAAYRAGLTADGA
+AGLPTAADVVPDPDAERADFDALLTAAEEQAWPLVSFTFGLPAADVFARLAAAGIPAGAT
+VTDATEARAALDHGAAFLVVQGHRAGGHRGTSDPAAEPTRAEMPTVLAAVRDVVGTGAAS
+AAPVVAAGGVGTAEDVRALLTAGADAVSAGTAFLLTPEAGTSAAHRAAVAACAAGTRFSA
+DDGRARTGLTRAYTGRWARSLATAFMAEHPDAPAAYPEVNVLTKGLRAAAAAAGDLERVH
+LWAGTEAHRVREAPAADVLASLAP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001692.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001692.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9359e453ec4196337f97bc9b2001572c79a14f77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001692.fa
@@ -0,0 +1,30 @@
+>0_2102
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLLHCLAGLDARTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRALGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR
+>1_1827
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR
+>2_576
+MSTTADSHSAHSTPPGAGASGPGMPSSSTTTTTAPAASARALTKTYGRGDAEVHALRGVD
+VDFAAGAFTAIMGPSGSGKSTLMHCLAGLDTPTSGSVVLGGTEITGLGDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRKPDRAWLDEITATLGLTDRLKHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDSATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELLDPTVESVTNALAALSAPGAADAAGTFDAPADGGR
+>3_500
+MDITSPRSAAHDAGAHALATPLAHAAAPPAPAVSARGLTKTYGRGDAAVHALRGVDVDVE
+TGRFTAIMGPSGSGKSTLMHCLAGLDTPDAGVVTLGDTVITGLSDAALTRVRRDRVGFVF
+QAFNLVPTLTAEQNIVLPMELAGRTPDRAWLAEIVDRLGLSDRLAHRPHELSGGQQQRVA
+VARALLTRPDVVFGDEPTGNLDSATGAQVLDLLRRATRETGQTVIMVTHDPVAAAAADRV
+VLLADGALAGELHAPTAERVAEALTALQQGRPLPQGRPLPQDGGR
+>4_2048
+MDTSSPAHPFSPTTPGPVAPGPGTPSSSATTTTAPAVCARGLTRAYGRGDAQVHALRGVD
+VDFASGAFTAIMGPSGSGKSTLMHCLAGLDAPTSGSVRIGGTEITGLDDTALTRLRRDRV
+GFVFQAFNLVPTLTAEQNIVLPLELAGRTPDRAWLDEITRTLGLADRLGHRPHELSGGQQ
+QRVAVARALLTRPDVVFGDEPTGNLDTATSAEVLGLLRRSAREMGQTVIMVTHDPVAASA
+ADRVVLLADGRLAGELVDPTVESVTAALTALSAPAEGGVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001696.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001696.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c1cf50236f20de16bc2d109a24cbf4c40f73d14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001696.fa
@@ -0,0 +1,33 @@
+>0_2109
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLALEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLETIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>1_1834
+MATPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERMLRLARQTLVLEDETLAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGTLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
+>2_564
+MNSDHLRALVSAVDHGTFDAAADALRISGSAFSQRVKALERQVGQVLLARTVPVRPTPAG
+ERMLRLARHTLALEEEALASLGRGDGGRVPVRVAINADSLDTWWELVLREAATWDDVVLQ
+LRTEDQEHTAALLRDGTVVAAVTDDPTPVSGCTSTPLGTMRYHAVCASFLLEMHRDERGR
+LDLATLPRVDYGLRDGLQRTVLRRAARGRAAFDPPHHLVPSVQSYLRAVELGLGWGMLPS
+AQLPPGVLEGRHPDLEPVPSLGTVDLTLHWQRWSAGTAALDRLTDAVLRAAPSVADAAD
+>3_491
+MNSDHLRALAAAVDEGTFDAAAAWLGISGSALSQRIKALEGQTGQVLLTRTVPVRPTEAG
+ERMLRLARQTLPLEEEALAALGRGTGRRAPLRVGVNADSLETWWTPVLREAATWDDVVLH
+LHAEDQGHTPELLRQGTVVAVVTDDPTPVTGCTVTRIGTMRYHAVAASFLLDLHRDAHGR
+VDVATMPVVDYGPRDGLQRTMLERAARGRVSVPRPPHHLVPSVGAYASAVGMGLGWGMLP
+TGQVPPELAAGSHPDLELVPELGTAEVPLYWQRWSAGTPALDRLTAAVTAAAPAG
+>4_2055
+MTTPTLDRMNSDHLRALVAAVDHGTFDAAADSLRISGSAFSQRIKALERQVGQVLLARTV
+PVRPTAAGERLLRLARQTLALEDEALAALGRGDGGRVPLRVALNADSLDTWWEPVLREAA
+TWDDVVLQMQSEDQEHTAVLLRDGAVVAAVTDDPTPVAGCTSTPLGTMRYHAVCASFLLE
+LHRDARGRVDFGSLPIVDYGPRDGLQHTVLRRVTRGRPVADPPTHLVPSVHAYLRAVELG
+LGWGMLPSVQIPPGVLEGRHPDLEPIPALGAADVHLHWQRWTAGTAALDRLTDAVLRAAP
+SAGDTAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001699.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001699.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2840ac9a22ed181782d76b59ad11f6ea46ab5ea7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001699.fa
@@ -0,0 +1,35 @@
+>0_2115
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAILTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRSGRTPGAPSPMALVLAGAALTAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>1_1840
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTTPGAPSPMALVLAGAAITAGA
+TAGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALAL
+GDDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALM
+AGCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
+>2_558
+MPRALLLIAPAVLAVLAALASLALGARPVPVDAAVGALTEAALHGPAAVTGMDGAAVLSR
+VPRTLAAILVGAGLAVAGAALQGATRNPLGDPGLLGLTAGAVLAFALGIALGVAGSLPAV
+MALAILGTLAAAALVTAVAAGAARVSGVPGPPSPLSLVLAGAATTAGATAVTSALVVLHP
+AVRDRLRLWTVGSVARADLGDALWLAPVVLAAVAAVVVLGPGMDALALGTDLAHGLGARP
+ERVRALLLAAAVVLTAAAVALAGTVGFLGLVIPHAVRRLRPPDARTLVLACALWGAVLVL
+VADTLGRLVIAPAEVHLGVTTAVLGVPVLLALLRRRGVAA
+>3_486
+MPSSPTRGALLFGLLPLALLLTAGLAALALGARPVPLTTTATTLQAMLAGEGVPAGVDAA
+AVASRVPRTLTAALVGAALAVAGAALQGATRNPLGDPGLLGLSAGASLATAIGLALGVSG
+STFWVLALAAAGTLAAALLVYAVAAAASRGAGAGGAPTPIGLVLAGAAVTAGAGAVTTAL
+LVLSPVVRDRFRFWAVGTVARADLGEAALLTPVIGLGIVLALAAARGLDALALGDDLAHG
+LGARPGRTRALLLAAVVLLTAAAVALAGPVGFVGLVVPHALRRLRPGGTRTLLIGSALWG
+AVLLVAADLLGRLVIAPAEIHLGVTTVLLGVPVLLVLLRRTGLGS
+>4_2061
+MPSTALASPARVRAGVLMGALPAALLLAALVAGVALGARTVPATTALDTLGAVLTGHPVP
+EGIEAAAVASRVPRVVTGALVGAALAVAGAALQGATRNPLGDPGLLGLSAGAGLAVAAGM
+ALGVAGSTFGVLALAAVGTLVAAALGYAVAAAATRRGRTPGAPSPMALVLAGAAITAGAT
+AGTTALLVLSPTVQDRLRFWAVGTVARADLGEALALAPVIAVGLLAAVAVAPGLDALALG
+DDLAHGLGGRPERVRAVLLGAVVLLTAAAVALAGPVGFVGLLVPHALRRLRPPSTRALMV
+GCALWGAVLVILADLAGRLVVAPGEIHLGVTTVLLGVPVLLALLRRPGVAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001709.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001709.fa
new file mode 100644
index 0000000000000000000000000000000000000000..51581b421d6a872a71b68107bfaa3f6d74f78c73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001709.fa
@@ -0,0 +1,25 @@
+>0_2128
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>1_1853
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAAMSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
+>2_539
+MSIPATEVEARWNEASEPFTAVVRAVRDWDAATPCEGWDALDLLDHVVGAERDFAARQGR
+EVPLFDGSRQQTANQWTKHSAALSALAGDEEFIMKPMHTALGEMTVGEAMIRFHAFDLIV
+HRWDLARSQGVDERFTDAEMDCIEESLDLFGDAAYTPGILAQPVPVADDADRQARLLGRL
+GRRA
+>3_467
+MSTQTDVEQYWMDCVEPFTDVVRAVEDWDASTPCKGWSAQDLLDHVVVAERDFAARQGRE
+IPVFDGSRNELWTQWVKHASAVTALAGDETFIMQSLHTATGDMTVGEALLHFHGFDLLVH
+RWDLARSQGRDEQWTDEEMDRIERALDSFGEQAYQPGILADPVPVADDAPRQVRLLGRLG
+RRA
+>4_2074
+MSIPATEVEARWNAAAEPFTAVVREVRDWDAATPCEGWDALDLLDHVIAGQRDFAARQGR
+EVPLFDGSRQQLATQWAKHAAALSALAGDEEFIMRPMKTALGEMPVGEALIRFHAFDVIV
+HRWDLARSQGVDARFTDAEIDCVEESLELFGDAAYTPGILGEPVPVADDADRQTRLLGRL
+GRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001713.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001713.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25ced05c95acdd11d436632becf4f36ed5f04f62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001713.fa
@@ -0,0 +1,30 @@
+>0_2135
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>1_1859
+MSSTPTDADHHGPGPAPDPAHLDDLPPATLVARGLTLRGSRGPVFGSLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLTDGVRRRAGRARFALLADAVRLTVAPEAV
+VRELSAPDRALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>2_530
+MSSTPTDADHHGPGPVSVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLRGVRGELVLTGGPVDVALDGPERPAARAYRPLIDATRHPYA
+LRARTAIAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLTVAPEAV
+VGELSAPDRALLAAVVACLRPARLVTFDDVDATLTLDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
+>3_462
+MTEDQTPAPIETDDVVAERAPEPAPGGSHQVGRALTARGLTLRSIRGTVFGPVDVDLPPG
+VPGAVLGTQGSGRSALLLALVGRLQGVGGELTLGDMDGIRHPHRLRRATTVARITDYVEL
+EPLLTIRECIDEHCLAEGISRRTGRKRFARLEAAVGFHPDHGDQVSSLPVEDRTILTCML
+ACLRPADVIVYDDIDSSLTRPQLEHVYRVLETLGRLGHRFVVSALTSAPVPRGAVVVELP
+TPGHDDLPAALPTRPSLED
+>4_2080
+MSSTPTDADHHGPGPAPVPAHLDDLPPATLVARGLTLRGGRGPVFGPLDLVLPPQTHLAV
+LGTQGSGRSALLLALTGRLQGVRGELVLTGGPVDVALDGPERPAARAYRPPIDAARHPHA
+LRARTAVAHTTDVVELEPALTAAEVVDERCLADGVRRRAGRARFALLADAVRLSVAPEAV
+VGELPAPERALLAAVVACLRPARLVTFDDVDATLTIDELVALHAALDVLKDHGHPFAVSA
+VASAPVPRDAVVLTLPPVREN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001720.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001720.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ff2a9b4a88042ffc4e2b067bfe06345a8f292e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001720.fa
@@ -0,0 +1,40 @@
+>0_2147
+MTQTPTAPDRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPRTAESRAAATTP
+GLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRVIRWQRRL
+ELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIHSTTWEWD
+FVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWRPRHLLNPVINAGLAPIF
+EWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVLTGSGKAA
+LVGTLLANGLRNIWAHAVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSANISGSKL
+MHFMTGNLSHQVEHHLFPDLPSSRYAEVAPRVREICARYGLPYTTGPLLRQVGSAWKKVF
+RLALP
+>1_1871
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
+>2_519
+MTQTLPATERTGATAPDDLSLAIPGTTVRGRTARVLPEDRPDTTSWAPQTADAGTDAAAP
+AASETPEAPTADAATRPAANAKPGLLGVVGSPAVRPPGAAHLTDEQVAELGRELDAIRDD
+VLSRRGASDAAYIRRVIRLQRWLEIGGRAALLNARHPAAFVAGTTMLTVAKIVENMEIGH
+NVLHGQWDWMRDPDIHSTTWEWDFVTPSRAWQNTHNDLHHRWTNVIGKDRDVGYNVLRMD
+ESEPWRPRHLLNPVINAGLAPIFEWGIALYDLELDRVHAGEKSRKELMTDLRSVGVKASR
+QFAKDYVATPAVAEFLTGSGKAALVAGLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVD
+GETRGDWYVRQMIGSANISGSKLMHFMTGNLSHQVEHHLFPDLPSNRYAEVAPKVREICA
+RYGLPYTTGPLLKQVGSAWKKVFRLALP
+>3_451
+MIRSATAGKIIENMEIGHNVLHGQWDWMRDPDIHSTTWEWDFVTPSSAWQHTHNDAHHRW
+TNVTGLDEDLGYNVLRMDEAEPWEPRHLLNPVINAILAPFFEWGIAIYDLELAKVRAGEK
+PVADLRRDLASVAVKAVRQLAKDSLATPIAAELVSRSGSAWRKVFRLALP
+>4_2092
+MTQTPTTPSRTGATAPDDLALAIPGTTVRGRAARVLPQDRPDTTSWAPHTAESRAATSRS
+TAAATTPGLPGVVGSPAVRPPGAAHLTDAQVAELGRELDAIRDDVLARRGTSDAAYIRRV
+IRWQRRLELGGRALLLNARHPAAFVAGTAMLTVAKIVENMEIGHNVLHGQWDWMRDPDIH
+STTWEWDFVTPSRAWQNTHNDLHHRWTNVVGKDRDVGYNVLRMDESEPWQPRHLLNPVIN
+AGLAPIFEWGIALYDLELDRVQSGEKSREELMTDLRSVGVKAARQFAKDYVATPAVAEVL
+TGSGKATLAGTLLANGLRNIWAHSVIFCGHFPEGAETFSEEMVDGETRGDWYVRQMIGSA
+NISGSKLMHFMTGNLSHQVEHHLFPDLPSSRYAEVAPQVREICARYGLPYTTGPLLRQVG
+SAWKKVFRLALP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..804deb92ec4d7969fdaf3d0e4ffb96bb2239f994
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001721.fa
@@ -0,0 +1,30 @@
+>0_2155
+MPAQPSPSGHTVHLSTSGVDARITPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALADRIRRA
+>1_1879
+MPAQPSPSGHTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDAASPTGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLALDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLHFLGAELGALEEAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLGEA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
+>2_507
+MRAHPSPTGRTVHLSATGEDARILADELGGSVLEIGGAVQSHVDPADPTALRYEYLRRMA
+NVLDGVAPAGAPLRVLHLGAGALTLPRYVQATRPGSEQTAVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLLMDGERFDAVVLDIGTGEDGAAHLTGAEFYGELLGLLTAAGVL
+LVNIGDDDGLRFLGAQLRHMEAACAEAGVPGPWTLASAAMLERLELGNAVLAAGPALRGD
+GAAAGGDAGPEEDGGPLTPAALLARGPHPGAVLDEAASADLARRVAGR
+>3_450
+MPTQPQDDASSPAPSPTARTVHLAASGVDARILPDPHAGGWMLEVGGAVQSHVDLADPTQ
+VRYEYLRRIANVLDALAPAGEPLRVLHLGGGALTLPRYVAATRPGSVQTVVDLDRELMGL
+VLEELPLPADADVYVVVADARAVVDDLLDPLEGESQAGAWDAVVLDIDTDAGAVAHLTGA
+AFHAELLELLAPGGVLCVNIGDDDGLAYLATQLTALEAACADAAEGAGVPGPWTLGPNSV
+LERRELGNAVLVAGPGLAGMDAAALHAAGPHPAVVLDAHESAALAERITAAP
+>4_2095
+MPAQPSPSGRTVHLSTSGVDARIAPDEFGGFVLEIGGAVQSHVDLADPARIRYEYLRRMA
+HVLDGVAPAGAPVRVLHLGAGALTLPRYLQATRPGSEQTVVDLDRELVSFVLAELPLPAG
+TDLVSVVADARLAAVDLAMDGERFDAVVLDIGTGEEGAEHLRGAVFYGELLELLTAGGVL
+LVNIGDDAGLRFLGAELGALEKAAAEAGVPGPWTLADQGMLERLDWGNVVLAAGAPLREA
+GCTERLAAAGPHPAAVLDPAESAALAARIRRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001722.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001722.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3161d9026a9a78faad6493ccb5c65c56585532d0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001722.fa
@@ -0,0 +1,35 @@
+>0_2158
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>1_1882
+MPPESSVPSAERGPSRPRPAAVAARPEAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLAVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGMIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEAGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGLPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVALASWPARRR
+>2_509
+MSARAARAARAGEGRQGSDAPAGADARPGAAGSALLFAMAIVAGSTIPVQARLNSALAER
+SGDPTLAAVASFAAGLVLVAAVTVLTPAGRRGLRAVRPALAAGRVRWWYLLAGTIGGAMV
+FSQATTVGLIGVAVFTVAVVTGQLIGGMVVDRLGLTPAGVRRMTPRRLAGAALALACVVL
+VVAPQLGARGDGGPPLWLLVALAPLAVGLATSIQQTLNARQAAAYGSVLPVTTVNFVAGT
+GILALVHLGGRLGGGVGGTLPGDWWLYLGGPMGVVFIAFSAYLVPRVGAFLTMLGLVSGK
+LLGSLAVDALAPVGEVAASPWTVVGTLGALAAVVLASGAARPARKG
+>3_448
+MPASSPALTPAPRSGATTALLFLLALVAGLAMPVQGRVNSALSLAVGSPALAACASFATG
+LAVLVLATLLLPSGRRGAARIPAAVRNGDVRWWQLLAGTIGAAFVLTQAWTIPLIGVAVF
+TVAVVTGQMLGGMLWDRLGWTPAGVQRISRRRLFGALLAFCAVTAVVWPRLQESGSPGAW
+LALAVLPLAAGVATSGQQAMNGHQTAHFGTPLPPTLVNFAAGTAVLAAATAVAAGTGAGM
+GPLPAAWWMYLGGPLGTVFVGLGAFLIPRVGAFLTTLGMVAGQLVGSLLLDVVAPAPGAQ
+VTWLTVVGTLGALAAMVVASSPQVPAGLRASRRRARRG
+>4_2098
+MPPEPSAPSGERGPARPHPADVAARPDAPSPRATALLFALAVAAGSVMPLQGRINSRLAH
+LTGDPVLAALCSFAAGLVVMVLVSVLTPRGRRGLARIRPALAAGSVRPWYAVAGVIGGLL
+VLTQSATIGPLGVAVFTVAVVTGQVVGGMVVDRLGLSPAGVQRLTPRRLTGAALALAAVA
+LVVWPSLGEVGGGPGWALLALLPLLAGLATAGQQVFNARQTTAYGTAIPATLVNFTAGVL
+FLGIVWGGIALASGHGMPALPHDWRLYLGGPLGCVFIGVGAMVVPRLGVFAATLGLVSGN
+LLGSLVVDLVAPTDGSTVTTTTVLGTLGALAAVTLASWPARRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001724.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001724.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93c7531a2fb529caef4dce929057c951ff89bc0d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001724.fa
@@ -0,0 +1,55 @@
+>0_2178
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAEGRPTGLL
+EETAMSLVTRLLQSESHEHIGACLARASQGYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHSVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRVVPSDQIAAIDVVATAVGGEFVH
+GGL
+>1_1891
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLTARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELGPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>2_488
+MQLDLIVENAHLLTGDPARPEATRLGVWRGAVVGVDEELDGLGARERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGAHTAQEVYDRIRARAAELTPGAWVTCTGFDPGHLTGPQPD
+RDGLDAAAAGRPVLIRHNTGHAFTVSGAVLFLAGVGEQVMQQPEGGRIITDAADRPTGLL
+EETAMNLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGIAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQAMVTLDALRPVDGHADDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTADYCGHGHGRGYLQQDAGEMRRECLGAAAAGWSLALHAIGDAALDFALDV
+IAEARARFGRPVMPHRVEHGGVVRDDQVARLAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLDVIQDFVLRRTETGEQYGPDLERLTVAQA
+LQAYTVGSAEATGWGGRKGRLVAGQLADFTVLSADPRAVPSEEIAAIDVVATAVGGEFVH
+GGL
+>3_425
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEELDGLAAGERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLATRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALRPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AALSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLAAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
+>4_2111
+MQLDLIVENARLITGDPARPSASRLGVWRGVVVGVDEQLDGLATRERLDARGRTVLAGFN
+DAHAHSVWFGQSRLDVDLEGARTAEEVHRRVRARAAELDPGAWVTCTGFDPGHLTGPQPD
+RDSLDAAASGRPVLIRHNTGHAVTVSGAVLVLAGVGEQVLQQPEGGRILTDAAGRPTGLL
+EETAMSLVTRLLQPESHEHIGACLARASQEYAAEGITSVTDAGVAGGWIGHSPLEFGAYQ
+RARDAGLLRTRFQTMVTLDALHPVDGHPDDGTHLTLDAGVRTGVGDEWLQIGPAKVFTDG
+SMLGQTAAMTEDYCGHGHGRGYLQQDAGEMRRACLGAAAAGWALALHAIGDAALDFALDV
+IAEARGRFGRPVMPHRVEHGGVVRDDQVARMAELEVVMATQPNFISAFGGSVRERIGPER
+AVLSYPAGRLLRAGLVLPGSSDRPVAGGRPLEVIQDFVLRRTETGEQYGPDAERLTVAEA
+LHAYTVGSAEATGWGGRKGRLVAGQLADFTVLSEDPRAVPSDQIAAIDVVATAVGGEFVH
+GGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001726.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001726.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8513fc27f4d7c9da99c93b48549f8f7dc30b3a58
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001726.fa
@@ -0,0 +1,55 @@
+>0_2180
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDREHPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>1_1893
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTD
+IVDLDPSQDGRPRRYSGGYAGWAKGRRRAQAAWEQEYAEQNAERERLELAVEDAREQMQG
+SWRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADMPDGDPRDG
+ADAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLR
+VLAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGR
+PLPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALV
+DEMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>2_697
+MTLTPPHAPALPAGASAHIRAECITLTLGDRTVLDQADVTVSAGSRLAIVGENGRGKTTL
+LHVLAGTLAPDAGTVTRAGTLALVEQDLDADDDRTVGDLIHDAVGESLAVLDRLEAATRA
+LAEGRPGADDDYARALETATALEAWDAERRIDVALEGLSACTDRTRPLNSLSVGQRYRVR
+LAVVLGSAVDLLLLDEPTNHLDAGALEHLTRALREHPGGVAVVTHDRALLKDVAETFLDL
+DPTSDGRPRQYAGGYAGWEKGRSAERAAWEQAHEQQVAEHAALAEAAEAARGRLQDRWRP
+DKGTGKHQRATRAAGVVQAFNRRVRDLEAHEVTVPEPPRALAWPASSTRAARPLLNAEGV
+DVAGRLRGPVSADLTGGDRLLLTGPNGAGKSTLLHVLAGRLDPTAGRVLRHTGARIALLT
+QEAPAWNPRHTARQAFEVHLHRRGLLADDDGGAPPLASLGLLEPRSMDAPVGRLSQGQQR
+RLHLALCLAERPDLLMLDEPSNHLSATLVDELTEALRATRSAVVVATHDRQMLRDLSDWP
+RLELTAEAVAR
+>4_2113
+MTSGPPSPALPAGPAAHLRGEHLTVSLGGHRVLTDATVRINAGSRLGIVGENGRGKTTLL
+HVLTGRITPDVGRVTRAGTLAFVPQALRARADGRSRTVGDLVRDALTGPHAALEALDAAA
+AALAEAPDDAGAGHRYSTALERAHLYDAWDAGRRVDMDLEGLHACTDRERPLTSLSVGQR
+HRVRLAVTLGSRPDLLLDEPTNHLDDVALDFLTRRLVEHPGGVAVVSHDRALLRAVCTDI
+VDLDPSQDGRPRRYSGGYAGWAKGRRRARAAWEQEYAEQNAERERLELAVEDAREQMQGS
+WRPPKGTGKHQRSSRSAGIVQMFNRRFDELEAHRITVPEPPLRLDWPFADRPDGDPRDGA
+DAAAGTAGGPGTAGDDVLLTADAVRVAGRLEQPMGAALVPGGRVLVTGPNGAGKSTLLRV
+LAGDLEPTSGLVTVGADVRVRLVAQETPAWDEERTAAAVFEEHVRRVGADEAGVDDLGRP
+LPAPTLPSLGLLTAEAADTPVGRLSQGQQARLHLAMVLIERPHVLLLDEPTNHLSPALVD
+EMTEALQVTEQAVVVVTHDRQMLADLADWPRVELRTDAAAV
+>4_2153
+MPTSRSLRSCVWNGTPQGHAAHIRAESIHITLGDRHVLNGVDVTVSVGSRLAIVGDNGRG
+KTTLLHLLAGILQPDSGVVTQAGSLVLVKQDMATEGDRTVGDLIAEATGPSKSALEALDA
+TSAALAEGDDAADAYSAALERATLLDAWDAERRVDIALEGLNACSDRDRVLSTLSVGQRY
+RVRLAVALGSTPDLLLLDEPTNHLDAAGLSFLTERLRDHAGGLALVSHDRALLRDVATTF
+LDLDPTRDGRPRTYAGGYQGWVEGRQRERVSWEQDHAAQVARHAQLTRAAAEARSRLSQG
+GWRPDKGTGKHQRATRAAGVVQAFNRRVEDLERHEIDVPEPPLRLAWPKSSARRGMSIVN
+ASMLTVERRLDTPVSIGVNGGDRLVVTGPNGAGKSTLLAVLGQRLVPTTGYVQVNPSARI
+ALLSQEVPDWDRTSPAHVAYETYLGKLGCRSQAPSLGSLGLLEASATSTPVGRLSQGQQR
+RLHLALCLAQDPDLLLLDEPTNHLSSSLVDDITTELLQTPCAVIVATHDRQMLDDLADWP
+HLDLDPKDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7e183b46ab51876d96973f743fb67cea5e01258
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001737.fa
@@ -0,0 +1,40 @@
+>0_2224
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTCVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRRLPATPILASVAEEAPAPEAPADDA
+>1_1926
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>2_434
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+ILPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
+>3_388
+MKLAILSRSLRAYSTQRLKSAALDRGHDVKVLDTLRFGIDLAGDEPDMMFRGKPLSSYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRASQILSRHGIAQPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGKDVRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVEQVELSEEYAETAVRAAHIM
+GLRVAGVDMLEGEDGPLVMEVNSSPGLEGIERATTLDVAGAIVDYIADQAGFPEVDVRQR
+LAVSTGYGVAEIAVLAGSDMAGQSIEDSGLLEKDLQVLTLHRGASVFPNPADSKVLEEGD
+RLLCFGKTENMRALIPARSQRPKRVKKLPKNPIIEAPPAEPAVRPDAESGES
+>4_2164
+MKLAILSRSLRAYSTQRLKTAALERGHQVKVLDTLRFGIDLSSDEPDLMFRGRPLSGYDA
+VLPRIGNSVTYFGTAVVRQFEQMDVYTPNTAAGIMNSRDKLRATQILSRHEIDMPATVFV
+RNRGEVSTAIDMVGGAPVVIKLLEGTQGIGVILAPTKKVAEAIIETLHGTNQQVLIQRFV
+EESKGTDIRALVVGDRVVAAMRRRAQGDEFRSNVHRGGTVERVELSPEYAETAVRAAHIM
+GLRVAGVDMLEGEHGPLVMEVNSSPGLQGIEAATDLDVAGAIIDYVADQAGFPDIDVRQR
+LAVSTGYGVGEITVHAGSGWVGQSIEDSGLLAKDLQVLTLHRGTSVFPNPADTKVLEEGD
+RLLCFGKTENMRALIPARARRPKRVRKLPATPILASVAEEAPAPEAPADDA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001741.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001741.fa
new file mode 100644
index 0000000000000000000000000000000000000000..475755ed309412ff75714364eb8b53efd274563d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001741.fa
@@ -0,0 +1,15 @@
+>0_2229
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>1_1932
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>2_430
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
+>3_383
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AIKNAREVALLPYAGAGRG
+>4_2170
+MAKAELRKPKPKSNPLKAAKITEIDYKDVALLRKFISDRGKIRARRVTGVTVQEQRKIAQ
+AVKNAREVALLPYAGAGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001748.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001748.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d7095f1b6b42c34218962b5a6075f9f8d6c6240
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001748.fa
@@ -0,0 +1,50 @@
+>0_2238
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEITEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
+>1_1942
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRTSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEEAMAAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYNHLLEWRLDEGPHEQAEAEAELRRWWAEQPEA
+QQD
+>2_419
+MDLTTATLALPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRVSGDLDFT
+TDAGPDAAEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEEDLLRRDFTVNAMALRLPGLELVDPYGGVQDLAAGVLRTPGAPEDSFSDDPLRMLR
+AARFASQLGFTVADEVEAAMTAMAERIGIISAERVREELVKLVCGAHPRRGLDLLVRTGL
+AEHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEAEYSPSAPDPVLRLAALLHDV
+GKPATRRFEKGGAVSFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNKRKAERLAHAYDDLERRIAEIAEQEEL
+AAVRPDLDGEQIMALLGIRPGPVVGRAYRHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+AEG
+>3_373
+MEPRTDTRPLPAGFPADAALPAVVVELGRRFEAAGHELSLVGGPVRDLLLGRPVVDLDFT
+TDADPDATERIGAGWAEAAWDVGRHFGTIGFQKGGWQLEVTTYRAEQYDPTSRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPAMELVDPHGGVRDLAAGVLRTPGAPEDSFSDDPLRMMR
+AARFASQLGFGVADEVEAAMTDMAERIGIISAERVRDELVKLVRGDRPRAGLDLLVRTGL
+AQIVLPELPALQLETDEHHRHKDVYAHSLQVLEQAMGEEERYSPERPDVVLRLAALLHDV
+GKPATRRFEPSGAVSFRHHENVGAKLVRRRLKALRFDNDTIKAVARLVELHMRFYGYGEA
+GWTDSAVRRYVHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIEEISAAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYAHLLEWRLDEGPHEQAAAEAELRRWWAEQPEA
+AGASSGGGARD
+>4_2180
+MDLTTATHALPPGFPADATLPAVVVELGRRFEAAGHELSLVGGPVRDLFLGRPSPDLDFT
+TDADPDASEAVGAGWADATWDVGRRFGTIGFRKAGWQLEVTTYRAEQYDPASRKPQVAFG
+DSLEDDLLRRDFTVNAMALRLPALELVDPFGGMRDLHAGVLRTPGTPEDSFSDDPLRMMR
+AARFASQLGFAVAPEVEQAMTAMAERITIISAERVREELVKLVCGAHPRAGLDLLVRTGL
+ADHVLPELPALQLESDEHHRHKDVYAHSLTVLEQAMELEGEYAPSTPDPVLRLAALLHDV
+GKPATRRFEKGGAVTFRHHETVGAKLVRKRLRALKFDNDTIKAVARLVELHMRFYGYGDA
+GWTDSAVRRYAHDAGDLLPRLHALTRSDVTTRNRRKAERLAHAYDDLERRIAEIAEAEEL
+AAVRPDLDGQQIMALLGIRPGPVVGRAYTHLLEWRLDEGPHEPAEAEAELRRWWAEQPEA
+QQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001749.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001749.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0afa8fcde94e7fb7ff5e5e1ea5b507e9fa19b416
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001749.fa
@@ -0,0 +1,60 @@
+>0_2240
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>1_1944
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTSAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLITMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGVAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAVASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGVVVVWLLGGYTGGFAWNSIGTALLTCAVAAVA
+MGPVYLMVLRAMRFPELDDALRPLVARVPALGRLLRVG
+>2_418
+MASPDPSAHRGAPLPSALGAWHRRPQPPARPEPAPAPGPRPAASGLPTVEEVSAGGVVVR
+EHDGGLEVAIIARYNRGGRLEWCLPKGHPEGVEDHRQAAVREVEEETGIAGDILEPLGAI
+DYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERRI
+VDLARQVVDRHFPRAPPGAPAPDPPPRTRGSSDHDWVTLEQQPLPAPRAGTPPAPAVADE
+EPTTADPAPATDPEAPAREDRPDETPEGERRAGRSTAIMASGTLISRVLGLVRAMLVTVA
+IGLSTDMADIFEIANSLPNVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGT
+LVMLGGTLVVMAVAAPLMTALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNAN
+GRFGAYMWAPVLNNVVAIAAIGLYLAMFGAYRAGEDVAGWTSTQTLVLAGGHTLGVILQA
+VILFLPLRGLGLGMRPRFGWKGIGLRETGRIAGYTLVTMMVTNVVLLLCQRYVTSATEAR
+DRGELRIPGTEAWSTEMAQAAIPGVAAYNMAMLIAVLPHSVFVLSLATVLFNRLARAMTR
+QDMPAVRRTTAQGLRAFTVPLMFSLAGIVVLAGPLGRVFGSTAETSMVAGIAVGAVLLAL
+ALSIPFRSGSFYLLRVFYAAEDAKVPMVVQVSSSLLMLLLSWAGAMLLPLWSMALWVAIA
+SSVSYVYQFALTHVLTVRRFGDYGFASVLRAHGQTGLAALAAAAAGAVVVWLLGGYTGGF
+AWETIVTALITCAVAAAVMAPVYVVTLKLLRFPELDDALRPVVSRVPALGRLLRVG
+>3_371
+MSSRTAPRRALPADDAPRPKEVEDVVLPASDPEAPAQAQEEVPEGERRAGRSTAIMAAGT
+MISRVLGFVRAALLTIAIGTTVGTVADIFEVANSLPNVIYLLLVGGVFNVVLVPQLIKHA
+KDADRGADYTSRLMTLAVLVMLAATVLVTAAAAPLMAALTRGWSPEMLQLGTVFALWCLP
+QMFFYGMYALVGQILNANGRFGAYMWAPVLNNVVAIAAIGLYLVMFGRYSGGDLLGRWTP
+EQTLVLAGGHTLGVILQALILFLPLRGLGLGLRPRFGWRGMGLRHTGRIAGYTLFTMAAS
+NIVLLLSHRYINGASAAREDPSVRVPGTEGWDPAMADALIPGLTAYNQAMLISVLPHSVF
+VLSLATVLFNKLARSMAAGDHAAVRETTARGLRTFAAPIMFSLAGVVVLAGPLGRLFGST
+AESAQVTGMAVGAVILLMSLSMPFRSGSFYLLRVFYAAESARIPMVVQVTTSLLTLAVTA
+AGAYLLPLWAITYWAALASVVSHAFQFFFAHVLAVRRFGDYGFTHVLAAYATTGAAGVVA
+GAAGAVVAWLLGAYSGGWAWGSILSALVTCAVVGLVMAPVYVVALRVLRFPELASAAAPL
+ARRVPALGRLLGAR
+>4_2182
+MDPADETPEGERRAGRSTAIMASGTLLSRVLGLVRATLVTVAIGLSADMADIFEIANSLP
+NVIYLLLVGGVFNVVLVPQLIKHARDADRGADYTSRLMTLGTLVMLAGTVVVMLAAAPLM
+TALTRGWSPEKLEMATVFALWCLPQVFFYGMYALVGQVLNANGRFGAYMWAPVLNNVVAI
+GAIVLYLGMFGAYRAGDDLAGWTTAQTVVLAGGHTLGVVLQAVILFLPLRGLGLGLRPRF
+GWKGIGLRDTGRIAGYTLVTMVATNVVLLLCQRYVTSATEARDRGELRIPGTETWSAEMA
+QAAIPGVAAYNMAMLMAVLPHSVFVLSLATVLFNRLARAMGRQDMSAVRRTTAQGLRAFT
+VPLMFCLAGVVVLAGPLGRVFGSTAETAMVAGIAVGSVLLALALSIPFRSGSFYLLRVFY
+AAEDAKVPMVVQVSGSLLMLLLSWAGAMLLPLWSMALWVAFASSVSYVYQFVLTHVLTVR
+RFGDYGLASVLRAHVQTGLAALAAAAAGAVVVWLLGGYTGGFAWNSIGTALLTCAAAAVA
+MGPVYLVVLRAMRFPELDDALRPLVARVPALGRLLRVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001753.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001753.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21bf49c18502cbba0444a30d75f45708040ef314
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001753.fa
@@ -0,0 +1,29 @@
+>0_2246
+MTERGSAYERRPGLDPQDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVAARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>1_1950
+MTEQGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
+>2_411
+MPEQASPYERRPGLDPKERGDRPAPVGQPAPPLIDALRPAAVELFGEDLPRAERYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELIPEGALVADVGSGAGLPGLCLALARPDCR
+FLLIEPLERRVEWLDMVVEDLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGDGQLLAIKGRAAADEIAAARKVLRKYGGDEPEILTVGEGLLPETTTVVRVSARA
+R
+>3_365
+MSAPQLTAELRPAAEDLFGEALPLAERYVDHLATTGIEWGLLGPREVPRLWGRHVLNCAV
+VARLLPEGSLVADVGSGAGLPGLCLALARPDCRFTLIEPLERRVAWLEMVIADLGLTNVE
+VVRGRSEQVADEIQVDIVTARAVSALKTLLPLTMPLLRSSGHLLAIKGRSAAEEITAAQK
+PLRKYGGGDPEIVTVGEGLLPEPTTVVRVPARRAR
+>4_2188
+MTERGSAYERRPGLDPRDRGDRPAPVGQPAPPLTDALRPAAVELFGEALPRAEAYVAHLA
+DTGIEWGLIGPREAPRLWERHVLNCAVVEELLPQGALVADVGSGAGLPGLCLALARPDCQ
+FLLIEPLERRVEWLDMVVADLGLENVDVIRGRAEQVSGNLDVDVVTARAVSALKTLVPLT
+MPMLQGAGELLAIKGRSAADEIAAARKVLRKYGGAEPEILTVGEGLLPETTTVVRVSARP
+R
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001759.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001759.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3c9961d5157864a3a26d24bb7f85dc6c1a8d0813
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001759.fa
@@ -0,0 +1,43 @@
+>1_193
+MTVESVDVSVIIPMHNGGELIHEQLDALAAQRTDLNWEVIVGDNRSTDGSPDAVRARADS
+FPVPLAVVDAFRVQGASHARNAAAAAARGEVLAMCDADDRVAPDWVEQAFRGVREIAPMV
+AGANRLLSHPQRPDAPLLNPRILHGRGAQTCNAAVRRDVFLASGGFDESLPPYGVEDSDL
+SARVLAAGHTIAPHPGLVLYFRETTGLKAKLRKIHSSGQAEAVLWSRGHEAQGTPLAESQ
+FVVALAALPADAVRTARARELRSLPKWTLREAAVRTGRWRGYRRWVKTGKAGEPRLPFLD
+GRGGAA
+>1_223
+MFADADDVVSRWWVRNGARAFESSDLWSGGAPFMTDEQMREGVEGARRAFDDSDEWHAPV
+PGDLRNAFPVLMGGDFGVTREVFERVGGFDHSLGAVYEDNDFAVRAHLKGIRVDEAAAVR
+IAFRGKWDMRFRTRLVRRSAKAHSLVTTRYELGRQSHFPNPWVEFVRTGASAALMTLGCK
+TPDWEGVRLRAQTAAGAAAGRVEYRWMRRGPQPQIGLGYRRADSSPFSQADAAGAGENSE
+EVLAASVVIPARNAEGWIGEQLDSLAAQCDAPLFEVVVADNGSYDRTAQIALSHPTPFQV
+RVVDASGVPSASHARNVGARLARGHVLLFCDADDFVGDRWAGELYRAVTSGPQLVARGVL
+EHSRFNDVDVLAAYRIDPAQDLHDTEDSPRIERVSDGFAGYLATVPGNNFAIRRDDYLKL
+GGMDPAYPGGSEETDFVWRAQEAGFTVVQAAGAVVYYRLRTTPAAIFRQQRNQQRGRMYL
+WTRYRGRGMSGPSVKASVFAISRHMPMWPFLRRDRGRALAWAYTVGAHVGALEGMARYRR
+PALLRSRRPGSDGGTAA
+>2_2379
+MSTRARSSSTPTAPSVSVVIPVYNGAPTLPLQLEALHTQVGAPAFEVVVVDNRSTDDLDG
+AVRPFMESGPPLRVVRADGHQGSSYARNRGIAAARAPYVMFCDADDVVSRHWVATGAAAF
+ATAPIWTGSVTHLPAAVFEQGLEAVRDLLGDGPRPQDGPGREVPGPFPVLMGGDFGASRE
+LLVAVGGFDQSFPHAGDDNDLAFRVLRAGHRLVEMPQVRVASRGKTSLQTAHRIAFRSAR
+AHALLADRYGLWERSRATTWASEPVRCLGAAVKMAAHPTRADWRGLACRTAMASGTLAGA
+VEYHLLRRRPAPQVGLGLDPDDTALPGEEPQGAGGPGHPELVSVIIPAYNAEAYIAEQIE
+SLAVQVDAPEFEVIVADNGSTDRTASTAREAAERWGLTLTVVDARGPASASHARNVGAMA
+AAGGVLLFCDADDFVGPEWVRELAAAVRSREDALAVGTLLHRRFNDAAVLAAYGIPPEAG
+EPRTDAAGYPVVHGGFAGHLPTVAGNDFGVRRSLYLAVGGMDSSFPGGSEETDFSWRAQR
+RGAVVVHAPRAIVHYRLRSTPQTVFRQQRIQQVGRMLLWMRHRGDGMSGPSWRVSVTEVA
+RHLPAYLLVRERAARLRHARIAGGHLGALQGMVRYRLLKRIPPRRLVDGSSVPRA
+>3_2262
+MNQAVSVVIPCHNAAGSMQRQVDALLPQLEETDELLLVENRSADGTRRIAEEAALRDARV
+RVLNAPDKAGANHARNIGAARAHNPIILFCDADDVVHSGWVRSLRQVLGTDGIAGGSATP
+VDEEGRRLGPDLGLHETFGGPAYPLGATMGVRREVLETIGGFDESYAGGHDETDLAWRAA
+RAGWPTHFVPEARIDYVQRPDARSALQQRRLYARTSIQVWVQNPDLVDQSAVSLRGALNG
+VRLGLPLGIKMIRGTATARDAARWGWALGVLEGHLRYRVLGRPPARVAPPIPPAPHPAEP
+NRPCA
+>4_493
+MSRPVSVIIPCHNAAAWVDRQISAVLAQLRADDELVLVDNRSTDTTYERLEAAAAGDRRV
+RTVSAPERPGANHARNVGIAAARNPLLLFCDADDLVTGGWVEAFRAALQNAGITGGAATP
+VDADGCRIGSDLGLHEIFGGPAYPLGACMAIRKDVVNAVGGFDESFAGGHDETDLAWRAE
+RAGWPTAFVPDARIDYLQRPDAAATVRQRRAYARTSIQLWARHPETVNPHGVSVKGAVRG
+VLRGLPNAVRVLRGRASADQAAQWGWSLGLLEGHLRYRILGKPPAAHTPRPDASA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001762.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001762.fa
new file mode 100644
index 0000000000000000000000000000000000000000..de117534fc1be471b0b4c59fd935fc94315b2c98
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001762.fa
@@ -0,0 +1,30 @@
+>1_1808
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIIGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGGLIGVPLVKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV
+>2_598
+MAWLAVVLAVAVGLLLGLMGGGGSILMVPLLTYVAGLDPKEAIAGSLFVVGVTSLVSVGL
+HARAGNVRWRTGLVFGLAGMVGAALGGVVGGFLPGTVLLIAFAVMMLVTAWAMIRPKRPT
+AAPAEGGHAPGRALGRIVLDGVVVGFVTGIVGAGGGFLVVPALVLLAGLPMSAAVGTSLL
+VIALKSFAGLGGYLTSVTLDWPFLLAVTGVAVLGALIGAALVNRVPDKALEKGFGWFVLA
+MGVVMLVTELVGLLA
+>2_2599
+MSGTLILTLVLAVGVGLALGTLGGGGSILTVPLLTYIAGMPPKEAIAASLLIVGVTSLSS
+LVVHARHRRVRWRTGLIFGAAGMVGAFAGGLIGGQLPGAVLMVAFAIMMIATAIAMVTRK
+PRRDTDQPTADAGTERAHSLPMLRTMLEGIVVGLITGIVGAGGGFLVVPALVLLGGLSMP
+VAVGTSLLVIAMKSFAGLAGYLTTVTLDWPLVAAVTAMAVLGALLGARLSGRIPADALQK
+VFGVFVLLTGTLVLVIELPPAWAIAAGGLGLITVVLVLVCRLTALNCPFGLARPTPG
+>3_523
+MVPLALLVVLAAVVGLLLGLMGGGGSILTVPLLTLTAGMDPQEAIAGSLVMVGASSLVAA
+LVHATRGAVAWRTGLTFGAASMVGALAGGFVGRDLPGPVLMVGFAVIMLISAVKMIRPRR
+KGAGHDDAAPVPLGRVLLQGVGVGLITGVVGAGGGFLIVPALVLLARLPMPVAVGTSLLV
+IAMNSAMGLVSQLGATALDWAVLGPMAAAAAAAGVVGVVLAHRVPAAALKRGFGWFVLAM
+GVLILAQQALELLP
+>4_2028
+MWIVLALALVVGLLLGLMGGGGSILMVPLLTYVAGLEPKQAIAGSLFVVGVTSLVSVLLH
+SRHGTVRWRTGLIFGAASMVGALLGGVVGGFLPGTLLLIAFAVMMLFTAWAMIRPKKTQP
+AAAPSVEASADVEPRRHPLGKILLEGVVVGFVTGIVGAGGGFLVVPALVLLGGLPMSAAV
+GTSLLVIAMKSFAGLGGYLTSVTLPWDLLLWVTGVAVVGALIGVPLMKRVPEKALKKGFG
+WFVLAMGLVILVRELIGLLV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001764.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001764.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4bc1d15308c5dc57a3d69ed01e0e0ff76d76bb14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001764.fa
@@ -0,0 +1,35 @@
+>1_2079
+MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA
+ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF
+YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS
+>2_81
+MTALASRPGAASRASRSAPVSPASRSTRRTHRRRTLVGAGTVLRRLAGAVGVVWATATLT
+FLMQFLLPGDRATLVFNLRAGQAQPRTAEELAPLNALFGFQDPVLVQYLHFLGGLLRGDL
+GTSYVTFEPVTTVIGDQLAPTLLLTGASIAIAWAVALVLLVATVRRARWVSGLASAVEAL
+LAALPHYWLGVILLVVFALGLGLFPVVGGTGPAALVLPALTMGLPLAGYLAQTMRSEYAS
+VLDQPFILTARTRGQSDAGIRVRHALRHALLPGLSLTGWAVGAQFSAAVIAEGVFSRPGI
+GGVLVDAANGRDLPVVCGVVVLIAIVYVLANLAVDVLYTVVDPRLRSAR
+>2_254
+MLRLIGKRLLLLIPTLFGLSVLLFLWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYTTYMGRLLRGDFGTSTMTNRPVLEEFADRFPATLELSLFAIVFAVAIGIPLGYWA
+ARHVGRWQDNIAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRLDATHYTNF
+YVWDGISTGEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQNADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALIYSLINLVVDVSYGLIDPRVRVS
+>3_125
+MARRILLRLALALAVLLGAYTAAFLILYVMPGDPVTAMAAGGLEAGAISDADLQALRAEH
+GLDRPLPVQYLSQLAAAVTGDLGTSVQTGQPVTEAILDRLPTTLRLAWAALLVAVVAGPA
+IALVAAGTRRRWVRATASAIPALGAALPTFWTGLLLVQVFSFGLGWLPALGDDGLAGLVM
+PALTLGLPLSALIAQVMLRALDESGTQEYVETALASGQSRRRVLITHMLPNAALPTLAML
+GVITGNVVAGAVVVETVFSRPGVGQLTVQAVTAQDLPVVLGVVLLSSLVFVLVTLTVDLL
+SPLLDPRVGPAGAV
+>4_120
+MLRLIGKRLLLLIPTLFGLSVLLFVWVRSLPGGPATALLGDRATPEAVARVNAAYGFDKP
+LLEQYVTYMGRLLRGDFGTSIMTNRPVVEEFADRFPATLELSIFAIVFAVVIGIPLGYWA
+ARHVGRWQDDVAVVLSLIGVVVPVFFLAFILKWVFAVKLGWLPTDGRQDPRIDATHYTNF
+YVWDGIITAEWDAALNALTHLVLPGIALGTIPLAIIARITRASVLDVQDADFVRTARAKG
+LAPRLIRDRFIMRNALLPVSTTLGLQLGLLISGAVLTETVFAFNGIGRFLAQAIFQLDFP
+VLQGFIIFIALLYSLINLVVDVSYGLIDPRVRVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001766.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001766.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c60a4914c6ffe0b6f80c4407161013f15710867
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001766.fa
@@ -0,0 +1,17 @@
+>1_2154
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
+>2_496
+MSLRLSHTTWDALDPHAVAEFWRELMGWEVTEPEAYELGSDECYLVTPHGYTILFYRVPD
+AKRVKNRAHMDLAVDDGTRDEEVERALGMGATMVDDRRGDLGWAVLADPEGNEFCILDI
+>2_510
+MALKWYTLVVDCRDPQAQAHWWARALDWEVVHDTPEEAVAVPKGVGEEPVADPDEWRARG
+QGLVFVPVPEGKTVKNRLHIDLAPHTSQDRDAEIARLEELGATRVDVGQDEEEVTWTVLA
+DPEGNEFCVLSSRDS
+>3_438
+MSLRLSHTTWDALDPYAVAEFWRELMGWDVAEPDSYAPGSDECYLATAEGYTVLFYRVPD
+AKRVKNRAHMDLMTAGTTRDEEVERALGLGASMVDDRRGDLGWAVLADPEGNEFCILDTG
+D
+>4_210
+MSLRLSHTTWDALDPHAIAEFWRALLGWEVDEPHLYRPGSDECSLVGPDGQVVLFFRVPD
+AKRVKNRAHMDLRAAAGSTRDAEIERALALGAAMVDDRRVDLGWAVLADPEGNEFCILDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df81dd5dd1ae878be2c68fc0f4cd00c039098a0e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001781.fa
@@ -0,0 +1,12 @@
+>0_124
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHWAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>1_2089
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
+>2_243
+MTSTPYEDGIDQRELQEDLLAEPDSATDPGPQDGRDGQPVRGSSDDPQHWAGDGRAEDSL
+RNAESEAMHIQQDAEDRTRADEGDVEIL
+>4_132
+MTDVPFEDREDERELETDLLADPNAAGDPEPEDGRDGQPVRGGSDDPQHRAGEGRAPDSL
+RNAESAAMHIEEDAQDRTRADEGDVEIL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001784.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001784.fa
new file mode 100644
index 0000000000000000000000000000000000000000..84d0a5e07df0562c353531650d16960a0ed6805a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001784.fa
@@ -0,0 +1,18 @@
+>0_147
+MSGVGNEREWRWRIGVASPLVGSAGVFAGLRQDLGLGWGLTLVAVTALGAMLALRGVHHR
+VEAEQARRNVFDAGAGSTAWVMLLMGAAVIPGLVLNAIDDAGVRAVVAGLLGAVVEMQRR
+VHTTRGELFAYQAGSGRRENWVSRWAPPRAPGIARNVGAVAALAGWLWRVMWRADRAGGS
+AHDAWRDPSPQTTDKGSGPSPSLAGARLSVWLAPLYGGVLSELSGGLQARGQEGAASEAH
+VPQADPSPGQRPTAGRRNRRRDRVHPAQQNRCERSNTPTQQSGPPCAATGP
+>1_2112
+MSRVGNEREWRWRIGVAPALVGSAGVFAGLRQDLGLGWGLTLVAVTALGAMLALRGVHHR
+VEAEQARRNVFDAGAGSTAWVMLLMGAAVIPGLVLNAIDDAGVRAVVAGLLGAVLAAAAH
+GILAATTTLEEQPRPEPVPLDRRRR
+>3_1439
+MDAVAQNTGRRVGEPLTERSDAGTGHTAASQGRDGTLRGDAPAWRAAGVGAAFGLASVVC
+SLQDHLAEWSAIGGAAAFMALGLLSMTGLRFVVDQEKARRTVFYAGERQGAWFLLNFLGI
+FQIPRFLISGIADPTGLVLAAAGLGIVVAVANQALVSRYMTGRRQPDPEPVPLG
+>4_160
+MCQHGAVSRVGNEREWRWRIGVASALVGSAGVFAGLRQDLGLGWGLTLVASTALGAMLAL
+RGVHHRVEAERARRNVFYAGAGSTAWVMLLMGAAVIPGLVLNVIDDAGVRAVGAGVLGAT
+LAAAAHGILAATTTLEEQPRPEPVPLDRRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001789.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001789.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88c161017df79f5b648fdb9a0aa33ffe6a062e6b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001789.fa
@@ -0,0 +1,18 @@
+>0_209
+MTANHSRHTAAADGQGAAAEHAGTGTATTDPRRDTRSRWGCSSRLGGGTGRLMGVSLAVG
+VVGALGLGSAAWATTVAAGHADSLAWIAAGAMALNGLLFGLLLTWLALVDRHSIRGADTN
+PEESIEGRWYEKATSGAFHDTLVVVGLGAAILSFGGYVISPAAVGAALFVLMGCAAAIRY
+QIQKRRG
+>1_2153
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG
+>2_158
+MNTTADPRSRSASGPERAASTSAAATPAGSAAPSAWGRSARLGGGTGRLVVVSLVFGVLL
+AAMLGVIAYGLAGTADPADPRRPWVLGLVVASGALPVLAGTVWMLLVDRATIKGAVRDPE
+ESIESRWYDAAAGGAFHDLLVVLGLGTFVVSMTGWTAELSLVGAGLVLFMMADVAIRYRV
+QKRRG
+>4_209
+MATTPHTTTDLARDRRPRWGRSARLGGGSGRLILVSLVAGVVIALLIGAASYGLASSQGD
+AGPRFPAVTGAVMAASALPVGAALAWLFLVDRTTLRGAVRDTEETIEGRWLEKAQSGAFG
+DLLVVLGLGTFVVALAGWQPSLPLVGAGLLLFAGASVAVRYALQKRRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001790.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001790.fa
new file mode 100644
index 0000000000000000000000000000000000000000..99a91a07cb14b777c8adee6db42d70f75ca38e11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001790.fa
@@ -0,0 +1,48 @@
+>0_211
+MTRTVPARRRTTLAAAVAAVSLAVTAAAPALSAPGNGNGNGNGNGSASQGQARSNDLSAT
+RGNKVNDAAALAPHLVGQTLDWEACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGH
+TITLRVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRG
+VGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKT
+SYIGYSYGTWLGSWYQRVFPQHTHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLP
+YVARHDEIFGLGDNPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAA
+YIRIMESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAA
+TQAGDAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQT
+SMPAQPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTEC
+VDAPIRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRI
+THDAIERQLIDSRAVTPDVEAFLED
+>1_2156
+MTRTVPARRRTTLAAAVAAVSLAVAAAAPALSAPGNGNGNGSASQGQARSNDLSATRGNK
+VNDAAALAPHLVGQTLDWDACDFGSERLNARFNAIPGTACADVTVPRDWKNPEDGHTITL
+RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS
+TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG
+YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR
+HDEIFGLGDDPMQIRQRWEDVGGTRTQLGMIVAGSFLLPAMYDTSQYLDAGSVIAAYIRI
+MESEAAATDPAGQRTQIERILAEARASLPAEERDSFDRFAARGLETVGEREQLVAATQAG
+DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS
+QPGGKGAPNTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTECVDAP
+IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA
+IERQLIDSRAVTPDVEAFLED
+>2_151
+MTRTAPTRRRTTLAAAVAAAAALTISAAAPALSAPGNGNGNGNGQSSASQGQARSNDLST
+TRGNQVNDAAALAPHLLDQELAWEACDFGSPALNTRFGAIPGTACADVTVPRDWKDPQDG
+HTITVRVAKTETSKGNPDRQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPR
+GVGQSTALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVMGEEK
+TSYIGYSYGTWLGSWYQRVFPQHAHRFLLDSAVDVSRDGLQTTWNLQPRSRDRQFQDMML
+PYVARQDAVYGLGTDPMEIRQRWEDAGGTRTILGQIVAGSYLLPAMYSTSQYPMAASMIA
+AFISIMETETAATDEAGMQAQLERITAEARATVPAADRAAFDRFIEQGSEVVAERDELAA
+AVRTGQPVTFSGTFSAIRCQDGQWNTSEGYWTSWVNDLGRKAPWIAAFMGPSECMYWPAQ
+TSMPSQPGGKDTPSAVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYRTE
+CVDAPIRDYFLTGEMPAEKSLCEAHPLPGETQTHQVAGTPTHKGDIKISMRTDAVREANR
+ITLDAIERQLLDSRAVTPDVEAFLER
+>4_212
+MTRTVPARRRTTLAAAVAAVSLAITAAAPALSAPGNGKGNGSASQGQARSNDLSATRGNK
+VNDAAALAPHLVGQTLDWEACDFGSESLNARFNAIPGTACADVTVPRDWKNPEDGHTITL
+RVAKTETSKGNPERQGIALVNPGGPGGSGLPWGPAMAERAPELAEQYDFIGFDPRGVGQS
+TALECTYTPNPEHDVWQDTKAQVDACLENELTPYITTEQTVYDMDFIRAVLGEEKTSYIG
+YSYGTWLGSWYQRVFPQHAHRFLLDSAVDISRDGLQTTWDLQPRSRDRQFQDAMLPYVAR
+HDEIFGLGDDPMQIRQRWEDGGGTRTQLGMIVAGSFLLPAMYDTSQYMSAGAVIAAYIRI
+MESEAAATDPAGQRAQIERILAEARASLPTEERDSFDRFADRGLETVGEREQLIAATQAG
+DAVTFEGAFSAIRCQDGQWNTSQGYWTSWVDDLGRKAPWIGVLMGPSECMYWPAQTSMPS
+QPGGKGAPSTVIVQSELDAATPYEGGHRAAGVLRNTSLISVDNEGTHGLFPYGTECVDAP
+IRDYFLTGAQPAEKSLCDAVPLPLETQPVQVAGTPTHKGDIKISMRTDAVREANRITHDA
+IERQLIDSRAVTPDVEAFLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001794.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001794.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46e1e84b0a35acfe662933f6b8b66f102516919c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001794.fa
@@ -0,0 +1,23 @@
+>0_243
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLVQDLQDA
+>1_2206
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RRPRRP
+>2_109
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADATVLHAPG
+LVSTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLAFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDLGVELGKILYRNAPGTAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLRDAWLT
+RRPRRR
+>4_243
+MLNLCAPERTVRRNTHLALVLTAIAGILNSVGFVAVATYTSHMTGIVASMADAAVLHAPG
+LVGTGLLALAMFILGAVVCALVFNWGRVNGLRSRYANILLLEGVGMLVFGLLAEHVRDAH
+RPLVVVAVLCFTMGLQNALITRIGAWPIRTTHVTGMVTDIGVELGKILYRNGPGAAAPVV
+GEPRRVGLLALLVALFFLGGVAGAAGYLWLGFEVVIPVAGVLLLIAHRPLIQDLQDAWLT
+RKPRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001797.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001797.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ceb644eba04b53f20c00b17e5235e10d055546e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001797.fa
@@ -0,0 +1,80 @@
+>0_264
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSPVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARRIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILARDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>1_2230
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
+>2_74
+MDRDAVNALAEEYSRGIGQALSMGVAAEPEAQLTVPFAAFLSRFAQEVELGRLDLLREAQ
+LDGVRPDFAAALDGRPCGWIELKAPGHTVVGERWRGREKSQWALLSQLDALLVSNGELLA
+LYVAGAPVETCALPVDGAAGWDPDRLRRVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLAEGLEHSYDSVVEAKAAWDHTMQHTTSPEEFSGDVAQVVAYSMAIAGLSGQADRNADG
+VVSLEEAKHALETAHRNVLAASLGPILGIPALMQHIAPEVGAITRLVAGMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPEARSRAGVYYTPISVVECQVRVVDALLRERFGQNLGFGAPS
+VVTLDPATGSGTYPLAIIDRAESVAREERGDAGAKQVAMNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMPTGLFGDARVLAEAAESARRVKRDQQ
+ITVAIGNPPYDRVTSGTGGWVEQGSGSGDALFDDVIKPAQDSGVIFSAQASLYNLYVYFW
+RWAIWKAFQQDPKDHAVISFITASSWLTGPAFVGLRRLAQATASEIWVMDLGGEGRGARK
+EENVFDIQSPVAIVTLVRTGKASREAKVFYRRFRGSRAEKFTALDRIQRLDAADGWEQIA
+APGGAPFMPASGGEDWTAMPQLADLFPWQQPGIMYNRAWPVASDQNTLRRRWQELLSDDD
+ADARAGKYVTGNSGRTIHTAVAGLPTLASLPADAEPRPIVRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFLVSPKTARINGGPAVTVSTAVPDKHHYVGSFGGKDVIPLYRDAA
+AAEPNVTVGLLELLADRLGHDVTPEDLAAYVMAVAAHDGYAQTFDEALETSPVRIPFTAD
+ASLWDAAVALGERLLWLQTYGERFTSADRPRGRVPRVPGLGWSEAVTHIPADTASLSYDA
+ASRELRVGDGVVTGVSPEVRAFSVSGMNIVDKWLGARTAKGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVALGDQQAELLAAILAGELITAADLPVPTAAERKVPKTIKR
+GVSPHQEGLL
+>4_262
+MIDAPLAQLAETYARDVRLASTSGVSAEPEAQLTVPVSEFLRAFSSVTGIGDLSLLREAQ
+LDGVRPDFAALIDGRPCGWVELKAPGHTVIGEKWRGREKGQWDLLSQLDALLVSNGDEIA
+LYVSGSLVDTAFLPVDGVAGWDADRLRTVLEQFTLAQPRPITRVSQLADRLAPLARFLRE
+RLQEGLSNNYRSVREAKAAWDHTVHHTTTDAQFAGDVAQVVAYSMAIAGLSGQADRNADG
+VVTLEEAKHALETAHRNVLAASLGPIIGIPALMEYIAPEVGAIMRLVSSMDVAAIERSTD
+SRGEPWLWFYEDFLQRYDPAARNRAGVYYTPISVVQCQVRVVDALLRERFGQTLGFGAPS
+VVTLDPATGSGTYPLAVIDRAEAAAREERGPAGVAQVAKNLTKNLLAFELLPGPYSVAHL
+RIGQRLAEAQGHAFQAEEIGVYLTDTLEDPSAGMAEGLFGDARVLAEAAEAARQIKRDRR
+ITVAIGNPPYDRVTSGTGGWVEHGDGEDALFDDVIGPAQEQGVIFSAQASLYNLYVYFWR
+WAIWKAFQQDPGDQAIISFITASSWLTGPAFVGLRDLARRTASEIWVMDLGGEGRGARQE
+ENVFDIQTPVAIVTLVRTGKAAREASVYYRRFRGTRAEKFAALDEVARLDPDDGTWECLP
+GGAGDPLAPASGGEDWAAMPALADLFPWQQPGIKYNRAWPVAPDQDTLQRRWRELLADPS
+ADARAEKYVTGHSGRTIHTAVSGLTPLAALPADAEHRPITRVAWRSFDRQWTFDDPRLIN
+LERPALWQALSDRQLFFVSPKTARISGGPAVTVATAVPDLHYFVGSYGGKDVIPLYRDAE
+AAQPNVTGGLLPLLGERYGREVTPEDLAAYVMGIAGHDAYVQRFDEALEGSPVRVPLTVD
+PALFARAVELGKRLLWLQTYGERFTGVDRPAGRVPRIPGLGWEAPVTALPASPRAVSYDP
+ATQRLKVGDGVVTGVSPEVRAFAVSGMNILDKWLGARTATGIGRAAGKAATPLDRIRPTE
+WADEWNDELLDLLRVLTETVSLGGDQADLLDEILAGDLIPANELPEPTPAERKVPKTIKR
+DFSTAQEEMF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001800.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001800.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fd6970866d17bf1497ae2d913a1494849de393b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001800.fa
@@ -0,0 +1,16 @@
+>0_277
+MSIDAAPPEDGGTAPTGTSPAPEALEDALPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+YLPVTEVRRDLFDDSSPRGAEWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDTLLAGGGRDYMPPDDYGFSRRFAWVGDRFGVTWQLNAA
+>1_2250
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLMFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDDSSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAVHDALLAGGGRDYMPPDDDGFSRRFAWVGDRFGVTWQLNAA
+>2_59
+MSETTTDPGLPDDVGVDAGADPTGTAPAPAALEESMPHPSDPSVTPFLMFEGDAGAAMDA
+YLSVFVEHLPVTEVRRDLFDGSSPRGAEWAGKVLHGELEVAGQRLRFFDSFTSHGFTFTP
+AISLFVELPDPTAVDAVHDALIAGGGQDYMPPGDYGFSRRFAWVGDRFGVTWQLNAA
+>4_283
+MSIDAAPPEDVGTAPTGTSPAPEALEDSLPHPSDPSVTPFLLFEGDAGAAMDAYLTAFVE
+HLPVTEVRRDLFDESSPRGAAWAGKVLHGELEIAGQRLRFFDSFTPHGFTFTPAISLFVE
+LPDATAVDAIHDALLAGGGRDCMPPDDDGFSRRFAWVGDRFGVTWQLNAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001806.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001806.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d42314e937225ff77931284328a3000fa9a5ee34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001806.fa
@@ -0,0 +1,31 @@
+>0_348
+MSTTPTPPVSHGSAPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGKPGSLLSVE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFELPTAGRVRARPRTRATVPGAADAVPAQTAEPASTTAPLPVVEP
+ASPPQPAAGPTPAAEPAAGAPARVRAPRPRPRHAD
+>1_73
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
+>2_2342
+MDAIRGTAILLMLLLHATMIPAVVGGMEPVPWLVAITDATAPFRMPVLMFLSGMLLDRAL
+AKPAKRYLSGKFRVLLWSYVVWAVVYFMVMGRPGELFRPWTWVQTLYLWFLAFLLAYYVL
+ALVLRRIPAIVVAVAALVPHVVLVGAERGFLARFFLYMTVFFAGAAFTRFLAARPGILEP
+RRRDGHLLVGLPLLVVGVVAIRSGGALPHPAGAVVGAVAAVAVAMGLVLVVQALVPRPRG
+PLVRVGQQSLVYYCVHYPVMVLVVRLGERLSWDVVVVSLVSLVAAVVVCAVIAEGRDRVP
+VLDALFRAPAPPRRRRPVTH
+>4_355
+MSTTPTPPMSHGSTPSRMTWMDAMRGFAVLLVMFTHTYTMPQGLDATFSSVAFANVVQVF
+QSWRMPMLVFLSGVLLPRSVSKPLGTYYRGKAERILWPFLVWMVVLALATGRPGSLLSGE
+FWRGGAWHLWFLWVLMLCYLIGPVIRRVPALVVAAVLFVLLLEFVSGPRDWVRPLYWGVY
+FFLGAASARLLPRIRTAPAALGVIAVILMVLTVTATRTGALVVAERQPWSVFAALPGILV
+VLWLGPRLPRLPFLEFCGRRSMVLYVAHMPVLILAVAAFRDLAAVRPVDFYVAIASFTFL
+VPLALALGYRRVRWLFEFPTAGRGRERPRTRAAVPEAADAVPAQTAEPAPTTAPLPVVEP
+ASEPQSTAGPAPATEPASDAPAQVPRPRPRHAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001807.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001807.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a2aca03fdabcc07ed6a264ba978229c26de038a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001807.fa
@@ -0,0 +1,28 @@
+>0_366
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRASHPPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
+>1_99
+MAPWPPTRSRRPFPQVTEGGGAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPEASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYAGRWPHLHFEVFP
+DKASITDATNNVLTSQIAMPAEQSAQVYATSAYDGSTENFAQVSLETDNVLSDGYETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPARP
+>3_2385
+MAPWLPTRSRRPFPQVTEGGEAPAVTPTFEGRAFHRPAEDVEDQGAAFDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSSSTSASAGSSSPAASSSAASASPSATLTEMVTETA
+GPYPGDGSNGPDVLDASGIERSDLTTSIDTGTVAEGVPLTVTMNVIDMANGDAAMTGAAV
+YLWHADALGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFPD
+KASITDATNNVLTSQIAMPEEQSSQVYATSAYDGSTANFAKVSLETDNVFSDGYETQLPQ
+ITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPARP
+>4_372
+MAPWLPTRSRRPFPQVTEAGEVPAVTPTFEGRAFHHPAEDVEDQGAALDVGTLVSRRNAL
+GIFGAGAGALVLAACGVQEGASSSSGSTSASAGSSSPAASSSSAASASPSATLTEMVTET
+AGPYPGDGSNGPDVLDASGIERSDLTTSIDTGTAAEGVPLTVTMNVIDMANGDAAMTGAA
+VYLWHADAQGRYSMYSDGITEETYLRGVQVVGDDGTVTFTTVWPGCYDGRWPHLHFEVFP
+DKASITDATNNVPTSQIAMPEEQSAQVYATSAYDGSTENFADVSLETDNVFSDGNETQLP
+QITGSVEKGFAITIDVPIDTTTEQEQGGMGGPGGGQPPAGGEGGQPPAQP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001808.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001808.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f44aa68008876d87466c4bf8222306bf2681899c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001808.fa
@@ -0,0 +1,15 @@
+>0_369
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>1_102
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARPIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
+>2_2510
+MAAVRALRTLLAEGYATPEAPVAVTGAGWPDYDARVLPGLAAAQELAGVDVDYLRHVDRV
+SDAGIDAASLADLGTLFTYVLRGERFSEGHIGAALANGKVGRMLDRLAELVPQVR
+>4_375
+MTEHPLPTPDDDATLTGPQTPTPQRVAAVRALRELLAAGYGTEARQIASYGAPAPGTLGG
+VYPDYDDRVFPGLVAAQELAGIDVDYLRNVDRVSEAGIAEASLADLGTLFTYLVRGERFA
+DGHVAAAIENGKVGRMLDRLTALVPEIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001809.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001809.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05145de667064a474caf39fb09697f136771c189
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001809.fa
@@ -0,0 +1,28 @@
+>0_374
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSGVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>1_107
+MDATPHARPAEPGPLPDPAEPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
+>3_2377
+MDTAANPALTTDLRSPRRVAGKDVRPVGLGCMNLVHGYSGFLSEREAVDLVVGVLADGTD
+HLDTATLYGGGLSEEYVGKALTRVGADVRDRVLLASKCGLSRDADRPIDGRPETLRAQVD
+ASLRRLGQDRIDLYYLHRLDPRVPVEESVGALAEAVAAGKIGAIGLSEVSGATLDRAATE
+HPVAAVQNEYSLATRNPEWGLLEACRRHGAALVAFSPVCRGLLTDAPPVVADLPDGDMRH
+AMPRFQGPAWEANLRLREEFASEAARLGVPAASLAVAWVLAQGADVVAIPGTTDPAHWRE
+DRGAEEVSLTLEDLARLDALVNHATVQGRRYSDAQQASVDTEDAPQQG
+>4_380
+MDATPHPRPAEPGPLPDPAAPRRLAGKDVHPVGLGCMNIVHGYSGFLDDDAAVDLLTRVL
+EDGTDHLDTATLYGGGRSEELVGRALARAGSDVRERVLLASKGGLVRDGQRRIDGRPETL
+RAHVDASLSRLGQDRIDLYYLHRLDPEVPVEESVGALAEAVTEGKIGAIGLSEVSAVTLT
+RAVAVHPIAAVQSEYSLATRNPEWGVLEACRRHGTAFVAFSPVSRGLLTDAPPRLGGLDA
+GDLRHRLPRFAEGHYEANLTLREALSAEAVRLGTSTAGLAVAWVLAQGKDVLAIPGTTSW
+EHWLEDRGAHEVRLTPADVARLDDLVNDATVAGPRYSESQQASIDTEAAPPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001815.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001815.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aceea5632c5cfaef7840cb9d1e0de846117d9cd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001815.fa
@@ -0,0 +1,12 @@
+>0_513
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAAHR
+>1_246
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR
+>2_2360
+MIRNGKAIDHSNVGGVWGSLIAFLVAYVAFLGSLYAMGFWTLENAWVPGLIALALAMVTF
+MIPQVFLGRSDTVDTAAIHTRPVAVEHPVSGAHAVETGAARRH
+>4_516
+MIRNGKAIDHSNVGGVWGSLIAFIVAFGAFLGCLYAMGFWSLESVWIPGLIALALATVAF
+MIPKAFLGRSDTVDTTAIHTRPVVEHAASGAHAVETGAAHR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001816.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001816.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4a26f9ac2030ba7d1172f11b9032f55665916f8e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001816.fa
@@ -0,0 +1,20 @@
+>0_545
+MDSRVNSGGVVGKVDNLTCLAGLVTTEDPARVRALRGTVLAVALLNGAYLVVEIILALGI
+GSVALVADSVDFFEDFAVNLLIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIG
+DPDPPAAGVLLGAAVGSLLVNLVCVALLARVRTDGGSLTRAAWLAARNDLVAGAVLIALS
+GITVLTASGWADIIVGVLLVLLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>1_278
+MNRAAVADRRRTRTLRGTVLAVALLNGAYLVVEIILAVGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKIGDPEPPAAGVLLGAAVGSLLV
+NIVCVVLLARVRVDGGSLTRAAWLAARNDLVAGVVLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD
+>3_2206
+MDAMTETSHPRPDPARVRALRGTVLAVSLLNLAYMLVEIGVALGIGSVSLVADSVDFFED
+FAVNMLIVIALGWPLARRARVGKVMAGIIVLPAIAALAMAAVKVGDPEPPATGPLFWTGV
+GSLLVNLVCVGLLARFRADGGSLTRAAWLAARNDLIAGIVLIALAGATALTASGWADIIV
+GVLLVVLNGGAAKEVWQAATEERLAAQALAGEFDDD
+>4_547
+MNEVPEADRRRTRALRGTVLAVALLNGAYLVVEIILALGIGSVALVADSVDFFEDFAVNL
+LIFVALGWTAARQAVIGKVMAGIIVLPAVAALVMAATKVGDPDPPAAGVLLGVAVGSILV
+NLVCVALLARVRTDGGSLTRAAWLAARNDLVAGVLLIALSGITVLTASGWADIIVGVLLV
+LLNGSAAKEIWEAATEEHLAAQALAGEVDDD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b3ec2c7fbbd6a568c3259e5461dc07a27948cfb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001828.fa
@@ -0,0 +1,22 @@
+>0_615
+MARPGDPGRECRRGLDVRIGTSGWIYKHGRGTFYPQGLRIADQLDHCTERDRVSRLRALP
+QRGPGPALRRIVLRRRARPWVGRLRELTGADAAGARPAHVSFYNDNHGHAAFNALTLRRM
+AEAEA
+>1_361
+MISGTLRLPRRVKARPGDPGRGYRRGMDVRIGTSGWTYRHWRGTFYPQGLRIADQLDHYT
+ERFRTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVH
+TLDLLGDHAGPLLLQLPAHLHRDDGRLAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+DGGPAGDAAGARPAYVYFNNDNHGHAAFNALTLRRMAETEA
+>3_2133
+MDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYTERFRTVELNGSHYRWPADSTVEAWRE
+RLPAGFEMAVKASRYLTHYRKLNEPQDWVERIVHTLDLLGDHAGPLLLQLPANLHRDDDR
+LAGFLGLLPERVRVAVEVQHESWLDEDVFDLLDRHGAGFVVSVIAGREPVLRATGRLAYV
+RFHNADPDWRYGGSFSDAELAPWVGRLRVLTGADNGGPAGDAAGARPAYVYFNNDNHGHA
+GFNALTLRRMAETGA
+>4_584
+MISGTLRLPRRIKARPGDPGRGYRRGMDVRIGTSGWTYKHWRGTFYPQGLRIADQLDHYT
+ERFGTVELNGSHYRWPADSTVEAWRERLPAGFEMAVKASRYLTHYRKLDEPQDWVQRIVH
+TLDLLGDHAGPLLLQLPAHLHRDDDRLAGFLGLLPERVRVAVEVQHESWLDKDVFDLLDR
+HGAGFVVSVIAGREPVLRATGRLAYVRFHNADPDWRYGGSFSDAELAPWVGRLRELTGAD
+AAGVRPTYVYFNNDNHGHAAFNALTLRRMAEAEA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001830.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001830.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b12fc27168c2f38fe03ac8b74f4a2b37a3cf40dd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001830.fa
@@ -0,0 +1,40 @@
+>0_637
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTRVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
+>1_383
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
+>2_2250
+MTASTTAPDSESAPTAAERNAAGHARLEQEVAELVARTALGGPERSRERHTARGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYDGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PLTVKKHLRAQEIALENHLPCLYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSRRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPPPAPAWEVAPAQEPAKDPAELTSVVPVDVN
+TPYDVREVIDRIVDGGSVHEFKPLYGTTLVTAFARIDGHPVGILANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMDAAEVEAF
+QAPVRQQYEDQGSPLYSTARLWDDGIITPGQTRRVLSLALDVISRPPLPDTRFGLFRM
+>4_607
+MTASTPAPAAQSAPTVAERNAAGHARLEQELADLVARTSLGGPERSRERHTGRGKLLVRD
+RIDALLDEGSPFLEVGALAAHGLYGGDSPAAGVVAGIGLVHGRLVMVVGNDATVKGGTYY
+PMTVKKHLRAQEIALENRLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFRNQALLSSQRI
+PQLAAVCGSSTAGGAYVPAMSDETVIVREQGTIFLGGPPLVKAAIGEDVSPEDLGGGRLH
+AERSGVADHLADDDLHAMQILRDIVATLPPAEAPAWEVAPAAEPAKDPAELTSVVPVDVN
+TPYDVREVIDRLVDGGSVHEFKPLYGTTLVTAFARIDGHPVGVLANNGILFGDSARKGAH
+FIELCDQRGIPLLFLQNISGFMVGRDAEAGGIARDGAKMVTAVATARVPKLTVVIGGSFG
+AGNYAMCGRAYSPRFLWMWPNARISVMGGPQASSVLTQIKQDQRAAAGEEPMSSEEVEAF
+QAPVRRQYEDQGSPLYSTARLWDDGVITPGQTRRVLSLALDVISRSPLPDSRFGLFRM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5717f8a080b6dbd4217188a9a63d02fbb58cd38d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001837.fa
@@ -0,0 +1,25 @@
+>0_759
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>1_499
+MSAPAWSALLRDAAARLTTVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALIGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPTAG
+VVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDAPGLRIPQAIVHRAAELL
+VPGGLFAMEHHETQGPALLAALGADPRFMGVRVHRDLTGRDRFLTARRSGEAAAGAEVEE
+>3_1988
+MTSSGPATPPADWSALLRQAAATLRAAGVDSPRADAELLLSHLLGGDRGTLLARVLAGAA
+PGPGQAEAFGALVERRAVREPLQHITGAAAFHGLTLEVGPGVFVPRPETELLVEEGIRAL
+AVLDGPARVVDLCTGSGAIAAAVAAWAEERHRDVAVTAVEREDAALAWARRNLEPRGVDL
+RQGDALVACADLDGTVDVVLSNPPYVPDAELPVQAEALADPPTALYGGDAAGLRIPRGII
+ARAAGLLRPGGRLVMEHHEAQGEALAAEARLGGRFEDVRVLPDHTGRERFLAAVRTGALV
+APPSDGRMEP
+>4_726
+MSAPAWSALLRDAAARLTAVGIDSPRVDAELLLAHVLGLDRGALLARVFAGAVAEPAQAA
+AFEALVGRRAAREPVQHLTGVAHFHGLDLAVGPGVFVPRPETELLVETVVADLAARPAAG
+AVVDLCTGSGAIAAAVAAWGEARGRPLAVTAVELDPTAADWARRNLAPRGVDLRQGDALV
+ACPDLEGRVDVVVSNPPYVPEAEVPAQPEARLDPARALYGGDTPGLRIPRAIAHRAADLL
+APGGLFAMEHHETQGPALLSALGADRRFTGERVHQDLTGRDRFLTARRSGEAAAGAEVEE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001844.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001844.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0817bb095d2e1d20023f7cfbb029f1591b35439
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001844.fa
@@ -0,0 +1,20 @@
+>0_972
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
+>1_695
+MAAVGRRLGVAPSALYNHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWA
+RSYRDVFAAHPPLIPLIATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFI
+YGSAYDVDAPADIFEVAGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLL
+LAGLGD
+>2_1839
+MDETPEPPRTRRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEAPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPGQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPAFGAAAEAFREGGGTRATGARNPYADAPFEEGLDLLLAGLDD
+>4_915
+MDETTEPPRARRRRGRPLSPALSREAIADAALAVARTEGYEGLTMAAVGRRLGVAPSALY
+NHISGKHELLVLLQDAVMGEVSLVELEAAIRGEVPVVAALRAWARSYRDVFAAHPPLIPL
+IATLPIEGAPSTQRVYETVCAVLARTGLAPEQVLARVIALESFIYGSAYDVDAPADIFEV
+AGAQERLPALGAAAEAFRAGGGTRATGARNPYADAPFEEGLDLLLAGLGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7910d31fe81db953da75e04af2af8340c3fe38ee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001845.fa
@@ -0,0 +1,36 @@
+>0_975
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAKAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQTYFVQD
+>1_698
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVTADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGIKRSGFGRELGPLGMDEFVNKQMYFVQD
+>2_1836
+MSTPTGYRVQDPSTDQVVETFPTLADGEVDQLLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETFEGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAA
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERVARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
+>4_919
+MSTPTGYRVQDPSTDQVVETFPALADGEVDQVLAAAETAQRAWAARPIEERATIVQKVAD
+LFEERKDELAQIIATEMGKRVTEGVEEAEFSSAIFGYFADKGPTLAADRPIETYGGGRAM
+IRHLPLGVLLGVMPWNFPYYQIARFAAPNLMLGNAIVLKHAEICPRSALAVQQIMDDAGV
+PAGVYTNVFATHDQIAEFIADPRVAGVSLTGSERAGSVIGALAGQHLKKAVLELGGSDPY
+IVLDAEDPAEAARTAWATRMYNMGQACNSNKRMIVSADIHDAFVAELVSLAEAMKPGEAT
+DEDPTVFTPLSSRGAAEGLAEQVERARQQGATVHVGGTVTDEAGARFAPAVITGVTSEMD
+AYREELFGPVAVVYKVESADEALALANDSQYGLGGAVFSQDEAQAERIARQLEVGMANVN
+TPAGEGAEIPFGGVKRSGFGRELGPLGMDEFVNKQMYFVQD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001865.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001865.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8702531c904a7e5d6690b43cc7c5f1a870b5b780
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001865.fa
@@ -0,0 +1,37 @@
+>0_1361
+MVQQRVVRAPGRSDPGGSVPPTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVA
+HTLTTALRAQTHEHANQLHTALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAA
+QARERGVALTWSAELTAPAPLRPLDLLTVLGNLVDNDLDAAAAPDLSAVDRWVDVEVVSD
+ATGLVVQVADGGPGPSDADRRRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVAT
+DSGTVFTVEVPREPTPQEET
+>1_1100
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRARLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVSGEASLAAGGRVLVVQQRVVRSPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLEAARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLGNLVDNALDAAAAPDLSAADRWVDVEVVSDAAGLVVQVADGGPGPSDADR
+GRLFDRGWSTKPVGAAGRGMGLWLTRRIAEEAGGVVDVATDSGTVFTVEVPREPTPQEET
+>3_1367
+MRHPWSIARRVAASLVLLLSVIAVFSGWAGWRQARDATFVVEERHVLGVARLAAREEVVV
+DALGSPAGAAALQARIPSVVDDAGVSWLTLLDARGTRVASWRPEQVGTAYPAPVDRALAG
+ESWTEVSATGPAGISVRALVPVRDAEGAVVGVLTMGVRVSELEVAASAQLPRLAVTFALT
+LAAGLGAALLVARYLHRVTLGRGPEDLAESFLLSAAAMDSLEASLVVLAPDGSIRQHNAA
+AVHALGLPARTEDGTVPAAARLPEELARALEEHADADFPARVGDRLFVVRQRVLGAARPR
+RGGAVDDAAREGISPAPAGTRVLMLHDRTDLQRLTDDLALSRTLTAALRSQTHEHANQLH
+TALALLDSGRTDAARDVLTRHRRPDQDAEDVVSALLEAKAAQAAERGVELTYAVRLSAPA
+PLAALDLVSVVGNLVDNALDAAADAAEPAGRWVDADVTCDADGLLVQVADGGPGLDPDGD
+RVFEPGWSTKPAGIAGRGMGLALVRSIASQAGGVVEVATDSGTVFTVEVPPAGPEQDGEA
+A
+>4_1310
+MRHPWSIARRIAVVHVALVAAIALFSVWSAYLQAREVAQRVEERHVQGVTTLVARDPALV
+SALRAGDAPALQAGIDGWIAEAQVSWLTVMDPDGMRLASWRPEQVGVRYPRPVDAVVAGD
+TVVELSSTGAAGRSVRALAPVVDPEDGTVLGVVTTGVQISDVAIMAQAQIPGILLGSAAV
+AAVGLLVAWLVGRYLNRVTLGRGPEQIAEQFLLAETAMDSLEAGVVVLAPDGRVRLHNDA
+AARLLGWEGAGEPRLPTELSAALPGAVGGEASLAVGGRVLVVQERVVRAPGRSDPGGSVP
+PTALAAAAREGVTTAPAGSRVLVLHDRTDLQRLGDELTVAHTLTTALRAQTHEHANQLHT
+ALALVESGRLETARAVLSRRAADEEASDDVLAALLDAKAAQARERGVALTWSAELTAPAP
+LRPLDLLTVLATWWTTPSTPPPHRTCPRQTGGSTSKWSRTPRAWWCRWPTAAPDPPTRTA
+AGSSTGAGRRSPSAPPDAAWGCG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001866.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001866.fa
new file mode 100644
index 0000000000000000000000000000000000000000..811d777335b5df21dbfa710a0e9f0d4837f1863a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001866.fa
@@ -0,0 +1,19 @@
+>0_1362
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTESTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
+>1_1101
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHADGRFPFD
+VVLLDMNLPDGHGLDFLHQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+>3_1366
+MSAERPYRVLIVEDEELTAQTCADHVTRLPGFTVVGAVGTVDAARRLVAAALDRDGRFPF
+DVLLLDMNLPDGHGLDLLQQLRAAGFQGGVLALTAATELSVVRRAIALGVVQYLVKPFGF
+EAFAQRMTGFRSAAALLAGPGRLSGQEHVDDVFRAGQRRGVEELPKGLSAGTLQAVLDLV
+HDADGGRSASEAAAGLGLSRVTARRYLEHLERIGRVRRRARHGGRGRPEQEYVWAPGAPS
+A
+>4_1311
+MTARPYRVLVVEDEQLTAETYVAHLDRLPGFEVAAVAGSLLAARQVAAAGLHANGRFPFD
+VVLLDMNLPDGHGLDFLRQLRAAGFHGGVLALTAATDLPVVRRAVAYGVTQYLVKPFGFD
+EFADRLGGFRAASAMLAGDGALDGQEQVDAVFRVSRERRAEALPKGLTEGTLREVVELLG
+ADPETALSAAEVGERLGISRVTARRYLEHLERIRRVRRSARHGGRGRPEQEYRWAGRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001867.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001867.fa
new file mode 100644
index 0000000000000000000000000000000000000000..00b3d607d048638e8eccfbc4f5d4abe372e8bba0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001867.fa
@@ -0,0 +1,44 @@
+>0_1368
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>1_1108
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>2_1453
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAAALADVDAVCVPGGFGVRG
+LEGKLDALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
+>4_1317
+MFVTGGVASSLGKGLTASSLGHLLKARGLRVVMQKLDPYLNVDPGTMNPFQHGEVFVTED
+GAETDLDIGHYERFLDEDLDGLDNVTTGQVYSTVIARERRGEYLGDTVQVIPHITDEICR
+RMRLPAEPRGDRPAPDVIITEIGGTVGDIESQPFLEAARQVRQDVGRDDVFFLHVSLVPY
+IGPSQELKTKPTQHSVAALRSIGIQPDAIVLRSDRAVPDDVRGKIARMCDVPQDAVVNCA
+DAPSIYDIPRVIHDQGLDAHVVQSLDLKFKDVDWTAWDALMDAVHHPEHELTVALVGKYV
+DLPDAYLSVTEALRAGGFAHRAKVGIRWVAADECATPEGAAVALADVDAVCVPGGFGVRG
+LEGKLGALRHAREQRIPTLGLCLGLQSMVIEYARNVLGLEDADSTEFDPETASPVIATMA
+EQEQIVAGEGDLGGTMRLGAFPATLRPGSVVAEAYGTTEVTERHRHRYEVNNAYRDRLEE
+AGLAICGTSPDGALVEFVELPRDVHPYYVSTQAHPEFSSRPTRPHPLFAGLVAAGLARRA
+DAAARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001873.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001873.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6e13e93fb039dc99a8cd0449fd83f74e09fc098c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001873.fa
@@ -0,0 +1,16 @@
+>0_1453
+MLATTLEQISVAGARGRPRIRPDRLIADKGYPSKANRAWLRRHGIAATIPERADQITHRR
+RRPGRPIDFGEDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARNYHAGLSLAATLHWL
+TTLL
+>3_623
+MTTKIHLVCDGKGRTLAFVLTGGQVADTSMFPDTIDEIRVVGVKGRPRTRPERVIADKGY
+PSKKNRAWLRQRGIATTIPERDDQIAHRRKKPGRPIDFGRDQKRRYKGRNAVERCFNKLK
+QWRGIAARSDKTPRNFHAGLSLAATLQWV
+>3_1709
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
+>3_2184
+MNYKKSGDEPADHAIGRSRGGLTTKSHLVCDGKGRVLAFVVTGGQVADTSMLATTLELIS
+VAGARGRPRARPDRLIADKGYPSKANRSWLRRHGIAATIPERADQIAHRRRRPGRPIDFG
+EDQRQRYRGRNVVERCFNRLKQWRGIAMRSDKYARSYHAGLCLAATLHWLTTTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001884.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001884.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e84a953b8a721132a4b5354a18ea50cc694cef57
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001884.fa
@@ -0,0 +1,24 @@
+>0_1629
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPVGAEDVTGFAHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>1_1343
+MRRTLPLAALAALALLAAGCGTPAAGPSSTPTTPTSGSASAAASSRAASSTAPSSGTHAD
+PATLDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAADLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPAPDYAD
+>2_1170
+MARRALPAAGLAVLAALAAGCSLSDGQPAPSETTSAPAASSASPSGTATGPAPSSAAPAG
+AHSDPAALDVVVNKARPLSPVDWAPQDLVPVPGSDLPLRAEAARAAGGLIEAAARSGHAL
+STLSAYRSHAYQAQTYGHWVDELGRQEADRVSARPGHSEHQTGLAWDVGDPESPQCHLEA
+CFGDTAAGRWVAEHAAEHGFVVRYPAGAEHVTGYAPEPWHLRFVGREAAAAVEAAGGVLE
+TAWGLPAAPDYPG
+>4_1558
+MRRTLPLAALAALALLVAGCGTPAAGPSSTPTTPTSGSASAAASSGAASSTAPSSGTHAD
+PAALDVVVNKTRPVAPPDWAPSDLVAVPGSELPLRAEAATAAGDLLDAAAAAGHRLTTLS
+AYRSYDYQVRTYGHWVDELGRAEADRVSARPGYSEHQTGLAWDVGDAATPACDLEACFGD
+TAAGRWVAAHAAEYGFVIRYPAGAEDVTGFDHEPWHLRYVGSAEAARVEAAGGVLETAWG
+LPPARDYAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001889.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001889.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4b8bed486562cb633cd37a929422a4abb74eba5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001889.fa
@@ -0,0 +1,28 @@
+>0_1787
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPELPADVVAKTRDR
+YVEAYERLTGRPFDA
+>1_1494
+MSGERVGFTGAEALWLPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRPQASFDKQFVRDWLTGPDSGWDKTSGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDA
+>2_1001
+MSHETPASDTTPHSGAAPRGFAGAEALELPGWRHVYSGKVRDLYEPADAAPGESETLLVV
+ASDRISAYDHVLSPPIPDKGAVLTQLTLWWFERLSEGYNGAAGAPVEHHVVSTDVPEAVA
+GRAMVVKRLRMFPVECIARGYLTGSGLAEYRESGTVTGLPLPTGLVDGSRLDPAIFTPSA
+KAEVGEHDENITFEQMSERVGAEAAERLRYLTLDLYSRAEAIARDAGIILADTKVEFGVD
+PATGQVVLGDEVLTPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTSDASGWDRASGAEPP
+ELPADVVEKTRARYVEAYERLTGRPFEA
+>4_1708
+MSGERVGFTGAEALELPGWRHVYSGKVRDLYEPADAEPGRSATLLVVASDRISAYDHVLE
+PPIPDKGTILTRLTLWWFEKLAEGYNGAHAEPVEHHVVGTDVPAAVAGRAMVVKRLDMFP
+VECIARGYLTGSGLAEYRASGTVAGLPLPAGLVDGSRVDPPIFTPSAKAEVGEHDENITF
+EQMVERVGTEAAERLRFLTLDLYARAEAIAREAGIILADTKVEFGVDPATGQVVLGDEVL
+TPDSSRFWDAEDYEPGRAQASFDKQFVRDWLTGPDSGWDKAGGEAPPALPADVVAKTRDR
+YVEAYERLTGRPFDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7fc4e98a22101fd06fbdcb0f75506791f9f5b063
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001893.fa
@@ -0,0 +1,33 @@
+>0_1833
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPPAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARPAGDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPVKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARVLSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>1_1540
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADASRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRWRLAGLVDAVLPPARPADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDPDAAPASP
+AAAVDEAAGAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPAEAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLAAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
+>2_945
+MFYNVVGGNVRAIDGPTTYSAFPANVSAKLPPADPDGVAREVSAMIRAADIPEWARRSFA
+GTVVMDANDIGRNALGRDTAASAAVLEAAFADNPLGQGRERTPLAVVVRMD
+>4_1754
+MRDTTADAAQVPARPDDAAVYRYLAFGEADRPFLVGGPRPAPLAPAATPSPVADLESVRA
+AIRAHGGPLASTAHVCGRPAPTPSAADAPRGLRGAARTLTATRRDVAARLADSRERADVP
+VEALLNSAFVDAHADERPADRGVPRGRLAGLVDAVLPPARHADDDAAAGLLLALREPVRE
+VFASDSFAARPYADAPTVRALFEDFLAHPRRHDPERFWRLLNLELWLRDAVDADAAPAGP
+ATAVDEAPTAPAPAKPDHEPNPGKELDLVSAEDGRRYRRFPVQTGLVDRDTDLQAYLRGE
+IEDFFRDLPADAMPQDAPWHFSVSEKIVAITQGRSYYTWEVRPSVAARALSRLVTRTPAG
+IGLGDPTTMQLAIQEAGLPRIVLSAAAGAAGKVAGKRGVFYNVVGGNVRAIDGPTTYSTF
+PANVSAKLPPAEPDRVAAEVSAMIRAADIPAWAKASFAGTVVMDANDIGRNALGKDTAAS
+AAVLEAAFADNPLGQGRERTPLAVVVRMD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f54a56794bf965d93ea6b568c3f646d54ca0191a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001905.fa
@@ -0,0 +1,13 @@
+>0_1907
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>1_1612
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
+>2_872
+MSELDELDFVAVEIHTAGTDPASVCAVDMALVRGGEIVAAERWPVRPPTGPTSFSRLHTQ
+LHGVDEAAVADAPEWPEVAAQLDLLGEHLPFVASGADRDRGAYEAATRATGGTPQAHEWR
+DALALVGRLRPDVDPPRIATAAQALGVPDGARPAGAGSEAVRTAEVVLALARQSGRGTVR
+RLWSEAAPPTPDEPIIPESLRRRHATEPSVPPAGAHRWAPPAPAPAPASAAPAGRGGGVG
+WKLAGTAMVGIALGAALFFVASVAVIMEYLEDGRGSDATVGMGIAALSAFLAWWFGKTGV
+DWIRRQDG
+>4_1834
+MSELDELDFAALSAFLAWWFGKTGVDWIRREDG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001910.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001910.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a8697b0ed04c66e64295da134a149c8c6ccef451
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001910.fa
@@ -0,0 +1,52 @@
+>0_1940
+MKILPPRSAASPRPLAPAVAVAALSILVGGLLPQSPSATTEGAPDARPRDDAARATTVGA
+AATPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VKRVEIRVRQDGAWGPWQVLDRPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGEEPAEARTVATV
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGVSTMGNYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPAAVTPAPTPAPTTERSTAGTYTVQPNDGWWTI
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPASPPAPAPAPGTYTVREGDGWWIIA
+HRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQRTG
+VSMERLQRLNGMTVSTMLHPGMVLRTA
+>1_1645
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALNSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPNDGWWVIA
+RRTGVSAAELQRLNGMTASTVLHPGMVLITAATAPTSPPAPAPAPAPAPDTYTVREGDGW
+WIIAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIA
+QRTGVSMERLQRLNGMTVSTLLHPGMVLRTA
+>2_837
+MKLSAPRSAAPARSPPAVVVAALSVLVGGLLPQQPVPTTAVPPPPPRLADAAALRTLAPA
+GSGRAPAAASEVRGAAVAAVPQEGEALADAPAGVVLGEPVVDRPFTVAAAVWDAAADHAV
+ERVEIRVRQDGAWGPWQVLERAVLPEGAAVTRTGTDPFVAFGADGAQLRLTTADGAAPAG
+LELSLIDPGTAATDEAVASAHPAVSADQAAQDAALPRGVKSSAVVGGAEPAPARTVSTAS
+EARARILPDVITRAQWGADESWAQASPQFEQVRALTIHHSAGTNDYTRAQAVEQMRAIYA
+YYTKTLDWGDFPYHLITDRFGNIYEGRRGALDANPLGTHAGGFNTGTMGISTMGNYDVVA
+PSEEVVDAMARATAYYLYRDGLDPYGRVTLTSGGSTKYAAGTPVTVDTIFPHRTTSNTAC
+PGRHLMARFDDVRDRAATIAAAAGQEAPAPEPEPIPTPEPEPTPRPEPEPIPMPEPTTPT
+TYTVQDGDGWWVIARRTGVPAATIQELNGMTESTVLHPGMVLRLVADVSAPAPTPVTTGT
+YTVQPNDGWWVIARRTGVPAEELQRLNGMTADSLLHPGMVLITAATAPAPAPAPAPAPAP
+APGTYTVRDGDGWWVIAHRTGVTMETLQRLNGMTADTLLHPGMVLVTGQNATAAAPAPAP
+ATYTVRPNDGWWIIADRTGISMAELQRLNRMTASTLLHPGMVLRIA
+>4_1867
+MKILLPGSAASPRPLAPAVAVAALSVLVGGLLPQQPSATTEGAPDARPLDDAARATTAGT
+ATTPASAAPVEGAGVATVPQEGENLVPAEEAPAGVVLGEPVVDRPFTVAAAVWDAAADDA
+VERVEIRVRQDGAWGPWQVLERPVLPEDAAPARTGTDPFVAFGADGAQLRVTTVDGAAPA
+GLELSLIDPGTAATDETVASAHPAVAAEQAAETAGLPRGVKSSAVVGGAAPAEAHTVATA
+SDARAKILPDVITRAQWGADESWAEDSPQFDQVRALTIHHTAGTNDYTRAQAVEQMRGIY
+AYYTKTLGWGDFPYHLITDRFGNIYEGRRGALDSNPLGTHAGGFNRGTMGISTMGDYDVV
+APSEEVVDAMARATAYYLYRDGIDARGRVTLTSGGSTKYAAGTPVTVDTIFPHRATSATA
+CPGQHLMARFDDLRDRAEAIATAAGQPPTPATPAPTPAPTTEPSTAGTYTVQPNDGWWII
+ARRTGVPAATLQELNGMTESTVLHPGMVLRTVADPTAPEPTPITTGTYTVQPDDGWWVIA
+RRTGVCAAELQRLNGMTASTVLHPGMVLITAATAPASTPAPAPAPAPGTYTVREGDGWWI
+IAHRTGVTMETLQRLNGMTATTVLHPGMVLRTGQTASAPAPSPATYVVQANDGWWLIAQR
+TGVSMERLQRLNGMTVSTLLHPGMVLRTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001916.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001916.fa
new file mode 100644
index 0000000000000000000000000000000000000000..23933e3754146e9b43ceb288638075e71323e1bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001916.fa
@@ -0,0 +1,32 @@
+>0_1988
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAMNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFVPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSSVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>1_1705
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDSFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLAKLKPSFEALGREAGFDAVAL
+EKYSSLAEIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
+>3_713
+MTRDAYLFDAVRTPRGLGKPTGSLHEVKPVGLLGGLFDALRERHPEWDPAGVDDVVLGVV
+TPVGDQGGDIARVAALKAGMPESVAGVQLNRFCGSGLEAVNQVAARIRSGWEDMLIAGGV
+EAMSRVPMGSDGSAWAMDPATALDLHFVPQGISADLIATRQGFSREDLDRFAVQSHHRAA
+QAWSEGRFEGSVIPVTDMNGLTVLDRDETIRPDASLETLAGLRPSFAAMGEQAGFDAVAL
+NRYTDVDEIHHVHHAGNSSGIVDGAALTLIGGEEAGRRAGLTPRARIVSAAVVGSEPTIM
+LTGPTPACRKALDVAGMTASDIDLVEINEAFAAVPLQLMRDLGWNEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLQTGIATLCIGAGMGVATIVERV
+>4_1923
+MTQDAFLYDALRTPRGAGKPSGSLHEVKPIDLVVGLTHALRDRHEGLDPADIEDMILGCV
+SPVGDQGAVLPRVAALKAGLPQTVAGVQLNRFCASGLEAVNQAAARIRSGWESLLVAGGV
+ESMSRVPMGSDGGAWAMDPATSLATDFIPQGVSADLIATREGFSRAELDRFAAQSHRRAA
+AAWQEGRFARSVVPVTDMNGMTVLDRDETIRPDSTVETLATLKPSFEALGREAGFDAVAL
+EKYSSLAGIEHLHHPGNSSGIVDGAALTLIGSEEAGRRAGMSPRARIVSAAVVGSEPTIM
+LTGPTPACRKALEVAGMTAADIDLVEINEAFAAVPLLLMKEMGWTEEQTNVNGGAIAMGH
+PLGATGAMILGTLVDELERRDLRTGIATLCIGAGMGVATIVERV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001923.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001923.fa
new file mode 100644
index 0000000000000000000000000000000000000000..55729015c89f050606505b9e5656ba8175ae3d56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001923.fa
@@ -0,0 +1,20 @@
+>0_2040
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR
+>1_1758
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGVLDWAAQAVLLLAGWLSVIGLYPRVPSLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRGRTR
+>2_660
+MLPLIPADLLRALGLVLIPAAWAVAGWPSAAVMLLVFGAQWLTRWLVPGSALDWGAQAVL
+LAAGWFSVTGLYHRVEALDLVMHAAASAAVVGLVAVAARARLRRRGEDPGALVRRLGPVL
+SAAALTGAGVGLGVLWELAEWWGHTVVTAEIGVGYDDTIGDLAADLLGAGAGAALAVRGQ
+LRAAGSAR
+>4_1981
+MPVGAAGGRDAAPTRAIADMLPLIPADLLRALGLILVPVAAVHAGWPSAAAMLLVFGSQW
+LTRWLAPGGALDWAAQAVLLLAGWLSVIGLYPRVPWLDLLVHAAASAVVACLTALVVGAW
+LRRRGTEAGQAVALLGPGLAGLGIAAAAVALGVVWELAEWWGHTAVTPEIGVGYTDTIGD
+LAADLVGAGIGAALAVRRERTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001926.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001926.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5b40f21abec94cfac1f42a871f2ff980799d8637
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001926.fa
@@ -0,0 +1,20 @@
+>0_2063
+MSTEPTPSSATPETESAAPSSSGLPQAAPQAAWPERVETGEHQVSYRATVAAPAHELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL
+>1_1782
+MSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHELWA
+MLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVE
+WAHPGGHRWRWAFRDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRL
+AGRHL
+>3_556
+MSTEPTPSPATPETEPAAPSSSGLPQSAPQAAWPERVETGEHQVSYRATVAAPAQELWAM
+LADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDELVEW
+AHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSLTRLA
+GRHL
+>4_2002
+MGDMSTEPTPSSATPETESAAAPSSSGLPQAAPQAAWPERVETGEHQVSYRVTVAAPAHE
+LWAMLADPHRHHEADGSGTVRPKVSGPHRLAVGDRFRVAMRKYGVPYTMTLTATAVDEDE
+LVEWAHPGGHRWRWAFQDNGDGTTEVTETFDYSWARPAVRRAYELLRVPADNGRGIQSSL
+TRLAGRHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001927.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001927.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dedad9cd7db97748af11ce60ee71fd24a219ce6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001927.fa
@@ -0,0 +1,28 @@
+>0_2074
+MSEHTPAHTPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVL
+DLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGLLPQ
+VQAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHAS
+SVHAAILGEHGDTEFPAWSSARIGPTPLLEWPTPADPLFTRADLDEVADTVVNAAYEVIQ
+GKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVI
+QPELDAAEMRALHASADALRREARSLGF
+>1_1793
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
+>2_619
+MSEHTPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRAEVLD
+LAHGTPFTSASAMTGGADPDVLADCEVVVITAGAKQRPGQTRLDLGAHNVEILRGLLPQV
+QAHAPDALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQVHASS
+VHAAILGEHGDTEFPAWSSARIGPTPILEWPTPAAPLFTRADLDEVADTVVHAAYEVIRG
+KGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVTRVIQ
+PELDAAEMRALHSSADALRREARSLGF
+>4_2013
+MSEHTPAHSPAAPASLGPAHRKVGVVGAGGVGTAICYAALIRGVAREVALYDIDEPKVRA
+EVLDLAHGTPFTSASAMTGGADPDVLAGCEVVVITAGAKQKPGQTRLDLGAHNVEILRGL
+LPQVQAHAPEALIVLVTNPVDVLTLVAQRLTGLPAGRVIGSGTLLDTSRLRWLLASRAQV
+HPSSVHAAILGEHGDTEFPAWSSARIGPTPILEWPTPVDPLFTRADLDEVADTVVHAAYE
+VIQGKGATTYAVGVATTRLLEAILRDQHAILPVSTVLDGVHGLSDVALSMPSVVGRDGVT
+RVIQPELDDAEMRALHASADALRREARSLGF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001929.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001929.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ddad4ee7cbb418b1906f954d56f19103b975873
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001929.fa
@@ -0,0 +1,20 @@
+>0_2095
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+APFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
+>1_1819
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHTAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
+>2_586
+MLVADDQQLMRTALAHFVSTAEDLEVVGTAADGVEAVEMAKDLRPDVVLMDMQMPRMDGI
+EATTAIMAEAPEVRVLAITTFSSEAYLVPALRAGASGYLVKDAPPEEVVEAVRQVHRGDA
+VFSPRVARELIETVTQQSERRESAAAHALTELEELTPRELEVVTELAKGSSNAEIAQALF
+LAEATVKSHLGKIMDKWQARDRVQVLIRASRAGLVSFDD
+>4_2039
+MIRVVVADDQALMRTALEHFVAQAEDLEVVGSAEDGVQALEAARTLAPDVVLMDMQMPRM
+DGVEATARISAEAPGVRVLAITTFSSEQYLVPALRAGAAGYLVKDAPPAEVVDAIRRVHA
+GDAVFSARVAADLVEAVTAAPEHAAPCPAEPLAPHERLTERELDVVRELAKGASNAEIAG
+ALFLAEATVKSHIGKVLDKWQVRDRVQILIRAARAGLVDIG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001935.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001935.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c9e3f4d9e985560d4cd2f45ada1043dd9378cd6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001935.fa
@@ -0,0 +1,17 @@
+>0_2132
+MSPADPTADVAAGPAGPAAVAEAFAAAWNAADADALADLFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
+>1_1856
+MSPADPTADVAARPTGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWRRRRQI
+RVNHALGFRWMFPHSRLELGRVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTETGAWEAVAGQNTDSVPGAQTHLADDEGLAAVHYHPSAWFDPDEDPDGPEAC
+>2_535
+MSPADPSPRLLARPPASPAAVAEAFEAAWNAADADALADLFAEDADFVTVLGVWWTRRRQ
+IRLDHARAFRWMFPESRLEMDEVRVRDLGDVAVVHAPWTMTGPGVGGEVGEATGTVGVRE
+AGGDGSGGGDGERTGVLLLVVRRDEAGAWEVVAAQNTDRSPEPRPRPADEDDLLAEVHPH
+PSAWLHPDDDGPASRLSARPRLGWAVHEPVPPLPLPNSPSPPLPLPQGELSCRWPV
+>4_2077
+MPPADPTADVAARPAGPAAVAEAFAAAWNAADADALAELFAEDADFVNVVGVWWTRRRQI
+RVNHALGFRWMFPASRLVLGQVRVRELGDVAVVHAPWTMTGQTAPDGDEAGERTGVLLLV
+VRRTEAGAWEAVAGQNTDSVPEAQTHLADDDGLAAVHYHPSAWIDPDDDPDGPEAC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001945.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001945.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6527190e0e485459301a1f9f4698f1566aba2af0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001945.fa
@@ -0,0 +1,12 @@
+>0_2198
+MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR
+>2_445
+MTRLLPGDSLTLDLAPEDPADLLARLRAAGVAMNESAERLITDARVCAVVPERVTVVERT
+LAELGLPDGGTLPELRRAVEAAGLRECPPTVAPLLRLVTLDQANAPDSLLRHGRAPDDSA
+HVFSPSLSDEPGVHRGLYLRVVDHVPWLRGFVCDDLHVFGPEDRWILAL
+>3_683
+MADLIDRAGIELTLAGDPHELLTQLQAAGVRFNDSARTLLFRPALARDLQTSRPVRVVER
+SLTDLGLPNGGTLPQLRRAALAAGLAPCPPAVAPLLRLRTLDQVNAPDSVLRHGRAPEGS
+VHVLSPSLGEDPRVHRGFYLRVVDEAPWLRGFMCDDLHVMGADDRWVLSAPTSAP
+>4_2130
+MNVSAEQLIGDESGVHRGLYRRVVDHVPWLRGFVCDDLHNFGPEDRWILAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9de68b67e774e1181d54b2312964c0b706bcdf7d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001947.fa
@@ -0,0 +1,32 @@
+>0_2211
+MGVNGLPGTGKTTTLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRAREL
+RPEVAGFEMVVASANNAAGESISEEIPQVESRIVV
+>1_1914
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHPQAARIDVVARADVVEAGGPGLMGVN
+GLPGTGKTTTLGDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRVRELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDSRNVDADYFAELAAALGGSRGEEDALGEDS
+LTSEQPGTSGLATAPMATAPTPPRSARRRPTRG
+>2_442
+MPAPSLGEEDKRAIPALQPSLSSSNVTAHEHTGHLQAACIDVVARSEVVEVGGPGLMGVN
+GLPGTGKTTMLRDILASNVVERARRLSACENPFDALTERTHEWTGEGRMRRRARELRPEV
+VGFEMVVASANNAAVENLSEEIPQRSAIKDGRHVDADYFACLATAAVGGSGGGRGRPG
+>3_393
+MGDTRGRTQQDIVRFWQLQELFDPQPLPKLTPRTSPPFGKRVITWRAEDGDVALPWNRLA
+PPPPTTKGAAREWRHTLYLRIYALEDAYQTLHSAFPADADAYDERPGGRSAAAGALVDAD
+GRLIGGTGVLSSALWGIGRLCRGEGFDDSLVDGFEAAGEAFVDAADRAAGVPDDDAFGEQ
+PVLTAGMLVALIRLAQHSAGVEGMPALAGHEVRIASQVVSASSGDETPDIDFLNSFYLSD
+LHRVGEAIARGDVGPALDAYLTPDGDVDTQRRVDVVARPDIVDAGVEPARVPAGRWPAKT
+SYALARSQQFAVNRALNELGAEPGLMGVNGPPGTGKTTMLRDILAANVVERARKLAGFAD
+PSGAFTGRTLAWTGEGRRHRTVHELRPELTGFEMVVASANNAAVENISEEIPHRDAIKDS
+GRADADYFADLATAALGLGVENADEDGAPGACDGPAAEQPAAASSGAWGLVAARLGNKVN
+RARFRDAVLFGGASGGRGARGRGLDTLLKDWAASPSAPAQWTAAREAFHRALHEVDRGLT
+ERRDAAQRTVRTAAAREAVRAAERRLAELSRQRTAKWAGAEAIRRELSAAQAEAGRIRDA
+LDLHRDAKPGFWETITSFGVAGQQWRETYQPLLEAWSTADAGRAALAADTEAAERRLSEL
+EAQIVHLDGECARRRGDLADLEAAVRADEERFGGRHPSAVVDAQTRETTTPWLDEEMEKA
+RTELFLAALELHRAFIAAAARDLRPSFQAAMEVMAGAAPRDLEAEKRRAAWQVFFLLVPL
+VSTTFASFDRMFTGMGRESLGWLFVDEAGQASPQYAAGAIWRANRAVVVGDPLQLEPVVT
+IPVTVSRSLAKAHGVSSTWIAPEASVQRLADRVSRYGTTLPQGEDDVWVSSPLRVHRRCD
+DPMFALSNDLAYGGLMVSGVQRKGPEEDPFERTGDGEIFASSWMDTPARTPGTHLQPNQI
+ERVRRGIEACRRWGIPCTEIIAISPFREVADALRVLSDEFPGLTAGTIHTAQGREADVVF
+FVLGGAPDKPGARNWASSRVNLANVAVSRAKRRLYVIGDREAWSRHNYFRQIAEALPRAA
+EPDAGRER
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001949.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001949.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6be8c607bba3b92a9879a8552eac95d8537d9374
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001949.fa
@@ -0,0 +1,32 @@
+>0_2222
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAQTAAHWRDVLQAERLPAGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPRHAPPALGADTAAVNTWLDAR
+>1_1924
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPERGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+EVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGAGVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAETAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPHHAPPALGADTAAVNTWLDTR
+>2_790
+MEHTDEPRGGGPLEGIVIADFTRVLAGPYATMLLADMGATVIKVESPGGDDTRTWRPPEH
+EGVSTYYLSVNRNKRAVALDLSDREDLDTAYALLDRADVFLENFKPGGLAKFGLDPDSVA
+ERWPHLVHASITGFGTASGTALPGYDLLAQAVSGMMTVTGEPDGAPQRSGVAIFDVITGL
+HAAIGVLGALQERTRSGRGQHLELNLLSSALSGLVNQTSAAIAGGVTPHRMGNEHPSLYP
+YGPFRAADRELIIAVGNDRQFARLVEQLGRPELAEDPRFLTMKDRNAHRGELGPLLEEAL
+AAQSAGEWFEQLRDAGIPCSPILTLPEGVEFAAGLGLDPVVEVGEQRIPTVRHPIRFSRT
+PARHELAPPALDADRDWVRAWIDQTPPSTAADAD
+>4_2162
+MPPATTAPSPASLPLDGVLVADFSRVLAGPLATMTLADLGARVIKVEHPVRGDDTRGWAP
+PRSATGATYFESVNRNKESVGWDLKDPEDQRRAAALAARADVVVHNLKPGTMERLGLGYD
+DVARENPSVVYAAVSGFGDREGRDLPGYDFIVQAAGGLMSITGEPDAPMKAGVALVDVLT
+AKDLTAGVLAALLRRERTGEGAHLRLNLLSSLQGALANQGQAWLGADVVPRRMGNDHPSI
+APYQLLACRDAPLAVAIGNDAQFRTFAAALGVPELAEDPRFTTNTDRVEHREELRTALED
+ALSAQTAAHWRDVLQAERLPVGLVSTVAEGVELAESLGLEPTVEVQDRSGAPAGRQFRHP
+VQWDPPVAHPHHAPPALGADTAAVNTWLDAH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001952.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001952.fa
new file mode 100644
index 0000000000000000000000000000000000000000..adebee60471468e1d0b6041d391b35c884e2bce4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001952.fa
@@ -0,0 +1,20 @@
+>0_2239
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>1_1943
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
+>3_372
+MSSPDPTAHRGAPLPSALGAWRRRPPQPPRPLAPGAPAARPQSGAGLPTVEEVSAGGIVI
+REHAGDLEVAVIARYNRGGRLEWCLPKGHPEGAEDHRQAAVREVEEETGIAGCILEPLGS
+IDYWFTVSRHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVSIDDVARRLSFANERR
+IVDLARQVIPQHFPTGRPPGRP
+>4_2181
+MTRPDPSAHRGAPLPSALGAWRRRPQPPLRPVTPAPAGPRSAAAASLPTVEEVSAGGVIV
+REHDGGLEVAVIARYNRGGRLEWCLPKGHPEGEEDHRQAAVREVEEETGIAGHILEPLGA
+IDYWFTVARHRVHKTVHHFLLRATGGELTTENDPDHEAVDVAWVRLEDVARRLSFANERR
+IVDLARQVVDQHFPPGGARGPRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001953.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001953.fa
new file mode 100644
index 0000000000000000000000000000000000000000..01092d5b4845a511084b6ea460c1168ce4a3268f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001953.fa
@@ -0,0 +1,32 @@
+>1_82
+MTRSTSTRIQGAVLQTLSATAPYAQSRPLEVQDLQLAPPQGREVLVRIEAASVCHSDLSV
+VQGLRPRPVPMLLGHESAGIVESTGPEVASVAVGDRVIMTFLPRCGECPACRTEGRLPCS
+EGTAANERGDLLSGGRRLSTEDGPVAHHLGVSGFATHAVVDARSVVRVEHDVPADIAAVL
+GCAVLTGGGAVMNAVSVPKGSTVVVVGLGGVGMAAAIVARALGHEVIGVDGISTKRDLAV
+ELGAQQVYAPQEALDAEVRGDLVVDATGNPRGFETAVELTGPGGATVTVGLPPADAMSSV
+SPMALVAQARTIVGSYLGSAVPQRDIPRFVELWRAGRLPIERLISSHISLEDINQAMDRL
+DSGAEMRQVILFDQEQPSQGQE
+>1_1746
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGVVAAVGPSVTSLKPGDRVVACLIAYCGACARCLAGQTTLCLNQEAVVRGPEEKPRLT
+LQDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPQAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVE
+AVLGITGTGVDHAFEAIGLPVTQQLAQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVAMGSSNIQRDIPLYADLYVQGRMDLDHMVSQEISLDEINTGYERLLNGEVIRSV
+ITSF
+>2_672
+MRAALAMKVGGKFEIHDVVIDDPVGREVLVDVKASGLCHSDLHLIDHDFGLPLPAAGGHE
+ISGIVAAVGPSVTSLKPGDRVVACLISYCGACARCLSGQTTLCLNQEALVRGPEEKPRLT
+LEDGTPVAQSVNVGGFAEQVLVHENQLAVVNEDIPFPHAALIGCSVVTGAGAAINTAHVR
+PGDTVAVVGVGGIGLNAVSGARLCGAKRVIAIDLDDSKLEAARRFGATDVVNSGSGDAVG
+AVLGITGTGVDHAFEAIGLPVTQQLTQDVLGPGGTAYLIGIAPPGTTAQFGASLDSLFAQ
+RRLQAVLMGSSNIQRDIPLYADLYVQGRMELDHMVSQEISLDEINAGYERLLNGEVIRSV
+ITSF
+>2_757
+MKTTAAVATAAETPLTITEVEIDDLRADELRIRMVASGVCHTDAIVRDQWYPTPLPAVLG
+HEGAGVVEEVGDGVHGFSAGDRVLLSFSSCGHCRACHEGQPAYCADMFALNFGGRRLEDG
+STSYTLDGEQVSSHFFGQSSFAALANVPARCAVKVDDDAPLELLAPLGCGIQTGAGAVLN
+VLRPEPGASLVVFGAGAVGLSAVMAAKVARCGTIIAVDMHPDRLRLAEELGATHTLQAGE
+PVAERIRELTDGGTEYAVDTTGVAAIFGDNVDALAPRGVLGVVGAAALGTEASFDIGTNL
+PKGITIRTIVEGESIPQVFVPRLMALHAAGEFPFDRLVKSYPFAQINQAFEDSKSGETLK
+PVVVFDQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001958.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001958.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dcb58b1d314cd2d3d8a98b51031601ce90b2180e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001958.fa
@@ -0,0 +1,52 @@
+>1_1594
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLADVRRARLRSEKPDTQG
+ASSDYYLGSLVVNRATTPEGVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRRRGAPAGTSFQVDAIGVAVETIAAACRRALERQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGGSWSALLTRDFASLRAALAPSQT
+AMASGARTIIGVLLAAGQTAVESGPSSDQCQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQGDAAWSQRFLVTLLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPEDGVDGVAFQHMLEDLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEALTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNSMRRVIQEWQGKRP
+>2_885
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLRSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAERVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGVEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWSQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLDAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP
+>3_825
+MQTEKHVPEALTIEEVFTAARHYRVPVYQRAYAWTQVEISTLLTDVRRARLGSEKPDTQG
+ALSDYYLGSLVVNRATTPEDVPIDEVVDGQQRLTTLTVLAAVAEHVIRAGVLDPRALAVL
+DYEGRPEAGEDLATLRHRGAPAGTSFQVDAIGVAVETIAAACRRAMDRQTPADDQEVMFD
+GDDLAYLWKHVRLLRTELPKGTDLNHYFEVMNTRGEQLAKHEILKATLMRPLQDATDRKV
+FAHVWDACAVLDRHIQLQFSTERPKDGGEAARDAVFGASWSALLTRDFASLRAALAPSLT
+ATVSGARTIIGALRAAGQTAVESGSSSDQRQDDADTGAYGTIVDFPNLLLHVLRVMQEKG
+EGAEPGLPRWGQDSTGAVRLEDGSLLEQFAQHGQDDAAWSQRFLVALLRMRLLLDTYVIR
+TLATTGTQADEENWVLSRAQKLETESGERSPRRRLGVKNTFQDPQVQDAVRNLQAMFQVT
+DTRRTSKYFLYRILRWLHAQPVDSVDGVAFQHMLENLARERLRAYEADKTWDAGVNVPNF
+VFNALDYILWDAGRTSPMEREHLREPLSDVEQEVLRRRADAFRFRYRTSVEHFYPVVPGE
+EQEVLTAEDVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGD
+WDVPQIKEHGNRMRRVIQEWQGKRP
+>4_1814
+MSERNAPETLTIGEVFAAGRHYRVPVYQRSYAWTEVEVSTLLADVRRARLRSKALESRGN
+VSDYYLGAMVVNRTQTPAGDQIDEVVDGQQRLTTLTVLAAVAEQITQAGVLDPVALAVLD
+YEGRAEAGEDLATLRRRGGHRHGAFQVEAIGIAAQTVRGACERATDRQATADGQTVVFDA
+DDLAYLWNHVRLLRTELPEGTDLNHYFEVMNTRGEQLAKHEVLKAMLMRPLRDESERQVF
+AQVWDACAVLDRPVQLQFASEQLDPDISPARDAVFGDTWSTLVTTDFESLRAALEPSLAE
+TELGGRTSLDSLLSSRGAGEGTSASAEKRSDETGSYGTIIDFPNLLLHVLRVMEESGMAS
+GSGRPAWGQEPKNAVRLEDNSLLEQCAERRQDDARWSKRFLVMLLRIRFLLDTYVIRTLS
+TTGTRADEENWVLVGALKVESGAEEGSSRRRRLGVKNTFEDPAVQEAVRNLQAMFQVTDT
+RRASKYFLYRILRWLAERPVDRVDGEAFQRMLEDLARERLRAYDADEGLDLGVKVPNFVF
+NVLDYILWDLGRNPSAEAGALGAALGDVERSVLSQRAGSFRFRYRTSVEHFYPVVPGEGQ
+KVLTSTEVNRFGNLCIMGRRENSQRNNLMPVSKVKQYSSDEQSLKFQLMAGILHAEGDWD
+VPQIKEHGNSMRRVIQEWQGKRP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001959.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001959.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f0342b667eabb291750c0d5bd2639abe50fabe4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001959.fa
@@ -0,0 +1,40 @@
+>1_1595
+MRTRPTALDAAVDHPRGAQSDARGPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTW
+STTNTGQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHIVENHRLILQTFRSWDSTEVEDFADYFLD
+HCTLVRLVVSDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNAALIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENRQFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVFARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSVDPAVVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>2_884
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTW
+STKNAVQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLILQTFRSWKSSEVEDFADYFLD
+HCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNATLIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLIRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>3_824
+MEMHSTAADAAVDHPWGAQNDAQGPGTGRSGSLTANVMTVADALRDPRLRVPEYQRPYTW
+STKNAVQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGD
+TAERAEHQRAALDRAAAIELPPGRRDVSERHVVENHRLILQTFRSWKSSEVEDFADYFLD
+HCTLVRLVVNDLDAAFQMFDSQNTRGRALLPTDLLKAYHLRAYGEATSDRAAILAAVREW
+EATPPFEIHHLFSRLLYPILRWSAGESLPRDGFTASRIGAFKGISAGPTGLGRLPWAHGL
+LMAKAHVDDYNGRNATLIAHGALPPLEFPFQLTQPVIDGEMFFRLVRHYTRLARDLGVSA
+TDAEQTAGDDARRGRENGRFQTITRLVRATGTGAGYRYTQELYGALLLAYADRFGDHDIE
+RAALVLARHAFALRTRLTRVYPRSVELHALGQHGAPDLEDRVNLFRLMRSSLDPAAVTGR
+VAALPGPYVDEASPVERLYSDTPWDTEEAHDAD
+>4_1815
+MRTRPTALDAAVDHPRGAQSDAQEPGTGRSGSLTANVMTVADALRDPRLRIPEYQRPYTW
+STTNTGQLVEDIRRFRAAASYRIGTMIVHAEDGWLDIVDGQQRYMTFALIALALQEVLGN
+TAERAEHQRAALDSAAAIELPPGRRDVSERHVIENHRLILQTFRSWDSTEVEDFADYFLD
+RCTLVRLTVTDLDAAFQMFDSQNTRGRPLLPTDLLKAYHLRAYGETTTDRGAIMAAVKDW
+EFTPPDEINHLFSRLLYPVVRWSAGESSPRDGFTSAQIGAFKGISAGAASFGRLPWAHGL
+LMAKAHVDDYNTRNAALIAHGALAPLEFPFQLSQPIIDGEMFFRFVRHYTSLARTLGVSA
+TEADQTVQDDARRHREIRRVHAITGLVRSSGNGAGYRYTQELYGALLLAYADRFGAEDLE
+RAALVLARHAFALRTRLRRVYPRSTELHALGLNKAVDSAEQVNLFRLMMGTMDPAAITGR
+VPARPGDVDNAPEPVRRLYSDRPWDPEEESHHV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001965.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001965.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6eb5a2e39989f1f0fa98de9e74db7f410475df62
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001965.fa
@@ -0,0 +1,20 @@
+>1_1650
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED
+>2_832
+MSFTQTDTPLTQDELAKVIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQVDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHIDVSVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAACTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEEAHPGVRFEKLEA
+>3_770
+MGFTHTENPLSHEELAQVIAADIAPGSYVNLGIGQPTTVSDYLDADQHVTLHTENGMLGF
+GPQAHGEQVDEDLINAGKIPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDRKLMPECTFPLTGVGCVSRIY
+ADKGVFLLDSSGVVKVRELHGITFEELQATHEGVTFEEVDASA
+>4_1868
+MSITQTDTPLTQDELARTIAADIAPGSFVNLGIGQPTTVSNYLEAEKNVTLHTENGMLGF
+GPQAEGEQIDEDLINAGKIPVTELPGAAYFHHADSFAMMRGGHLDVCVLGAYQVSATGDL
+ANWSTGKPGAIPAVGGAMDLAIGAKDTYVMMDLFTKKGDPKLLAECTFPLTGVGCVSRIY
+ADRGVFLLDASGVVRVRELHGITWEELEAAHPGVRFEKLED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001968.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001968.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb9e94ecb0b718aa686f8e063ad517ddac85c6d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001968.fa
@@ -0,0 +1,24 @@
+>1_1653
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVNLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
+>2_829
+MLRSFTPGRPSLTVSDAAAAAGTTRATARRVLHTLVHEGYAVQEGRDFRLTPRVLELGHG
+YWTGTSLAEILSPVLTRASQELEQSCSAAVLDGPFLLYIARVHTERIIRVNLDVGTRMPA
+FLTSMGRVLLADLPPATVRRVLEAAPRTPRTPRTVTDVEALLEEIAQVRRQDHAVVTAEL
+DDHLSSVAVPVRGPDGAVVAAINTALPHRTPGAAEPSADEQTRAAVAQALPVLRAAARDA
+EDALVALRR
+>3_767
+MSLPSTEITSPAPGDGYVRALATGLAVLRAFTPDVPRLTLTEAADAAGVSRATARRSLLT
+LVELGYAVQDGRAFELTPKVLELGHGYWSGRSTSEVLRPVLTRASQRLHQSCSAGVLHGA
+HLMYIARVHTERILRVNLDVGTLLPAFSTSMGRVLLAGLDDAEVRRVLEGAPRTPATAQT
+LTDVDALLEEVRRVRERGHALVHGELDPNLSSVAVPVRDRDGRVVLAVNTALSTRRGRLG
+EALSPAAAEAAAAEALPVLREAADDAEAALELLGR
+>4_1871
+MTDDVDAPGARPASGGDVVRALASGLAVLRAFTPDTPTLSVSEAATAAGVTRATARRMLL
+TLTELGYAVQDGRRFALTPRVLELGHGYWSGRSVSEILRPILTQASQRLHQSCSAGVLHG
+AHLMYIARVHTERILRVSLDVGTRLPAFTTSMGRVLLADLPEDEACALLAGAPRTPATEH
+TLTDVDALMAELARVREQGHAVVTAELDAHLSSVAVPVRDAEGRVAVAINTALSLGPDHR
+DPGARRAALRTGARVPAPRTPEVAAAVVQALPVLRAAADDAEAALAALQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001971.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001971.fa
new file mode 100644
index 0000000000000000000000000000000000000000..15cbe90d6bebeac15277b68d867ae0686bb06180
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001971.fa
@@ -0,0 +1,32 @@
+>1_1658
+MTSAAADLAAVADVGLLDPAWAGSRAEAATADRTFLGHLLDVEAAWVRVLARHGLATEAE
+AAAAAAAGDPDAYDLAALARAAQGGGTPLIPALKALRAQLPAGSRAVHLGATSQDVVDSA
+LMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLPSTFGLRAANWLDGL
+GQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVTAFTLVEDLAAELGL
+AAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGELGEPLAAGRGGSSPM
+PHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEWPALRRLLRVAGGTA
+ALTRELVSGLRVHEDRMRRNLELTGPLLVSEPIMAELAPELDEASGEPGSGKRLIQDVVD
+RSLACEGNFRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRLLAARRGTTTPPRT
+>2_825
+MTDLDALDLSADAGLLNPAWAGRPVARATADRAFLQRMLEVEAAWVAVLAAHGLATDEQA
+RQAEEACDPAGYDLVALARAAQGGGNPLIPALKALRERLPAGSTAVHMGATSQDVIDTAL
+MAMAAEVGRGLGEDLRGLAAALAGLAREHRGTPMVARSLAQHSLPSTFGLRAANWLDAVG
+QAAQRLERATAALPVQWGGAAGTMASLAGHVDRAHRAGRLDESVTVFTLVEDLAARLGLS
+APAGPWDTNRMAVTGVAAALADVTAACGKIANDVLLSSRIENGELGEPLAAGRGGSSAMP
+HKQNPVLSVLVHSAALSAPGMLAQVYTAAGAANDERPDGAWHAEWPALRQLLRVAGGAAS
+LTRELAEGLRVNADRMAENLAQTGPVLVSERLMAELAPAIDEACGEPGAGKAAIQGAVDD
+SLAGRGEFRALLREAVPDTVSDDRLDELLDPAGYTGEAGALVDRILAAHAELIDT
+>3_759
+MTRPRVGIVGAAPAGPWDTNRMAVTGVAAALADVVAACGKVANDVLTSARIENGELGEPL
+AAGRGGSSAMPHKQNPVLSVLIHSAALSTPGLLAQVYTAAGAANDERPDGSWHAEWPALR
+QLLCVAGGAAALTRELVSGLRVHTGRMAANLALTGPLLVSERIMAELAPELDALFGGPGS
+GKAVIQGAVDASLAGEGDFAELLRAAVPAEVSDARLADLLDPVAYTGEAETLVDRILAAH
+APRLRASA
+>4_1876
+MHLGATSQDVVDSALMVMVGRVGAILAEDLAAAQDALAELARAHRSTPMVARSLAQHSLP
+STFGLRAANWLDGLGQAADRLAAAVADLPVQWGGAAGTLASLSGHVDRAHRAGTLGPEVT
+AFTLVEDLAAELGLAAPAGPWDTNRMAVTGVAAALADVVAACGKIANDVLTSARIENGEL
+GEPLAAGRGGSSAMPHKQNPVLSVLIRSAALSAPGLAARVYTAAGAADDERPDGAWHAEW
+PALRRLLRVAGGTAALTRELVSGLRVHEDRMRRNLELTGPLLVSERIMAELAPELDEASG
+EPGSGKRLIQDVVDRSLACEGNSRALLRAAVPESVPDARLDDLLDPAAYTGEAEALVDRL
+LAARRGTTTPPRT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e492b46d0638be095d40b1ae7aef441a4dc0827c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001972.fa
@@ -0,0 +1,20 @@
+>1_1736
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>2_684
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VGSFDIEVQSPDEFFMNQLDLDPARVMTALAAQASATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
+>3_595
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRTLETMHPDMRASGAA
+RHRAEVMDAAFDDARVEGWEQLVLGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVSDVLERLVPCGAPLFA
+EAARAQLWRVDAERP
+>4_1960
+MARFSAVLDACVLVPIAQADTLLHLAEAGLYRPVWSGRILDETVRALEAMHPDMRASGAA
+RHRAGVMDAAFDDARVEGWEQLVPGIDLPDPDDRHVVAAAIQGRADLIVTANLKDFPREV
+VESFDIEVQSPDEFFMNQLDLDPARVMTALAAQAGATRNPPLTVRDVLERLVPCGAPLFA
+EAARAQLWRVDVERP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001979.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001979.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1c684e8dc712f0a8cdd9d49b09833851d27bdd5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001979.fa
@@ -0,0 +1,23 @@
+>2_2140
+MSTHQHDHGHPRPEASEQTGREHGAPAPQVDPDEDPRAFWEGRYGGERVWSGKVNATTAA
+LVAGLGVTPGRALDLGCGEGGDVLHLAEAGWDVTGIDLSEAAVARARDAARERGVTQRTR
+FLAADLSDPAADWGAHEAGAAGYDLVTASFLQSPVALDRRRILRRAADSLAPGGHLVLVS
+HGAPPPWAPPQLAERGDFPSPAAELAALGVPADGDARWEVLTAELRERDTTGPDGRSTRL
+KDTVVVVRRR
+>2_2525
+MHSTTDQHAASGRYGDEHAELYDLMYGSLPDWKQLPALCRRVRPAARTVLEFGIGNGRLA
+LPLAEEGFEVTGLEASGVLAGQLAARARDLPVDVVVGDFRERLTQDRFDLCLLMTNTLFM
+TEGVADQRRVLRRAAEALAPDGMLIVETYDPQVYLEKPAVSNFSMPLGDDALLTDTVIVD
+RLNCSVHIHHTVVRRGEVTVLRERSSWLTPRELDLVCEEVGLKRTLRFADLAGSPITDST
+RNVVSCYERR
+>2_2610
+MTGATRHDSPSQNPQEFWEGRYRYAERVWSGRPNPSLVNAVQHLAPGKALDLGCGEGADA
+IWLATQGWLVTGVDISATAIARARREAQRQQASAATRFVTADLARWEPDDGPYDLMTASF
+LHSPVPLPRIAILQRAATTVRAGGHLVVLSHAALPPWVDAADHPAHSFPSPARQFVELNL
+NEHDWLVLSIQTHTRHATAPSGEAAELTDGVLLLQRR
+>3_2038
+MSDQHSPGHEHRHGGAAPQIDPGMDPREFWENRYGGEQVWSGKVNATTAALVAGLDLPDG
+PGRALDLGCGEGGDVVHLAEAGWHATGVDISEAAVARGREAAAARGVAERTRFLAADLTD
+TSADWGARDDGAAGYDLVTGSFFQSPVALDRARILRHAASLVAPGGHVVLVSHAAPPSWA
+PPEVAARGDFPTPAGDLEALGIMTEGDEDWEVLVAEVRGRESTGPNGEAGHLDDGVVVVR
+RQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001990.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001990.fa
new file mode 100644
index 0000000000000000000000000000000000000000..760368e1a1b6cd14baf7815052f4e65e1c8135bf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001990.fa
@@ -0,0 +1,30 @@
+>0_27
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALDPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMAASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSVKRRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>1_1995
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTRFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGAERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMVVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
+>4_26
+METLGLLMEGFAGALTPMNLLWVVLGCLLGTAVGVMPGLGSSMAVALLLPMTFALEPTAA
+FIMFSGVYFGGLFGDSTMAILMNTPGQASAIASTFEGHRMAQDGRAAQALATAALGAFIG
+GMVASVCVVFLAPVLAEFSTSFGPAEYFALALFAFVATSSVVADSVLRGLASLVLGLGIA
+VVGIDAVTGTERFTMGSPQLFDGIPLVTVTVAILALGEVFHVASRVRREHEDLRIRRTGR
+PWLSGAEFREAAPAWLRGTAIGLPFGIVPVGGSEVPTFLAYSAERRLDRRRAHPQFGRGA
+IRGLAAPEAAGNSTTGMAMGALLTLGLPVSATAAIMLAAFRQYGLQPGPLLFDRSPDLVW
+ALLASFFIAMIVLLAINLPFAQLWAKLLLIPKHYLYAGITLFCGLGIYATTGAVFDLLML
+LGIGVLGFLMRRYGYPLAPLMIGMVLGPLAETSLRDALLSSVGDPAVLVSTPITWVIYGI
+LAIVLAFSVRAAVVRRTRQDV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001995.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001995.fa
new file mode 100644
index 0000000000000000000000000000000000000000..614873286f292686be2fba39be1471de4cc700fe
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001995.fa
@@ -0,0 +1,15 @@
+>0_168
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRITGAEELRRFLGLG
+>2_624
+MTRTLEEIWPPYGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMQGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTGEVFFELRPEGFVRGDEPVRIMGAEELRRFLGLG
+>3_41
+MTRTLEEIWPPSGLVVEAGDLRMTALREADVPEVLDVVAGGIHDPSWTPFLFPWTDAPAE
+EMPANYLRFYASTLTRTVDGDVSLELVVRRNGQVIGMRGMNGPDVAGTRRLETGSWLGLP
+FQGQGLGTRMRRMMCALAFDGLGLDAVTSSAWEDNAASRRVSEKVGYLETGRGQAERRGV
+PTPEVYFELLPEGFVHGDEPVRITGADELRRFLGLA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001996.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001996.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c84195572eb6f67930fe4f544966a0bd5db325df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001996.fa
@@ -0,0 +1,21 @@
+>0_197
+MSGAGSARLTRRTALGLLAASLPLGLSGCVLQGEATTGPVNGPDTLSIDYATYNPLSLVI
+RHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAALLNRANGAPTRIV
+GVASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEAAGVDPADVEIQN
+LQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVLNATESFLEADPE
+TAQTVLDTYERARAWALEHPDETVGILAEAAKISPDVARTVILERTNADVSPVPGQELLD
+ALTGVGRILVGTGSVDYQHQVDAALASILDTRFAEEAIR
+>2_189
+MRRPVVARPGARTLGRRALLAGGLGLGAAAAAGCVVPGEQTRPGPVDGGDWAWTLNIDYA
+TYNPLSLVIRAKGWLDEALNPDDVGVHWVFSAGSNKANENLRAEAIEVGSTAGSAALLSR
+ANGTPIRTIAVANRPEWAALVRAPGSDVDDVAALAGSVAAATRGTDPYFFLVQALREFDV
+PRERVEILNLQHADGRTALFGGSVQAWSGLDPIMADAQRDGAELFYRNLAFNTFDVLNAT
+QRFLDERPEVAQTVVDVYQQARAWVLASDANLAETARILAEEAGLDAAVARTVLAERTNL
+DVSPVPGADFTTALNGVGPIMAESGDARSLDAVQQAIEQIVEPAFAQRAAARPTPAGGNA
+>3_129
+MSGAGSARLTRRTALGLLAASLPLGLSGCVLQGEAGAGPVNDRDTLSIDYATYNPLSLVI
+RHQGWLEETLAPRGVRVNWVFSAGSNKANELLRSNSVDIGSTAGSAALLNRANGAPTRIV
+GIASRPEWSALMVPPGSDITDVAQLAGRTVAATRGTDPYFFAVQALEAAGVDPADVEIQN
+LQHADGRAALAGGSVAAWSGLDPIMAKAEAEGARFLYRDLALNTFSVLNATESFLEEDPE
+TAQTVLDTYERARAWALEHPDETVGILAEAAKISPDVARTVILERTNADVSPVPGQELLD
+ALTGVGRILVDTGSVDYQHQVDAALASILDTRFAEEAIR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001998.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001998.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a5664e3dac2a147099ded43ab5b43f5627e65573
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0001998.fa
@@ -0,0 +1,12 @@
+>0_262
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
+>1_2228
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
+>4_260
+MFNGKDDWTAAPVGVRAWASQRAVELIAAHTPWFGFQGVDVDRLRQRPGWEDAKPHIVVS
+AQLLNRVHRRTSLRADGLLVIADDHHLRDDSRLTYRRMRAASVQGLSDGALDHLLDTMYF
+GPSNQSRLLQAVDVLTYFEQRRRHVTERHRDAVRRMNAIGRSLNKIRQHSYVWTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002003.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002003.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1757d5e542927e569832c5b73831bada42557500
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002003.fa
@@ -0,0 +1,15 @@
+>0_431
+MTAITVVGGTGYAGAAIVAEAARRGHTVTAISRTAPGTQAESVRYVTGDLTRSVPDIAGA
+EVVVAALSPRGDNAGKLRDAYRSLAQAAATNGARFVGIGGFSSLRPAQGAPRFVEGDDLP
+PEFAAEAREMNDILTDLATGSVDVDWLFVSPAAEFGSHAPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTRHRAQIHFAY
+>2_2448
+MTAITVVGGTGYAGAAIVTEAARRGHTVTAISRTAPGTQAEGVDYVTGDLTQSVPDIAGA
+EVVVAALSPRGDNAGRLRDAYRSLAQAAATNGARFVAIGGFSSLRPAEGAPRFVEGDGLP
+PEFAAEAREMNDILADLATGSVDVDWLFVSPAAEFGSHVPGEALGRYRVSGEVALFDQDG
+KSAISGADFARAVLDEIETPTHHRAQIHFAY
+>3_2430
+MKIAVIGATGMVGSRVVAEARARGHEVAAGSRSGSRQDGWFDVDVADTAAVARVIEDNDI
+TVLAVPPVRTGDGDVTAIRRSHQALIAAAPQGRFIVVGGAGALQLPDGSLLKDSAEFPAE
+YKAESDVFGDILEDYRASQGLAWTMLAPAPMIAPGERTGAYKTETDIPAGETVSAEDFAV
+ALVDEAESGAHRGTRFTVAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c4eeea5854d50ae59c3adb4fc20948bd8e32572c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002004.fa
@@ -0,0 +1,10 @@
+>0_433
+MVTMRQAGAKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQK
+MLTQTLRALEEDGLVTRTVYAEVPARVEYRLTEAGHSLRAPLQALEEWSITHLADVLHAR
+NHYQT
+>2_2447
+MKRGNPYEQGCPTRHILDRIGDKWTVLIVGALGEESLRFSELRRRIEGISQKMLTQTLRA
+LEEDGLVMRTVYAEVPARVEYRLTEAGHSLRAPLEALEKWSITHLADVLHARTHYQT
+>3_131
+MNRSWNPLLASCPSRTSLARIANKWTALIVIALAEGPLRFGGLHDGVDGISRKVLTDTLR
+DLERDGIVARTDHGGVPRRVEYELTALGRTLETPLAALVDWAAEHHDAVEAARVDYDERR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002006.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002006.fa
new file mode 100644
index 0000000000000000000000000000000000000000..dc34e116f624b989dbe4b6619388db1a3af65230
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002006.fa
@@ -0,0 +1,21 @@
+>0_476
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>1_206
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
+>4_475
+MGVPVDRARRLLGAVIVAQMLPEGVVVKGGNGVRLRHGATGTRATRDLDLLARDPQQALK
+DLTGFVDRGWGAAPGSKRELKADPAATRVAFFGTVHEDDPAEPLGVPDPYVLSRAKVTLH
+FLSARTSWVSVPIEIGRDEFEGSTLAQPVEVVAPQVAEAVTALGCGTPRSVAVMAVEQQL
+AQKIHAVTDPHQTRGHDLVDIQLLWHGAEAEGGVDIPLLADLVSRTFMFRSPGRTAAGHT
+PHEWPPPVAHVRTLEQGYLDALEETRVGAEGQARLLQPRVSDAADWLESLITRIARAAGA
+EGSGAQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002007.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002007.fa
new file mode 100644
index 0000000000000000000000000000000000000000..da4b190877cadd6cd2927fdeda22431f1262c0c3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002007.fa
@@ -0,0 +1,21 @@
+>0_492
+MASFDILYIRPAGSGWGPVHELVQLTRRLFDARLIEVDDTGDVNRLQRASALLPRGPRVR
+DRHLLVMGPQPAAIAHVAHPRLWLPGYRSVAVWIIDSFWTDRTPRLLRDRPHVDRLFITD
+PQLVSEWSGQTGLPVGVLPWGSDTTRFTSAQEGTDRPVDVLRVGRQPRAWSDDARTSRDA
+AAHGLHFAGRPPFSDDPARNQMLVREAMGRARVVLAFSNLVSPAPYTHPTRDYLTGRWTD
+ALAAGCLVAGTAPASAASLLWPGATVEISPTSRDDAWPVLAQLASEWTPQAAADRQSEAR
+RRLDWRYRLRDLCMAMDWAVPDRLTAELATL
+>1_226
+MSVDVLYVRPGGSGWGPVDVLARLAARLLEGRLVEVEDRGAASWAQRASVLLPRGRRARG
+RRLLVLAGNPAALALAARRDLWWPGHESTAAWIVDSFWTDRIAGIARHRPHFDRLFVTDP
+DLVDEWSALTGRPVDALPWGSDTLAVAADDGPRPVDLLRLGRQPEAWDDDARTAREAQDH
+GLVFRGRPPSSPDPLQNQEAVRAALAQARLVLAFSNLVSPAPYTHPTRDYLTGRWTDALA
+AGCRVAGVAPRSAATLLWPEATLEVSPNSRAEAWPVLAEAAAAWTPERAAEQRRRARREL
+DWRLRLQRLCTAMGWPLPPTLDAELAALG
+>2_2383
+MTLDILYVRPRGSGWGPVAELVALAARLFDARVAVVDDHGEVSLFRKTAASLPRGRRRPG
+HHLLVVAPHAGMAAYAARPRLWFPGYDSTAVWVIDSFWTDRTPRLLRGTAHVDRVFITDP
+QLVEEWEQITGTPVSVLPWGADTALYPSAAHHRDIDLLRLGRQPKAWADDDATAADARRR
+GLRFAGRPPMNDDPGQNQHNVREALMGAKLVLAFSNLVSPAPYTHPTRDYLTGRWMDALA
+AGCLVAGTAPAAATSTLWDGATLEISPTSREDAWPVLTAAAEGWSPERAAEQQERARRTL
+DWRWRLRQMSSVMGWPEPPRLTQELERLISSPQQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002008.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002008.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2feb5d839635a521dabf2e8dcee114d41df7ad48
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002008.fa
@@ -0,0 +1,27 @@
+>0_502
+MGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFEAVLAIGLVMEAFTA
+PGLPIPFAEFSAILLLLLASFRQPRRDLSQYGVLALVALALVAYLVAVTVHNDLDPTRRA
+TRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDTYGGYLTGFLGDKNV
+SGLFYALLPVLLVATMQRMGPKLLVLGAGFALTFLTGSRTSMAGLLCAVVWILVSPYLGR
+VLRIALGVVLGWFVSWAEVNLADLGIFGDRTGTDWFREQIQEASAEKVADTSFFGQGLST
+AFVELDNVTMFFHNSYLGLLVEGGWPFLIVVVGAYLWLCLRPFARTHRSPSRVAVEAAAL
+IILVTSLQLGEVFITIFGAVVLGCGLLLSAQENEESQGAPAKDRAHRRKLDRIIERSRRA
+GV
+>1_232
+MRPSTPRDRTAARAMGAVAPPEARPARRHASLGLVPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGVLYGMTAGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGSVLTFLTGSRTSMAGLL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRAGR
+>4_502
+MRPSTPRDRTAARAMGAVAPPEARPARRHPSLGLFPDGQAAWTRSPWNPLVTPASPRLFE
+AVLAIGLVMDAFTAPGLPIPFAEFSAILLLLLASFRQPRRDLSHYGVLALVALALVAYLV
+AVTVHNDLDPTRRATRITLLILLIYAIASERIDIKGILYGMTVGALINVPLFYAGLAPDT
+YGGYLTGFLGDKNVSGLFYALLPVLLVATMQRMGPKLLVLGAGAALTFLTGSRTSMAALL
+CAVVWILVSPYLGRVLRIALGVVMGWFVSWAEENLADLGIFGDRTGTDWFRAQIQEASAE
+KVADTSFFGQGLSTAFVELDGVTMFFHNSYLGLLVEGGWPFLVVVVGAYLWLCLRPFART
+HRSPSRVAVEGAALIILVTSLQLGEVFITIFGAVVLGCGLLLSAQESDESHGAPAKDRAH
+RRKLDRIVERSRRANR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002010.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002010.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2e6d16a521c63429d61402a36e55ecb2b5ae23cf
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002010.fa
@@ -0,0 +1,9 @@
+>0_558
+MVGDMSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGAGAARTEAP
+RTAGTGPAQAAAEAEPSTEAGSARG
+>1_300
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQAGSARG
+>4_559
+MSLSFVSSARRRHGGLASAALFHPLVEAATGALPVIDPATGRPASEGVDAARTEASRAAG
+TGPAQAAAETEPSTQGGSARG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cb38ab586ed36e5a392269e253ee7d579a0da6a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002011.fa
@@ -0,0 +1,18 @@
+>0_563
+MSAQQMWEARTSGPKRAEAPASGQAVGASENAQSETVHIPKNTLVEHSKDSTGARPTDSG
+IRTLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGESARASWWALGAFTGLSMIANGAHAWSAENASVWQSVVGALIA
+VMVPVAVFVATDQLARVAVENPDSRRAERASQVSEEAEQLKAQAELDRQRAELEAELAAS
+RWQIEAQRREAEREAEVAEARHRQELERMERQAKLETEREAREVPQAVVEESQVAQGIEV
+VETVASSEPVAAETKTVEKASGADITAWIVSRAQEGQVPSAAEVAEKFGCSERTGRRRLV
+KSLEVV
+>1_306
+MSAQQMWEARTSGPKRAEAPSSGQAVGASENAQSETVHIPKNTLVEHSQDSTGTRPTGSG
+IRSLPRRVNPNDGRFIRAVVAGTAVAGLVAFSISFAALYEVAAWLGLPPFMHWAVPVFID
+LAILVYAGSVLVHESRGE
+>3_1743
+MRARRWAVRTAVAGTVFIAIGAFWLSFTALADLAARSGIGAGQAWAWPLIVDGIIVVATV
+AVVALAGQKAAWYPWALLIGGAVVSVTANALHAIVAADADVPALLAAAIAAVPPVVLLAI
+THLTVILTRATSPETQTVIWQTIAQQNDQPTPAPRPGIEAEPPPAALLQHDVSDTVGLGD
+ERPTTPESGPSPMKHAEAKPAPEASTPTAPNGETVRGVSEMAGVGRRERAAGLRSEGWSN
+KQIASELGVHPSTVGRWLTSTPTRSSEPDTNPSIKEES
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53a2a55137e4ebc5a39b8b87147908a853e221bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002015.fa
@@ -0,0 +1,38 @@
+>0_676
+MHRLGPELQGILAWCRSRGVPTAFWNKEDPVHFNTFLTAAGEFDAVFTTDLDCVPRYKRE
+LGHENVHFLPFAAQTAQSNPVEVFDRVEGCAFAGAYYAKYPERLADLRELSAELSADGRR
+FDIYDRNHGRATSGYTFPEDYQRYIVGGALTPGLLDVPYKGYTVNLNLNSVKQSQSMFAR
+RVFELLASNTLTVSNFSRGLRLMFGDLVVSTDSGRQMRRRLEAIEAQPNGNERLRAVALR
+KVLREHTYTERLEFVASRSGVTLPDAAVERPLMVVPSTLGRDAAAVVELVRRWAGQTWND
+WVLAVQGKVEEFAPMPLELQDPRVVLFDELADLDGLARTRGCTLAGMLDPNDWYGPHYLE
+DMVLTLRWADVKTCGHVEHYAVDSVDGSLERRELGTAWRLQDKILPCRSLSRLDWAQVAD
+CNGVARQLDAAQLSGLAVSPLEYCAGGATSEEPALAPASSLDVYEGLTLTEIRQHADDLV
+FAESSDDMPVMDLGTIFEGMKSFDEMTLTWEDGVPRVTSSLGAGRHQYWINSLARPVEFH
+QNGNDQPVYFDVSVGLDIMLVAYWLDADGQRFGHAMIPARQYTTVKIPEQARAMRWGLRV
+SGSGSAVVHRVVNGPYVAPSVPMLAGSSDVLITNIYPAYDNLYRNGFVHSRLRRYREMGH
+RLETILVGEGDGPRFREFEDVDVAVLRVQDLIATLATGEVKTLVVHCLLPETWNVLKATS
+DLPPTTVWVHGFEIQPWWRRRFNYATEEELDAAKMLTEQRLAMWREVFDSSPDNMHFIFV
+SRWFAETVFEDVGIRLPDHRYSVIHNPIDDTVFPYQEKTAQHRLRVLSIRPYHSHVYAND
+LAVAAVLELSNEPWFNELDFTFIGDGPLFEETLAPLWDFENVLIRKGFLTHAEIASEHAR
+HGVLLVPTRSDTQGVSRDEAMSSGLVPITSAVAAIPEFVDEEVAFLAPPEDHRALADAVR
+TLRAEPARYLRMSAAAARRVRRQSGADHVLDAELRLAFRTDGDHSAPSVRPHPEREAHRP
+>0_858
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA
+>1_589
+MLRAVFDTLPQDSDAVRRLRAAAAPPRRRRTSPPRPAAPAGAHGDTPGYRGYLHLADVGD
+TYTAQEASTLLQLENAALKRRLFAEPAPPLPPTGHEDEDLAAAPRRVADHLARADAADQL
+GDDAPRHLVVVGVYPTLENPYGNGFVHRRVKYFQAAGVRVDVAVIDRSAEPRSYEYDGVH
+VLVGRGAEAAEMLRTRHYESVAAHFLVRSLWEPIQDALAGHRFFVFMHGFESRRWIRTVR
+NHRTQGQVDDAIVDTLERQRFWREVLEHPHGPERFVFVSRWWRRAAQEDMELVFPGQRTA
+IVHNVIDTDLFRFVPKDPEQRFRVLWVRSAANLNYGADLAVRALERLRDTPLWDRMQVTV
+IGDGKHFGLFEAAFADDANVTVERRYAVQEEIAALHREHGVFLVPTRLDSQGVSRDEAMA
+SGLVPVTNDAGAVREFVDEDCAMIAGVEDVAGLADGLRRLMEDPDLFLRMSQAAAARVRA
+QTSPEHTVDHEMALMGLAAGPGGRGEENA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002019.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002019.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c7a332ca69342a048a8187c08b87290a693e54d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002019.fa
@@ -0,0 +1,14 @@
+>0_855
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG
+>1_586
+MSGNVFTAASADVAEDAVLGDGTKVWHLAQVREQARLGERCIVGRAAYIGTGVELGDDCK
+VQNLALVYEPARLGRGVFIGPGVVLTNDTYPRAVNPDLSQKSGDDWEAVGVDIGDGAAIG
+ARSVCVAPVRIGEWALVAAGSVVTRDVPDFGLVAGVPAKRIGWVGRTGRRLEEKDGVWVC
+PDTGETFIERDGALRPAEPAQEEENHG
+>2_1190
+MSKLRMLSRMPKKGRFMFIISGGDRARYMSRKGLVRGMGENVWFQPRALPNDPNLIRFHN
+NIVVASGVTFVAHDVINLMIGRKNGVRLPVNEDCIEVMDDVFIGSGSVILPGVGIGPRAI
+IAAGTVVTKDVPPDSIVRGVPAKRLGDFSVLEAQRLADAGRFDGMTRAQIDDVLWE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0eb21fb5e4ac6bb5bf5f3b81f1bced17029914c5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002020.fa
@@ -0,0 +1,24 @@
+>0_856
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
+>1_587
+MAEFIPAAKPLIGDEERAAVDRVLRSGMVAQGPEVAAFEEEFGAAMVDGRACVAVNSGTA
+GLHLGLLASGIGPGDEVIVPAFTFAATGNAVALTGATPVFADVDLDTYTLDPQDVRAKVT
+ERTAAVMPVHLYGHPARMDELEAICREHGLQLFEDAAQAHGARWKGRPVGTFGAWGMFSL
+YPTKNMTSGEGGMVSVGEADVARRLRLLRNQGMEVQYRNELVGFNNRMTDIHAAIGRVQL
+TKVGAWTRRRQEIAARFDAELRGVTVPTVLEGAEHVYHQYTVRLPEELAGTRADVLARLK
+DEFGVGTGVYYPVPTNELPSFGVEADLPNTRVAASTVFSIPVHPSLTDADVTRVVEAVNT
+VVAEAAA
+>2_1198
+MTDRIFLSSPDVTQAEEDALVRAFRSNWIAPLGPEVDAFEAELAEYTGRAHAVVLSSGTA
+ALHLGLLNLGVGPGDLVPTSSLTFAATANAIAYTGAEPVFVDADESGNMNPALLEQALAT
+LRGEGHEVKAIVPVDLLGKTADHAAIGRIAAEHGAVVLSDAAESLGATRDGKQSAAYGVA
+AAVSFNGNKIMTTSGGGALLTDDEEMATRTRYLATQARQPVVHYEHTDIGYNYRLSNILA
+ALGRAQLNRLEEMIERRRALRIRYRELFAAVPGVEMFGEPSGADGGPTRDNFWLSSVLVD
+PDAAGFTAEDLRAHLAGQDIEARPLWKPMHLQPVFAGRRAFTDGTGERLFTTGLSLPSGS
+VLDESRISRVLDSITAFLESRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002024.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002024.fa
new file mode 100644
index 0000000000000000000000000000000000000000..54786262931bbda97ce41fd45b886ed4a93f8318
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002024.fa
@@ -0,0 +1,31 @@
+>0_934
+MTTAMTTTTDVRPAPRDESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWR
+DNTYPGAACDVPSHLYSFSFAPNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADML
+EAHWDPETERWTVRTPRGTYTGRWLIMGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTV
+DLKGKRVAVVGTGASAIQVIPELAATAAELVVFQRTPAWVTPRVVKPYSAAVRRMFERAP
+HTMQRERDDIFWFAESNYAQRRGVPAALDQVRAQALGHLAAAVSDPELRERLTPRYLPGC
+KRVLVSNDYYPAMARDNVTLEDSALDRVEGSRLFGVSGHGYEVDVVVLCTGFEAAQPPFA
+ERVHDGEGRSLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYIL
+EALDRVEHEGIRTMVPETLAQEEYVDRLQERAATSVWLVDGGCHSWYVDPRSGKLTLIWP
+DYAYDFRARNGHFTGEGFLSSASGEPEPMPVREPERSVALI
+>1_656
+MTTTTTTTDVRPALRDESAEILIIGSGFAGLGMGAQLRRHGREDFLILDRAQQVGGTWRD
+NTYPGAACDVPSHLYSFSFAPNPQWSGFYTPGPEIQDYLVRFSEDEGLTPHLRLGADMLE
+AHWDPETERWTVRTPRGTYTARWLIMGTGHLADPRLPDVPGLDAFEGEVIHSARWDHTVH
+LKGKRVAVVGTGASAIQIIPELAATAAELVVFQRTPAWVTPRVVKPYSAAARRMFERAPH
+TMQRERDDIFWFAESSYAQRRGVPAALDQVRAQALGHLAAAVSDPELRERLTPRYLPGCK
+RVLVSNDYYPAMARDNVTLEDSALDRVEGSRLFGVSGHGYEVDVVVLCTGFEAAQPPFAD
+RVHDGEGRSLADHWSSGMAAFDSTAVAGFPNLFAINGPNTSLGHNSIVYIIESQIAYIVE
+ALDRADHEGIRTMVPEALAQEDYVDRLQERAATSVWLVDGGCHSWYVDPRSGKLTLIWPD
+YAYDFRARNGHFTGEGFLSSASEDPEPMPVREPKRSVALI
+>2_795
+MTTQTTETTAPTTDAAPGAAAGGDVQTVDAVVIGAGFGGCYLVHRFADEMGMSVIGLEKG
+DDIGGTWYWNRYPGALSDTQSHLYRYSFHKGLLEKGDWSHTYVNQKDILEYFELVDRELD
+VRRHFRFGEEVASATWLEDEQRWELVTKSGLTLRATYVVNAVGLLSAVNMPTIKGIDSFQ
+GEILHTGAYPEGKDLSGKRVGVIGSGSTGTQVVTALGPQVKQLTHFVRSPQYSVPVGRRE
+VTDEEKARIKANYDEIWEQVKNSSVAFGFEESSTPAMSVSAEERERVYEKAWNEGGGFKF
+MFGTFSDIATDEEANETAAAFIRNKIGEIIEDPEKARKLTPHDLYARRPLCDDGFYATFN
+LPHVDVVALKETPIKEITAEGIVTAPESGVEGGEQLHELDVIIFATGFDAVDGNYRRMDI
+RGRDGVEINEHWEGQPTSYLGVATDNFPNWFMILGPNGPFTNLPPSIETQVEWITDFIDY
+ARQNGIATVEPKAQTIEEWTQTCTEIANATVFTKVDSWIFGANVEGKKPSVLFYLGGLGN
+YRGVLDGERDAGYPGFELTRADGTQAAASPQPADVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002026.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002026.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0a8176416119861fb7fcf1aa25d438ab5b9181d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002026.fa
@@ -0,0 +1,12 @@
+>0_999
+MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWSK
+RQGDDASVAELSWGPRWGTLWRDTALEFSPGFTTSPTRHTRPTTASFATGRWTG
+>1_721
+MAALDDETAGIPEGNRGPSAGLVYAWGEHSRADPVFGDYPERVLALKYAEPGVELPLWSK
+RQGDDASVAELSWGPRWGTLWRDTALEFSPGFTTSPTRHTRPTTASFATGRWTG
+>4_941
+MAAALYDEAAGTPEGNRGPSAGLVYAWGEHSLADPVFGDNPEWFFTLEHAESGVLLPFRS
+EGLGDDAAVAELSWGPRWGTLWRDTTVDSFTGFHYLADATYPTDDRLVLDWSLDGMTKSE
+DVIITQDAARSDVFALVELLADGQKPWALNVPAGEDAPSPGEADPVPPAEQEPVDTPAPV
+AGEEPGEGTGGEETHTTPDTVETGREVRRARSERSRPSARDSCSWPGGGCAGSDTPGRRG
+GRGAVDGRPSAAPRSVLSRPERIRWGRCSPRLRSRRCSHRRHCG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002030.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002030.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cf79f15632f79625ea9a204537c68e9bbea6507d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002030.fa
@@ -0,0 +1,21 @@
+>0_1337
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>1_1074
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
+>4_1291
+MGNAVGSNIINVLLILGLSALVVPLAVKRRLIRFDLPLMVVLSVLLLLVSLDGRISAVDG
+LILFFGVVVHTIMSVVISRRDAKTAVNAREGTGDSATVDPADEEGAALGASVSRSLFFVL
+LGVALLVAGATLLVEGAVNIATTLGVSSLVVGLTVVAVGTSLPELATSIIAVRRGERDLA
+VGNVVGSNIFNIGVVLGLTALISLEGIPVSGAAVAFDIPVMLAAAVALLPIAFTGFAVAR
+WEGGLFVVLYAAYTGYLVLAATAHDALEGFTVAMAWFVLPLIALTLISFTAYEIGLRKGR
+RDLDQTTTST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002033.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002033.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ec2fa5c5d737a41e326d17bbcfd4e2a9697a633a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002033.fa
@@ -0,0 +1,9 @@
+>0_1347
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>1_1089
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
+>4_1296
+MAMPETDLLRIGRWCRERVPEHLWDQVRVEAEIADRHVTIIETRPPWDGQGDWTRFPVAR
+LRYTVKTGQWSIYWRDRHMKFHEYTKRRPTKNVQSLLDYIGSHQDPIFWG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002041.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002041.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b346082e092dc5066aa79bb4602bd5a3ce6dd684
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002041.fa
@@ -0,0 +1,21 @@
+>0_1567
+MTLPANSIRIIEANNWVSAETAARMKLKLTPPGAVAFAKIGEGLKAERLRRITVPTAMDN
+NMMAAIPKPAVVDSGFLIYLIESVHIAEWAQGSALPYLSQKLLADIPVHVPSLPEQRAIA
+ATLGAFDDKIESNRQAMATGESLIRAVVESTLDASEGEDGTLGDYCALVKAPVEIDKIDP
+DDNYIGLEHMPRGSIFLTEWKKAKGLGSNKTAFKRGDLLFGKLRPYFKKVGIAPIDGVCS
+TDILVVRPKSPRDIALVTAVAASDALIDSLSASSTGTRMPRASWKDLAAWRVPVLTATER
+IELSARVDPLVERLTQLTFESHRLVALRDALLPELLSGGLRVPVTS
+>2_200
+MKPGWTTVALGDVAEVRRTSVHPAHMRPDDPYLGLENIERGGRLLSVSTVAGEGVKSTKF
+RFSPGDVLYGKLRPNLAKILKVDFEGLCSTDILPIAVNSGTLSADFLAYYLSQPQVVAQA
+ASRASGANLPRLAPAEFLALRIPLPPLDEQRRIAAALDRATVVIGGIGDLRRRTRSIGES
+VVQQSSTGAGRWSTIGKSLTLRSGSTLPATRRRPGGVPVYGANGAIGEHDEATHEQPHVT
+IGRVGAVGAVNVTAGRAWISDNALIVVKAPEHLSNGYLAIALAMADLGRFASQSAQPLIT
+QRKVADVPLWIPSQAEALRIDAILDRLAEVERANVERVARADALFASLQSRAFRGEL
+>4_181
+MKPGWTTVALGELCELKYGKSLPAKARSGEGFPVFGSSGLVGAHEKAIQRGPGIIVGRKG
+SIGEVHWSEDDFWPIDTTYFALPRRANVDLRWLYLALRWLPLKTLNKAAAVPGLNREDAY
+RLTLALPPLDEQRRIAAILGTSLHSIGCRVRACIWIDDFLDNVYNSTLRSGDIPRRPIRS
+LGEVSTGKTPATSKADYFGGVIPFVAPGDLGGLVSAKRTLTDLGAQESRLVRAGATMVCC
+IGATIGKVGIVAEQSAFNQQINAIEWGPDMDDLYGYFTMRAQSDVVAARGSSTTMPILAK
+SKFEELLIPVAPFEVQEEFARVASIVSRVRSNLVAAWEAERQLFASLQSRAFRGEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..40824495591cb2ac0feba4490d3124767b91f094
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002043.fa
@@ -0,0 +1,33 @@
+>0_1569
+MSTFNENVVELAALEHFAELGYRRVHAPEIAPGEPDAERDSYEDVVLWGRLRDALRRINT
+SADAALIAEAVKTVQRAGSQSAVDENARLHKLITEGVPVEHRGDDGLLRTTRLWLVDFDE
+PANNDWVAVNQFTIVENGKNRRPDVLVMVNGLPLALLELKNPAAGHATLKSAWNQVQTYR
+HDIPSVFVPNAVTVISDGTSAAMSSYSGAFEHYAPWKTIEGREVVSNRPALEVLIKGVFE
+PKRFLDLLKNFVVFSDETVTDKSTGQPTRALLKRVAKYHQYWAVNAAVESTVQASSPDGD
+RRGGVVWHTQGSGKSFEMVFYAAKIMRDPRMANPTLVFITDRNDLDDQLFGETFAPARIL
+PETPVQAATRSDLRAKLKRASGGIVFTTLQKFAPGEDGDANPVLTDRRNVIVIADEAHRS
+QYGFSETLDRHGRLKSGLAKHMRDALPGATYLGFTGTPIESNDKSTRAVFGDYVDVYDLT
+RAVEDGATVRIFYESRLAKIELSEADLAALDDLADEITESVEKDTATAAKSRWSRLEAVV
+GAEARLDLVARDIVEHWEKRRESLFGKGMIVTMSRRIAVRLYEKIIALRPDWHSDDPAQG
+KIKVVMTGSASDPAEFQPHIHSKDVRKDLKLRAKNADDPLELVIVRDMWLTGFDAPSMHT
+MYVDKTMQGAGLMQAIARVNRTFRDKPGGLIVDYIGVFANLQNALSEYSPSDRDQAGVPI
+DEMVQVMLEKHDIVRGLLHGVQFDSSPELTAAQRLNEYAKVLDFVMADPDRTSRFNDQVL
+ALAKAFALAGARDEAAAIRNDVRLFTDVRAAILKIQNPDSGRGGSGAVEVDTALSQLLNE
+AVTANQVVDVYMLAGIETPEISILSEEFLDSFAEKDRPNLQMGLLRRLLNDQIRTVQRTN
+VVQGRKYSEMLEETVNRYTNRSLTTAEIIAELVKLAKQMRDAQKRHEELGLREDEVAFYD
+AVVQNDSAVMELGDETLKAIAQELVTSVRQSATIDWNLKESVLAAMRSKVRRILAKYDYP
+PDAEAKAIELVIEQAELFARGVSA
+>4_2143
+MTHANAPLTPTGRLRMVHRHLRDLLTQSNSGGIYFTTLQKFGLTQAERDAGADHPVLSDR
+RNIIVMADEAHRSHYDTLDGYAAHLKNALPNASLIAFTGTPIAEGERDTRRVFGDDIDVY
+DLHRAVEDGATVPVSFEPRLITLSRVDGVDDESLDAAADELTAGLDEADRDRIQRGVATL
+EAVYGAPHRLQTLAEDFVRHWEDRRDAMQPTMGVPGKAMIVCATRSIAARLYERIVALRP
+EWHDDADDKGRIKVVYDANPSDTGEIKKHMRRPSALAAVKKRLKNPADELEIVIVKDMLL
+TGFDAPALHTLYVDRPLKGALLMQTLARVNRTFRGKEDGLLVAYAPLAENLQQALAEFTR
+DTRTAGTKTLAQNTEEAAEIIETMVGMLADTVGVDWKATYQSDPKNGWRKALLEVTSRLR
+SPGTPGNTDPEDPTVRPVADTFRSQASRLHRAWALAGRVAAVERFRLDVKFYEEVRTWLA
+KLDAQDRIARGEPIPEEIARLLGEMVVDSTEATGVMDIYAAAVG
+>4_2146
+MEEAAAPSKAELAIEGLRTDLLKEATRVTGGNEIRRAQFSERINAVMAKYTNQQLTAAEV
+IAELVEMAKEVVAEADRGRRFTPPLHDDELMFYDVVAQNEAALDVMGDDVLAQIARDLVA
+TMRRDIKTDWTVREDVKAKLRASIKRLLRKYGYPPDQQPEAIVEVMRQMEAVAPRMAEGQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002058.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002058.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1d22504030e55adaec9a05d4bd55a983d120d2d3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002058.fa
@@ -0,0 +1,14 @@
+>0_2130
+MGGRPAAGLDPPQTAQSGHADDPSSARTVFDRFVFGNHIRSFSVD
+>2_533
+MTTTIQDPWAQPTPAGAYDDLLVRALPVTRAQRRWEPADGPMPSLFVSHGAPPTLDDPQW
+LADLFDWAQSMPKPRAIVIVSAHWEDAPVAISSAAAGTPLVYDFGGFHPRYYELQYATPD
+ATDLAARVAGVLGQGRPGSVHQTGRGLDHGAYIPLMAMYPDADVPVVQVSMPSMDPSALL
+DLGVKLRSLREEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDKWAAEMTHAGDVDSLIGY
+LDKAPGARIAHPTADHYVPLLLTMGAANDPSSARTVFDRFVFSNHIRSFSVD
+>3_457
+MTLADPWAQPTPAGAYDDLLARALPLTRRQKLWEPSDGRMPALFISHGAPPTLDEPQWLN
+DLFEWAQTMPKPRAIVIVSAHWENAPAAISASAAGTPLVYDFGGFHPRYYTLRYDTPDAT
+DLARRLAGVLGAQGQEVHQHTDRGLDHGAYIPLMAMYPDADVPVLQVSMPSQDPADLLRL
+GERLRELRDEGVLVIGSGFMTHSFAAMRDPRLFGHVDAFDTWAAEMAHAGDVDALMGYLD
+RAPGARIAHPTADHYVPLLLTMGAAHDPSTTRTVFNRFVFSNHIRSFTVD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002059.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002059.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fdd2dd5396c466432bbd2bc672fdca301726ac3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002059.fa
@@ -0,0 +1,24 @@
+>0_2138
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVVGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>1_1862
+MAQHSSTPFPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPEPTVLEDLPDAVELRRGVTVTHADLGARTLRVGEEPVRFERLILALGAHPKPLPVAD
+DDAEVHLLRSLDHARRLVASAGHARSAVVIGSGFIGCEAAASLALRGVATTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYMDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
+>4_2083
+MAQHSSTPYPLVIVGSGPAGVSAARAYVDAGGPGPVLMLTSDVDHPYERPPLSKELLRGT
+AEPDPTVLDELPDAVELRRGVTVTHADLGARTLWAAEEPIRFERLILALGARPVPLPDVE
+ADAEVHLLRSFADARRLVTSAGHARSAVVVGSGFIGCEAAASLALRGVETTLVTPDEVPQ
+QKRLGREAGDRIAQWLIGAGVELRTGVRVGQVRAPRTVHLDDGATLAPDLILAAVGVEPG
+GGWLEDSELTMHEGRIVADEHLAAAPGVWVAGDVARAHHAVAGRPIPVEHWGDALGMGEV
+AGHNAARTEVGVPGGAGQASVLAHAATADPESLRRWEAVPGFWSTIGEHTLKHAAWGDGH
+EQARMVERTGGFTLWYTDAQDRVVGVLTYNADEDYERGRELVAGRDAVGEGRGRPDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002066.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002066.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14ea966366af40ff5ac25c57f68ad8f0c56ce7c0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002066.fa
@@ -0,0 +1,12 @@
+>0_2181
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>1_1894
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
+>4_2114
+MIRTPWTRTPAGARRARRPRQFRRVTTTGPAAVDVAWARYADLRLWPRWAPQIRAVEAPR
+RRLRAGLRGVVHAPLGLRVPFVVEEVDDDARTWRWTVRVAGTAVSMTHDLTATPRGTRAG
+LTVHGPAVVALAYRLPARVALRRLCRAHL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002070.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002070.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77d81255c78bf73af699bea6a08deb2f853b706e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002070.fa
@@ -0,0 +1,9 @@
+>0_2203
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>1_1909
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNSLDITLRKVAA
+>4_2135
+MEAHAFADNAPILRVMEKVGLRHEGTFKEESLHRTRGWVDGVTYAMLASEHRARGRRLST
+SRRPEVRNALDITLRKVVA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002071.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002071.fa
new file mode 100644
index 0000000000000000000000000000000000000000..371c62b3b6c67dde67131be615d9d6b98dda706b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002071.fa
@@ -0,0 +1,12 @@
+>0_2206
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPHTW
+>2_450
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELIVLPSRGMSQAGPLASAGWVVTYHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+CEPVLPETPRPDEWLLDLEILEDLGPHTW
+>4_2139
+MDITVGAVGRASLSDWEQECCGDPIAVGEVHELILLPSRGVSQAGPLASAGWVVTHHDDG
+SPAGSIPLRRVRAVVRAAHEVWPSGRLAEIDRVPGHADLTILEPEEATGLGLGEVVYVGA
+YEPVLPETPRPDEWLLDLEILEDLGPRTW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002080.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002080.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8322b3361cc0d638d19985de0331d5b0774ec7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002080.fa
@@ -0,0 +1,20 @@
+>1_350
+MTRISPLSAAGTDFDGTRLTVARRLRRKTKATLAREVGVTPTAIAQFEKNLSKPTQSVLA
+RLCLQLGLPREFFGAGRPLALLPASGAHFRSLRSTSATSREQALAYGELCLELVDLIGAY
+VDLPPVSLPELELPEELTDEAIVEAARLTRSTWGIAPGPLPSVVQTLEAHGIIALRLPVE
+TDAAVDAFSTYSGARPLVFLSPTKDDKARSRFDAAHELGHLVLHPDTEPGSKLVEQQAHQ
+FAAEFLMPRDEIIEDLPRRINWPAFHELKRHWGVSLRALVYRAHSLGRLSEASYRRANQQ
+LSAWGHPEPGPLGPAESPQVLGIARQLITDGGYDFEGIMAAGRIAPEVAEAVMDAASTVR
+PKLRFVI
+>3_306
+MTMMHELGHVIYDRDVSTPWRSTKSPEEERAFRFAGAMLIPANVMKKRVTESLTLHGYLA
+IKADYGVSVGALVKRAESLGIISKSRARSLYIQISSQGWRYNEPVPVAAERSLLIQQATA
+RAFGENLEGVAQSTGVPHRLVEHWTGFKRDLRAPMADVIPLRR
+>4_163
+MSLEPSRIVRARRRAGISKKRLADLIGATPRTISNYETRGAPDALAATLADVLNVDPTFF
+SMPATSPLEEDRVFFRARRRTSAAVRHAASEAGRTGVEFYSLIAEHFKLPEVDLPDLVGM
+GPAIAARQLRAHWKVGAGPLPNLIQLAESRGLRVMSLPGTTDEVDAFSVWEKGVPYIFLS
+QRKTAERSRFDLAHEIGHLVLHSGLGNGDSVERDAEREADAFASEFLLPGEVLRGAMPRQ
+PSTEAVLKAKVSFGVSAMAMAYALFRNGLLSEWAHRQMCIDLTRRGYRSSEPGGIHRETS
+RVFGLTLSLARQRLGLGTEEIAQALGVCPQEIHELTFGHAVTPVASVGGSSAAPEPGPRP
+SLRVV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002085.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002085.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a13c5a344d57459f7b2fc889897830790be90aa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002085.fa
@@ -0,0 +1,12 @@
+>1_1080
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRLGISAY
+GT
+>1_1916
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWVARYRAQGEAGLQDLP
+SRPHRSPAQLDPVLVAQIHALRRERKWSARRIHHHLVSEGHRVCLRTVGRWLHRAGLSRL
+RDLTPGQVPGSGVTVFEAVGA
+>2_136
+MTHANAPLTPTGRLRMVHRHLIDGIPQAHVAAEFRVSRPTVATWVARYRAKGKAGLQDRS
+SRPHRSPARLDPAIVAELEALRRAEKWSARRIHHHLVGEGHQVCLRTVGRWLHRLGISRL
+RDLAPTGEDLRQRPQKITARGPGHMVHLDVKKIGRIP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002089.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002089.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6044a1a741d04f80921987073da2368145f8475c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002089.fa
@@ -0,0 +1,27 @@
+>1_1654
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
+>3_765
+MTERVALIGAGPSGMALLRALALAEDEGAVVPEVVAFERQADWGGQWNLDWRTAADRFGE
+PVHSAMYRDLWINGPKECMEYPDYSFDAHFGRPVSSYLPQEAMKDYILGRVAHVAERIRP
+LIRFGTVVRWVQPLDDGTFEVTSVDLTTGAARTEAFDRIVVATGHFHAAHTPSWPGVEDF
+PGLVQHAHDYRTPEPFAGRRVLVIGSSYSGQDLALQLHRGGAAHVTTAYRKAPQELDWPA
+GMDERPEVQGFAGSRVAFADGSSAEYDAVLLCTGYRHHYPFLPAELALSGPNLPFVPSLW
+KSVVWQADPRVLYLGATQQWFTLTLLDAQAFFARDVLLGRAPVPSAQERQADIDAWTARM
+AAIDSTPVALAFQADQIRDLTAGTGYPEMDLDGVIATFLQMGEDKRESLTRYRDRTHRSL
+VTGTRAAAHPVPWMHHPDGSLEGYLAHFPG
+>4_1872
+MRERVALIGAGPSGMALLRSLALAEDAGAAVPEVVAFERQDDWGGQWNLDWRTGADRHGE
+PVHSAMYRDLWINGPKECMEYPDYPFDAHFGRAVSSYLPREAMRDYIVGRVAEVAGRIRP
+QIRFATAVRWVQPLDDGGFGVTSEDLVTREAVTERFDRVVVATGHFHTPHLPSWPGVETF
+PGQVQHAHDYRSPEPYTGRRVLVVGSSYSGQDLALQLHRAGAAHVTTAYRARPQDIAWPA
+GMDEAPEVQGFDGAEVTFADGSTAEYDAVLLCTGYRHHYPFLPGELALAGPNLLAPFGLW
+KGVVWHADPRVLYLGATQQLFTLTLLDAQAFFARDVLLGRVPVPGDEERRADMDAWFERM
+TRIDGPPAALAYQGAYIQDLSSHTDCPEVDVEAVARTFLEMRDARIEDVRTFRDRRHRST
+VTGTLAAAHPVPWMDRPDDSLEEYLRRFPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002095.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002095.fa
new file mode 100644
index 0000000000000000000000000000000000000000..12ece39a8da767cd58efee52be711d1dc8937aa3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002095.fa
@@ -0,0 +1,14 @@
+>1_1725
+MRVSKADGSQATDLQRDALLEAGVEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVW
+KLDRLGRDLRHLVNIVHELTERGVGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFEREL
+ISERTKAGLASARARGRKGGRPYKMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYR
+HVSPTGELREAGQKVLAQRR
+>2_713
+MEPEALYEDKASGKSDDRPHLAACLKALRAGDTLLVWKLDRLGRDLRHLVNIVHELTERG
+VGLKVLTGQGAAIDTTTASGKLVFGIFAALAEFERELISERTKAGLASARARGRKGGRPY
+KMTPAKIRLAMASMGNKDTNVGALCKELGITRQTLYRHVSPTGELREAGQKVLAQRR
+>3_662
+MGHLLGYARVSTTDQDASLQIDALGAAGCYRVFVDTMSGSLQHRPELDKLLDQLRPGDTL
+VVWRLDRLGRSIRHLIDQLHALAERGIGFRSLQETIDTTSPGGRLVFHVFAALAEFERDL
+IKERTNAGLAAARARGRTGGRPSRLSADQVRTARRLYEQQDMTVAQIGDVLGVSRTTIYR
+TLAKHAEPVARRRAKPSPTM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002098.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002098.fa
new file mode 100644
index 0000000000000000000000000000000000000000..611e2e96c30784d7727021284dba54e1fb934b55
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002098.fa
@@ -0,0 +1,29 @@
+>1_1747
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADANIDAAVDGALMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRHGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
+>2_671
+MTETSNSPMTARVRAFLDRPHRLLIGGEWVDAASGKTFETRDPATGEVLATVAHAEQADI
+DAAVAAARAAFDEGSWVRMRPNVREDLLWRISNLITERLEDFALLESLDQGKGVGIASAF
+DVRAAADCFRYYAGWPSKLQGAVNAPSMLLAPPEAEFHSYTRREPVGVCGQIIPWNFPLL
+MAAWKIAPALATGNTVVLKPAEQTPLTALMLGELLTEAGVPAGVVNIVTGHGDAGAALTA
+HPDVDKVAFTGSTEVGKKIVGAAAENLKKVSLELGGKSPNIVFADADIDAAVDGSLMGFT
+LNSGQACESGTRVFVHADVYDRFNEALAAKMRQMSIGPGTEDAAITPLVSQEQLDRVMGF
+VEEGKRDGAVALTGGQRYGDAGFYVEPTLFTETTPEMSIVREEIFGPVAVSVKFTDEDEV
+IRAANDSVYGLAAALWTRDVSRAHRVAARLKAGTVWVNTFHALDSQLPFGGFRQSGWGRE
+LGAESLELYTQVKSVTIAL
+>2_805
+MTETLTYADLLAAVVAPEGAGTEIKDPATGDLIGYAPQSTTADLDAAVELARTAQRDWAK
+LSHAERSAALNRAADAIEANSAALAELLSREQGKPVKNGPNAAFEVGGCVAWTRATAGFE
+VQPETIVDDETGRAELHWMPIGVVGGIGPWNWPMMISVWQIAPALRMGNTVVLKPSEYTP
+LSVLGLVHVMNQALPEGVLQVLAGDGELGRAFTSHDGIDKITFTGSTATGKAIMKGAADD
+LKRLTLELGGNDAGIVLDDADPKAIAEGLFWGAFINTGQTCAALKRLYVPDSLYDAVCEE
+LVAVARRMPMGPGLEEENVLGPLQNRAQYEIVERLVQAAKDGGGRVLLGGDPDPERPGLF
+YPTTIVADIDNDNPLVAEEQFGPALPIVRYTDLEQAIEWANGLDVGLGASVWSADPERAK
+EVAMRLEAGSVWINKHGTIDPRVPFGGVKHSGMGREFGVLGLKEMAEAKSISV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002099.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002099.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b6f66b51f0873c3765c0d5923a919cb31e47b14
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002099.fa
@@ -0,0 +1,7 @@
+>1_1804
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY
+>3_532
+MGMKQRISKVGADVAVAGLLAVSGAVPGQALTDSGRQDCSAGGGYVGARGEQQRYGDRMS
+FDVGGRTTKVVNRYTYGFDSGLRMSQNWRVSSESLLLSGTYGYCYYPY
+>4_2024
+MGMKQRISKVGAGVAVAGPLAVSGAVPAQALTDSGRQDCSAGLLLSGTYGYCYYPY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002103.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002103.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8bad3b32e1746c355d968c96c53b1d72622d1c9d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002103.fa
@@ -0,0 +1,15 @@
+>1_2129
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPGESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRLDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRS
+>2_806
+MSARTEFDPAALGDRETTLLVKSLLIPRPIAWVGTLSADGVPNLAPHSFFTVASSEPPIV
+LIGSAGRKDTLRNAEATGEFTVSLVTRALAEAANRTSAPFAPEVDEFAAASLTPEPSVVV
+GPPRVAASPAALECRLHEVHPVGDSFLLMGRVVHVSVDTDVLTTDARGRTLPDPAALGPV
+SRLGRMEWGGLGEVFELERPSAG
+>3_147
+MKYRPQHEANPLPFSPFKSSTVPRPIGWLSSVSTDGRENIAPYSQWQNLTFDPPMVMFSA
+NQYPDGRRKDTVLNAEQTGWFVWNMATYDLREAVNVSAMALEPSESEWDRIAEHGVTKVY
+ADNHPIPMVAESPVRFECRYHSTHRIKGDSNVGTIDVVFAHVDTIHIDDDVITADGRIDI
+PRIQPIARLGYFDYTVVRETFEMRVPGADGDAQAGLEGRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002104.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002104.fa
new file mode 100644
index 0000000000000000000000000000000000000000..62a71acfdaa9e3a53456cfab5bfcc3b0b7193408
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002104.fa
@@ -0,0 +1,24 @@
+>1_2246
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
+>2_791
+MADRPAVIDHPDYFLLDSDLTDAQRALRDRVRDFGREQVLPIINEWWEKAEFPEPLLPGL
+ADLGIIGTYIEGYGCPGMSRIEAGLVAREMGRIDGSVNTFLGVHSNLCMGSIYILGSDEQ
+RQRWLPAMAKLEKTGAFALTEPKHGSDSVSLETSARRDGDEWVITGHKRWIGNGHAADVV
+VLYARDEADGEVKAFVVEKQEDGSFPAGYNPTVITGKVGKRAILQADIVIENLRVKEENR
+LVNCESFAGVNRVLKATRGGASWEAVGHGMAAFEIAAAYALEREQFGAQIGGYQLVQERL
+ATMLTDLTTMQLMCVRMAELQERDELTLAMASMVKMHTSRKALDMTRTARDIVAGNGLLL
+ERHIGRHLTDMEVVSTYEGTDSMQALIVGRDITGISAFTRSRRKS
+>4_279
+MSETRSGVLPDHDIYLLDDELTEEQREVRDRVRAFVDAELMPVINDYWERAEFPFELVPK
+LAELNVAGTVIEGYGCPGMSRMAGALVSMELARGDGSFNTFFGVHSGLAMGSINAFGSDE
+QKERWLPRMARMEMIGAFALTEPDHGSDSVALETTARREGDTWVLDGAKRWIGNASYAHV
+IVIYARDVADGQVKAFVLEREPDTEFPAGFEPTVITGKIGKRAILQPDIVISGLRIPEAD
+RLPGCSSFKDVNRVLSTTRGGVAVETLGHAVAAYEAAVAYAGQRVQFGKPIAGHQLVQGQ
+LATMLADVTNIKLTCFRLLELQDQGRLTGPMASLAKMSAARQARRVTSMARDILGGNGLL
+LENHVARHLTDMEVVYTYEGTDSMQSLIVGRAITGVSAFA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002112.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002112.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9551d7b1ca4d8999c6c26e66fb1ed70b99e95b34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002112.fa
@@ -0,0 +1,36 @@
+>2_1056
+MTTATPRQPLIEDHAYLSNQHSGALLTREGDVTWLCLPRFDAPSVFTSLLGEPEHGRWSL
+RIADGEVRERAYLPGTLVLRTRWRGPDGEAEVLDFMPLTSHRGSGRAHDDDAGALADEGE
+AARADLVRLVRCTSGSVSVDQCLQFRMDYGEVVPWVSRQTDPADESFLAVVAGGDALAVH
+GPDLRPDSTAHRGRTRLEAGQSAAWTLAWYPSWSMAPAAPDPERALEATVTDWVEWLGEP
+LATGPRADRVARSLLVLKGLTHRDTGGIVAAPTASLPEDFGGVRNWDYRYVWLRDTALTL
+EALMAHNHTDDACAWRDWLLRAIAGDPRDVQIMYTLSGERRMPERDLEHLPGYEGSRPVH
+VGNGAADQWQADVIGTVMLALGRLRDAGVDEDRWSWTLQKRLVERVLEHRDTKEHGLWEM
+RGEPAYFTHGRVMMWAALDQALHAARDHGLPAEDEELAAWEQARDELREEILTEGVGPSG
+GFRQTYGSEETDASLLQIPHTGFLPHDDPRMLATVADVERDLVTETGLVMRYRASGMDGL
+PGEEAPFMMCGFWLVEQYARSGRLADAERLMARLDECSNDLFLMAEEYDDGRDRMAGNFP
+QAFSHLGLIRAVDALEEARGAAGGEG
+>3_992
+MTAQTAPASPLIEDHAYLSNQHSGALVTRAGDVTWLCLPRFDGPSVFTSLLGAPEHGQWS
+LGIADGEVVERAYLPGTLVLRTRWRGPEGEADVLDFMPLADHAGSGVVDADDVGILMGEG
+EGPLRRADLVRLVRCTSGTVEVDQWIRARLDYGEVTPWVSRQEDPAGEEFLAVVAGGDAL
+AVHGPDLRPDGMRHRGSTRLEEGRSQAWTLAWYPAWTTAPAAPDAEHALEKTVTGWVEWL
+GDPRARGPRAERVARSLLVLKGLTHENTGGIVAAPTASLPEDIGGVRNWDYRYVWLRDTS
+LTLEALMAHNHTDDAAQWRDWLLRAIAGEPKDNIQIMYTLSGERRMPERELGHLPGYEGS
+TPVNVGNGAADQWQADVIGTVMLALDRLRDAGVDEDQWSWPLQKRLVERVLAHRDTKEHG
+LWEMRGEPAYFTHGRVMMWAALDRALHGVREHGLDATEEETAEWERVRDELREEILTEGV
+QEDGAFRQTYGSDETDASLLQIPHTGFLPHDDPHMLATVAQVERDLTTETGLVRRYRATG
+MDGLPGEEAPFMMCAFWLVEQYARSGRVEDAERLMARLDDCANDLFLMAEEYDDDRGRMA
+GNFPQAFSHLGLIRAVDALEECAEDARAAE
+>4_1660
+MSAQPRIDDHAFLSHQLSGALVSREGAITWLCLPRFDSASVFTSLLGTREHGEWSLGIED
+GEVAERAYLPGTLVLRTLWRSPSGVAEVLDFMPLLDADGVGDAQGDDGGPDGTGASEAAP
+RADVMRLVRCLAGRVRVTQSVFARLDYGEVEPWVSRQEDADGESFLAVVAGGDALAVHGP
+DLEPVDGHHEGTTELVAGESAQWCLTWYPAWGMAPSAPRAEDVLEATVRRWRGWLEESTR
+QAPRADDPLADRVQRSLLVLKGLTHRATGGIVAAPTTSLPEDIGGVRNWDYRYVWLRDTA
+LALEALLAYGHVEVATAWRDWLLRAIAGEPHEVQVMYTLSGERYMPERELEHLPGHADSR
+PVVVGNGAADQWQADVIGTVMMALCALRDAGVPEDEWSWPLQKRLVERVVAHREDPDHGL
+WEMRGEPAFFTHSRVKMWAALDRALHAVATHGVPATEAETAAWERHRDELREEILTRGVH
+ADGHFTQAYGSDAVDASLLQIPHTGFLPPDDPRMLATVRRIEEELVTDTGLVLRYRPDGS
+DGLPGEEAPFLACAFWLVEQYARTGRLDDADALMERLDACANDLDLMAEEYDDGQDRMAG
+NFPQAFSHLALLRAADALALVRAGDGAGEAGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002120.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002120.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0bb82a7052aa75040b3c65a96f24b20f0f066a7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002120.fa
@@ -0,0 +1,8 @@
+>0_163
+MDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLMLGILAAFAEFERRR
+IKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIEMGIPKAEVARTFEVSRQTLYTSL
+RRVVSS
+>2_2279
+MKYVREGDLVKVASMDRLGRDTRDLYAIVDELTDKGCAVQFVSERITVDKSGTSPVDGLM
+LGILAAFAEFERRRIKERQAEGIALAKARGKYVQAPKLSDTDVEQARVMIQMGIPKAEVA
+RTFGVSRQTLYTSLRRQASD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002127.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002127.fa
new file mode 100644
index 0000000000000000000000000000000000000000..14959b6228bdc98231e57682fdaeb2a076dc2271
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002127.fa
@@ -0,0 +1,11 @@
+>0_466
+MVNETRAISRRQVTKGVTWSVPAIAATAAAPAFAVSSVGVVAGATLYANPLMTKYVQAQN
+GTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAGIVDFRKVLNARKAGTPYNTYTN
+GSVGDSKTFYTLKVGDRFVTGTNPAYWEVTKLASDGSSITLTYSAPITGCYYYAQPSFNP
+YFWAKDVASMVNQVHLTAYIGTQRVAFDTGAASNVTWSADRLEIIGPKTTN
+>1_195
+MSECLMPVEVPQVLRSATKGIGMVNETRVISRRQVTKGVSWSVPAIAATAAAPAFAVSNP
+GVVAGATLYANPLMTKYVQPQNGTTALYLNATPGVGIPDATACQSVQNKKISIVYTAPAG
+IVDFRKVLNAQKAGTPYNTYTNGSVGDSNFFTLKVGDRFVTGTNPAYWEVTKLASDGSSI
+TLTYSAPITGCYYYAQPSFNPYFWAKDVASMVNQVHLTAYIGTQRVAFEKGAGTNVTWSD
+DRLEIIGPKTTN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002142.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002142.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f3565ce22462810d4325f38fda95b7e10c7b2f66
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002142.fa
@@ -0,0 +1,32 @@
+>0_860
+MAVATPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVSHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDVTDWSAVLDPEEAAAMTAWDLAHEVGAGLLQAVVR
+GLSPHALPDRARGRLGRAARRLGRLGPARGRRDPAAMRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDLVHVHDRHPLPAAAAYDHYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDELAERMREYHALQERPVTVINGPWGTQLPM
+GPAERLPLRTELGLSDDVPLLVYLGKLAAVRGVGTLVDALPLLPGVHIAFVGSPDPDARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVPTKLRECLLA
+GLPLTVSDLREQARFVREQGVGTVFAPGDAADLARAVRDLLARRTELTAAARSPEIAARH
+GWEAAERALHGLWRRLVPTPAAPPPVEIAPDPAREPQPRGLLVVGDPPTVRPLADAWPAG
+AGPVTLRPPRDFPEGRGLVVGGPEAVWGVLQDWVTDDRAHGTVLIGGEGPLWGRAEQSPV
+HELLSLRARGRQVALVAGERILAGVERRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGRDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFHGDVVVAPLHTEDLEVAALQALAAGSA
+VVAGPPVTPAPDECAPPVTETDDATLLATVLGLLEETSAAAGERRERAREHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
+>1_591
+MPVDTPAPRRPRMAMLVGNQVVGDSRVEKAAVSAVRAGYEVVVVGVFHRTTFNLGRYGSV
+PILRVPVTFRRHLAWQTLHGTARPDATDWSAVLDPEEAAAMTAWDLAHETGAGLPQAVVR
+GLSPHALPDGARGRLGRAARRLDRLGPARGRRGPAATRGRRALKNFAAGRTGAWREVWPL
+IADYEDGFLRALIDLAPDIVHVHDLHPLPAAAAYDRYRAARGLPPVPWVYDAHEWLPGQM
+MPGPVDQRIAWKAAEAELIHEADAVVAVTDGLADRMREYHALQERPVTVINGPWGAQVPM
+DPAERLPLRTELGLSDDVPLLVYVGKLAEVRGVRTLVDALPLLPGVHVAYVGSPDPGARQ
+GLRDRAAQLDVADRMHIVDYVPSASVTWYVSSATAGVSPLLPTPAHESAVATKLRECLLA
+GLPLIVSDLREQARFVRDQGVGTVFAPGDAADLARAVRALLARQAELTAAARAPEITARH
+GWEAAERALHGLWRRLVPTPAAPQPVEIAPDPARDPRPRGLLVVGDPPTVRPLLDAWPAD
+AGSATQRPPRDVPEGRGLAVGGPEAVWGVLQDWVTDDRAHGTVLSGGEGPLWGRAEQSPV
+HELLSLRARGRHVALVAGERILAGIDRRLAAVPGHPWGGLDPDARAALDRRIRRQGRPFQ
+AALAAGVPVLSHRRVEALLTPGVLWLPAPIPTPTDRGPGHDGASAPRSVLILPGDRTSAE
+SAAVDELVAELAARGIPVEAPSGPRFRRRPDAFRSDVVVAPLHTGELEIAALQALAAGSA
+VVAGPPVTAAPDGCAPPVIETDDATLLATVLSLLEETSAAARERRERAHEHHARLHAPEA
+VLVRLQALLSPAETTDGPAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002148.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002148.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bea11b6f613f624baec4f06eec31b29fcf4d5a13
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002148.fa
@@ -0,0 +1,12 @@
+>0_932
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEQGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLASLPPERRRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG
+>1_654
+MTPPTGVLPRAALVMRLLHEAGPAGLRLSQLVQRTGLPQPTAHRLLADLAEEGAVTRRGA
+AYALGDRWGPVGFEPVTPRCLIEREASRAVVQAAADELGDTVYLAARAAGGVAYLLRCDG
+DSPVRVFTVEVGEVKRLAAGYAGIALLAALPPERQRAEVDAVVARPPRRWNLTDDGALHD
+LLDTLLRQMDEQGWCGGVPVVPGVAGVACGVPARTGGIPQVSLTASAAEQRMPPARVPEV
+AEVLRAAATRLAEIGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002158.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002158.fa
new file mode 100644
index 0000000000000000000000000000000000000000..35329bad9e63890b575da985f11ff76121d6d6ad
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002158.fa
@@ -0,0 +1,6 @@
+>0_1444
+MSAPATAVTFPGVTLFLPDGVMTGDLTYDARTSQLAITYADGETEVLSIDLTLEGYVAAP
+GEALIKDWSEHSGFTAALVDAGIVMRVETLQIGPFDSRAYRVLVLTEAVTGR
+>2_2159
+MSASTATATFPGVTLFLPDGVMVGDLIYDARTSQLAIVYSDGETEVLSIDLTLEGYLPTP
+GEALIKDWSEHSGVTSALVDAGLVMRTETLVVGPFSSRAYRVLVLTPEVTGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002163.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002163.fa
new file mode 100644
index 0000000000000000000000000000000000000000..95f50e805469e82737b89adb5d4a3885a0c98151
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002163.fa
@@ -0,0 +1,8 @@
+>0_1554
+MSFLIPSVPVSCGCRREVREETGLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAA
+DVAAIRLQEDEASEHSFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPA
+G
+>1_1276
+MVNLLLSVTFACGVAIAGLHVVNRRFIAPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAA
+LAVLAWLILAVRTVRARRAGHKLEVTAGRLVAVDTRPSKADGRIGLRFLFRAVHPLTAAD
+VAAIRLQEDEASEHRFVTCQEARKLLRPAIARRVDAAWDAAHCVYLEDGRPAAGVDQPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002164.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002164.fa
new file mode 100644
index 0000000000000000000000000000000000000000..08defa312b78bb04c1682d5bd946c00a6a03f200
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002164.fa
@@ -0,0 +1,6 @@
+>0_1559
+MSGNAFQDLPFPVSGPILGSVGERFRLETASDEGTATFSAGGTEGGTYSCGAGQTLLIGD
+SALLCRAVGENSLDFTISRPR
+>2_1251
+MRTRVTTSLLGLGLTAAALVGCQTQTWISMCFTDATLRSCEVSVSGNAFQDLPFPVSGPI
+LGGVGDRFRLETASVEGTATFSAGGTYSCGAGQTLLIGDSALLCRAVGENSLDFTISRTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002168.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002168.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5530a572d313efeaf0e10520419d8d6a951223c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002168.fa
@@ -0,0 +1,20 @@
+>0_1733
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGSAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALIIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRLAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENALAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVLREIPRNLSGKILKHRLRADLTEPGVPA
+>2_1063
+MATLPSVLATTARRVPQHPALKWGDSSLTYADLDATVDRLAGELISRGLRPGDRVVLVAG
+NTPEFVIGLYGALRAGAIVAPVNPRSARPELEHFLADTEARMLLVDPTVGEGVQALAAAD
+SGPAQLLALGALDGFDDVLAAADGRPEGAVAHPDLAEDDDALNIYTSGTTGRPKGALFDH
+HRVLWVGQNMIMGLGMRVGETMVHVAPLYHSAALNLLLFSGVMLGATHVLLPAFDPDEVI
+ATLERERATIFFGVPTMLAYMLRSPRMAASDLSHLRGILYGAAPMPASTAEALVAALPHV
+HIIQACGQTEGGPGGILLTHEEVMAKPHTSGRMAMPNTEVRVVDADGRDVGPGEVGEMIM
+RGETMMKGYWRNPEATAVTVVDGWVHTGDLTRVDEEGFLTVVDRLKDLIITGGRNVYSAE
+VENSLAGCPGVAELAIIGRPHPDYGESIVAVVAPMPGATVSLEALRDYGEGRLSHYKLPH
+ELVVREIPRNLSGKILKHRLRADLTEPGDPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002171.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002171.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a6050efd476b75bf14116e903dc5360a378dd547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002171.fa
@@ -0,0 +1,12 @@
+>0_1737
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
+>2_1059
+MTRDIIRTERIGPVTVIHLQDDRALNALGSALVAGLADALEHAQQDPEVRAVVITGSDRA
+FCAGAHIPEVLALREALTADPDAEVYLDRLFDLLAASPQPVIAAVRGLALGGGCELALAC
+DLVVAGESASFGLPEVRLGVIPGAGGTQRLVHAIGKAKATRMLMTGESVDAAWAESAGLV
+AEVAADEDVVARAVDIARRAADNAPGAVRLAVGCARRAQDLSLTDGLAHERRAFLEALAS
+DDAAEGMSAFAQKRRPVFGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002172.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002172.fa
new file mode 100644
index 0000000000000000000000000000000000000000..053eab253fe3fa8d1c0455f860aa2481e88a645c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002172.fa
@@ -0,0 +1,16 @@
+>0_1738
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
+>2_1058
+MILDSYRSPWLTEDAEALLEHCRDFLAREVVPHEERWAEQHGVDRDLWTKAGEAGLLCPS
+LPEEYGGAGGTFALEAAILTEQGRCFDDAWGFSIHSPIVAHYILAYGTEEQKQRWLPGLA
+SGELVGAIAMTEPNTGSDLQAVRTRATRDGDHYVINGSKTFISNATHCGLLLIVARTGDE
+PGGRGLSLIVAETDGLEGFERGRVLKKIGQHGQDTRELSFSDMRVPVSHLLGPDEGQGFV
+QLMAQLPQERLTLAVLAAGVCEAAVRETIRYTKERHAFGEPLMSFQNTQFVLAECVADTL
+ATRTLVDQCIVAHVDGTLTAADASMVKFFASDMQNKVVDRCLQLFGGYGYMEEYPIARAF
+TGARVQKIYGGTNEIMKMLVARAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002179.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002179.fa
new file mode 100644
index 0000000000000000000000000000000000000000..845f8e19c2c1d173164bb377cab198fa042d3228
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002179.fa
@@ -0,0 +1,12 @@
+>0_2154
+MLRPRLARPTALLTAGLAALALLTGCSVDGDAAAGSSAGSPSAASSSSGASSSGRVSDGA
+APSSSRAAGSSSAVASASRAVESSQAAEASRAAAASREAEKSAAAAAAEASRSAEAEAEA
+VAEAEREAEASAEVEVGAAEEESAASAGGDGLSAEGQQAVRQAQSYLSFTAFSRSGLIDQ
+LEFEGFSNADATAAVDSLDVDYAAQAVKQAQSYLTHTAFSRTGLIDQLEFEGYSNADATA
+AVDGLGIDYNEQAAKQAQSYLSHSAFSRAGLIDQLMFEGYSASQAEYGVDAAGL
+>2_511
+MLRPRHTRPALLLTAGLTSLALLTGCADGDPAPGAAATTAAATTAAATSSAPTTQAASSS
+PASSPRTSSAAASSSAKASDAAAAASSSAAAASASEAAESSRAAEAEAEASREAEAEAEA
+ARAREAEESAAAEAEREAEAAATVEEDSSTTAGEGTVSSGQAVRAAKNYLEVLPFSRDGL
+VHQLVAGDGYSDADAAAAVDSLTVDYEAQARRAAQNYLDVLPFSRDGLVHQLIAGDEYSD
+ADAAAAVDSLTVDYQEQAARAAQNYLDVMPFSRDGLIRQLMDGDDYSASQAEYGVDAVGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002186.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002186.fa
new file mode 100644
index 0000000000000000000000000000000000000000..46d64359340e932ed97f39756a2179779f2c30f5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002186.fa
@@ -0,0 +1,12 @@
+>0_2189
+MTWISANLDFILSLTWRHIAIASPVVLLSLLISVPLGRLANATGWGRRLIVGGSSLLYAI
+PSLAVFVILPGLVGTKILDPLNVVIALTLYGVALLTRSASEAFDAVDDELLTAATAQGHS
+AWQRFWRVELPLAGESLLAGTRVVSASTLSLVSVGALIGVQSLGTLFTEGYARSFVTEIV
+VGIVGTVILAVVFDLVLVALAALLMPWTRRAKVRKASGRRRSSQDTTTTALATVPDLAVQ
+EGRR
+>3_440
+MTWIAENLDLILDLTLRHVALAVPAILLSVLIAVPLGRAANVSRWGRRLAVGGSSLLYAI
+PSLAVFVILPGLIGTRILDPLNVVIALTLYGAALLTRSASEAFDALDPDVLHAATAQGHS
+PSQRFWGVELPLAGESLLAGTRVVSASTLSLVSVGALIGVPSLGTLFTEGYARAFLTEIL
+VGIAGTVLLAVLFDAALVALAAALMPWTRRGRRTVPAPEDARHDAALTDAVTDPVTAPAE
+GVTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002189.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002189.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2043d5ed48caaf25c4c3087766926b9ff951cafd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002189.fa
@@ -0,0 +1,6 @@
+>1_14
+MSAPLPSHLTIVQSADLLQVSRDTIRRLIASGDLKAYRIGPSTNRRRPIRVDRDSLLALR
+EPVTSLAALKAGEAA
+>2_28
+MAAAASKPRPSFDPRPRLTIAEVADYTGTSPSSVRRWIARGELRAYKYGPRAIRIDPADV
+DAMRQPVTSLADLRGGDAQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002194.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002194.fa
new file mode 100644
index 0000000000000000000000000000000000000000..008e2e98e2d31ed8f0dfc5b9860d0f3ca7ba84e6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002194.fa
@@ -0,0 +1,12 @@
+>1_284
+MSAALDRLKQQNAQSGSQQQLDSPETMEALTSILAAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERITASASTSSPSSDASARIASIESRLNEIASTLGEFAQSLNGESLNAASQ
+SLVAEAQRNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVVKAVEQVAGEA
+SATIAANLDASNERAERIIAATAKLEARQLWSAAAAMCLALLPVVVVVAGLWMGIAGLIT
+GAQWALDVDGSVWLGIGRWLVIAAGLAAAGYGVFASVRWVAGLVETWKGRGMPTWPNWRR
+>2_2315
+MSAALDRLKQQNAHEQPPQQLGSPATMEVLTSILTAVEAQNARLDRLAEQQKKLAGFVKV
+MDEETTRRLERIAAPASTSSPSSDVSARIASIESRQNEIASTLGEFARSLNGESLNAASR
+SLVAEAQKNHAATASAIEGLKAQAAANQKLVSQVGGAVQRIEKRTEERVEKAVEQVTGEA
+SATMTANLDASNERAERIIAATAKLETRQLWSAAAAMCLALLPVVVVIAGLWMGIAGLIT
+GAQWALDVNGSVWLGIGRWLVVGVGLAGASYGLFASVRWVAGLVETWKDRGLPKWPRWRK
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002195.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002195.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f76b0b984a5b04f9c0ebc4fb791f4f620829b637
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002195.fa
@@ -0,0 +1,10 @@
+>1_285
+MSTERDALFQGVEGAGGPSQAAGEDMSASETSDTATACHSGVQVEQQTDSQVNTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDDATLAALRTRAKRLGLAPSTWVRTVVRDALHASRSE
+ELDAAVAAQLLGVEERVQASADARELAAQVRPLAINVNDLDRRARAGEPVALSAEVPELI
+ELLHEVRALLGDRAAS
+>2_2316
+MSADQHPLFQGIEGGGAPSQAGLEDTSVSDVSDRPTACHSGVQVEQQADSQVKTGRADAE
+AVRQSHGGAKRRRGGGGRLDTRFDEATLGALRTRAERLGLAPSTWVRSVVRDALHASRSE
+ELDAAVAAHLLGVEARVQASADARELAAQVRPLAINVNDLDRRARAGEAVALSAEVPELI
+ELLREVRTLLGDRTAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002196.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002196.fa
new file mode 100644
index 0000000000000000000000000000000000000000..101c4e8664791150a0ae8b88cce10164c0195fc2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002196.fa
@@ -0,0 +1,18 @@
+>1_286
+MAKQENNPTSIGLTQYLDPSYWAWAAEDPNGAALLQQGAEAILAYVVQRLEATGCQVVEA
+YGIVHDKDEREVWSDTEKALVVEPKPEHLHAVIKFASRAKSAPLDRLAFGIGVEPQYVEK
+PGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDAQRRETWLKGRAHVKKK
+IVAENFEDMRERVLQGEITRDQIMLTDELFDIYSRHQREIDDALSAYGQRRAYRAAAKLR
+AGEFSTHVVFVHGDAGIGKTRFATDFITEAINAANAHGERWQVYRAATGNPLDDWRGEEV
+LLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVEFFYYARQ
+KGNVDEALDQFIRRLASVVKVYRADDINRYLVQHIGKIEPYEWHQCSVPTAAHTPGMYGN
+AYHQNVGSRELTYGPETSAEHDAEGAVAELLGGLAVRSPDVPLALIGGAA
+>2_2317
+MSRAVVAVAKQENNPTSIGLTQYLDPSYWTWAAEDANGAALLQQGAGPILTYIVQRLEAV
+GCEVVEAYGIVHDKDEREVWSDTEKALVVEPKPDHLHAVIKFASRSKSAPLDRLAFGIGV
+EPQYVEKPGRGRYAFDNMLSYLTHVKYADKHQYAPSEVATVRGPDYLGIDALRRETWLKG
+RAHVKKRVVAENFEDMRERVLQGEITRDQIMLTDGLFDIYSRHQREIDDALSAYGQRRAY
+RAAAKLRAGDFSTHVVFVHGDAGIGKTRFATDFIMAAIDAANANGERWQVYRAATGNPLD
+DWRGEEVLLLDDLRASAMDANDWLLLLDPYNASPAKARYKNKGEVAPRLIVITATIEPVE
+FFFYARQKGNVDEALDQFIRRLASVVKVFRADDINRYLVQHIGKIEPYEWHQCSLPAAAH
+TPGVNGNSYHQQVAPSRELTYGPETSAEHDAESAVVELLSGLAVRSPDVPLALIGGAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002202.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002202.fa
new file mode 100644
index 0000000000000000000000000000000000000000..34d9c427c60224fa7b1df51794dbdbf136a8caed
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002202.fa
@@ -0,0 +1,25 @@
+>1_351
+MVMSLSRVLWKVRSKAPTVTASVQGTVSVTGEGYTTIRDSTCGAGNFLNLAYAKLREIET
+DLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDHQANRQLAA
+ALGQAPVRLPIKITATIYQHDALTLDWSQALPKPAGRTFVFGNPPFLGDHTRTAAQLALM
+QAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLFAPIFAAGW
+RIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDPGTKARLFKYEHARGEAREVPGVKTINAY
+LVDGPNVLVDKRSTPLAPDLPEVTYGSKPADAGNLVVTAEQYQAVMADPVMAPYVRPYVG
+AVELIRGQQRWCLWLADMDPDAPSHSPELKRRLEGVAAERAKSKAASTRDWARFPHLFRQ
+RGLVSDVPFVGIPEVSSEARAYLPVAHFEPDVIISNKVYGALDPDGIVFAVASSSMFITW
+MKTVGGRMKSDLSFSSTITWNGFPLPALTDKDRAALARAAEKVLEARALHPRRSLAQHYA
+PLGMDPALVKAHDGLDAVMDKIMGAPRRCRTELERQELLFARYAQLTS
+>3_2157
+MTKTEEQEASIAAAQLMASMFTALVGDEVDVPVGEEAPEDAEEEEFATQQASILLTRLLF
+LLYGDDAGLWEADLFQRWVEWDTTADNLGPQLDALFRVLNTPENRRRGVPDSLARFPYVN
+GGIFDGTSTAGFLTRDFRDALVAACRFRWTQISPAVFGSMFQLVKSKQARRGDGEHYTSE
+ENILKTIGPLFLDEYRARADRLIQNKTTTRREVIGLIEEIASNIYVDPACGAGNFLNLAY
+AKLREIETDLLADQRRRTGSQDLSLDVSLDQRIHIDRFYGIEINWWPAKIAETAMFLVDH
+QANRQLAAALGQAPVRLPIKITATIYQHDALTLDWAQALPVPAGRTFVFGNPPFLGDHTR
+TAAQLALMQAAWGEGKQLSRLDFVTSWHALTLRLLAERDGEWAFVTTNSIVQGDQPARLF
+APIFAAGWRIKFAHRTFAWDSQAPGKAAVHCVIIGFTRDRDAKARLFKYEHARGEAREVP
+GVKTINAYLVDGPDVLVQKRSTPLAPDMPEVVYGSKPTDDGNLIVTAEQYQAVMADPVMA
+PYVRPYVGAVELIRGQRRWCLWLTDMDPDAPSRSPELKRRLEGVATERAKSKAASTRDWA
+RFPHLFRQRGLVSDVPFVGIPEVSSEGRAYLPVAHFEPDVIISNKVYGAVDPYGIVFAVA
+SSSMFITWMKTVGGRLESRISFSSTITWNGFPLPALTDKDRASLAKAGQKVLEARALHPE
+RSLAQHYAPLSMDPVLVRAHDGLDTVMDKIMGAPRRCRTELERQELLFTRYAELTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002207.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002207.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4fb0b4e7e126504d321e1d9d38af134abe93d02f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002207.fa
@@ -0,0 +1,10 @@
+>1_736
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDVGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
+>4_955
+MSAVTPPQTTVDGAAASAARRVELRPVGAQDHPLLHRWVTSPHAVYWEMTEAGLADVVAE
+YEAIAAHPHHHAHVGLVDGTATFLVEVYDPAHSELAGRYAGAPGDIGLHVLVAPTDTPVP
+GTTDLVMAAVVRWCLAQPGARRVVVEPDERNAAIRAKNLAAGFTELGPVALGSKTAMLSI
+ATPESFTASRIGVLAAGLDLTLPEPPLLLTPDRQVSA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002210.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002210.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0506384aa9ffda109bd641a1df0d8f9f336e0ec7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002210.fa
@@ -0,0 +1,12 @@
+>1_739
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
+>4_958
+MKAYRGLAALGQAMPVDRDEYPQWTMTVRATWLLAPRLRRLTFAAEEFRTFTPQGCDEYF
+GLLTPPPGRALVMPDPAALNARRAVGRIPEDVRPDLRWYTVAEHRPSVGEIDVDVVVHDH
+AGPAGTWARTARPGDVAGFRTGTGAYRLPAAGESHLVVGDETAVPSIAAALAAQRRTPRG
+GRMDVVLEVPGRDHVPALEVPEGATLTVLHRGDAVPGALLTPHLEDLPAAPRDHVWACGE
+QSLATAARRVIVRRGIAPKRAIMFSGYWRVDGPRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002220.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002220.fa
new file mode 100644
index 0000000000000000000000000000000000000000..baf873916d6f196d75b79af8e3773e37ec7ab7da
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002220.fa
@@ -0,0 +1,10 @@
+>1_1919
+MTAPQLHLPRTVVSDQTDRAVDLLGHYFTPGKFIGGRWDGFDPSGTRAASANVFTSDDVA
+SAALLNTPVPGHAVVHLLITQRVHFAGLLEAVGPDRDFIDVDPDPSGKDMAPVYELYEAL
+KTLPKIGPTIASKLVARKRPRLFPIIDAELRQTVFHETRKDGYVGRALLHAEFSAQERTI
+WQRLASYHSAASLPTEVSVLRVFDVLAWMEAKAYWGPVP
+>2_440
+MTAPQLHLPRTVASDQTERAVDLLQLYFKSRKFIGSQWDGFDPSGRRAASANVFTADDVA
+SAALLNTPVPGHAVVHLLITQRERFSELLRIVGPDRDFIDADPDPSGKDMAPVYELYEAL
+KDLPKIGPTIASKLVARKRPRLFPIIDSDLRRTVFHETRKDGHVGRALLHADFSAQERTM
+WQRLESYRCAAALPAEVTTLRVFDVLAWMEAKAY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002221.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002221.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e41aed49580788285175c80a4dcb2633cf5ff024
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002221.fa
@@ -0,0 +1,12 @@
+>1_1929
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGRRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVFTVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
+>4_2167
+MTARPVAPGIHLVQHANVNCYLIEDTDGLTLVDAGLPAVWRPLGHAVRALGHRPEDIKAL
+VLTHAHFDHVGAARRLVERLGVPVYAHRAEHYLAAHPYSYAHENPRALYPLRHPAALPIL
+GSMVAAGVLAVKGVRATAELTPGETVPVPGRPVVVPSPGHTHGHCALHLPDRDVLISGDA
+LVTLDPYTGRRGPRIIAGAATADSGLALRSLDALAATGAGTVLPGHGEPWHSGVASAVEE
+ARRHGPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002231.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002231.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b465ec4dd8b71823caf7cb63dc796ba4ca3b05b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002231.fa
@@ -0,0 +1,6 @@
+>1_2242
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
+>4_275
+MITAVSSAWVGAMSTEGPGASSSAKSRVPAGRSPAPVETTYTVGPPSDPPAWAAPLTAAS
+AAVSTVMSTAVSESDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002241.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002241.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9634dd1b2300036255a54b300a0d61149df256fa
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002241.fa
@@ -0,0 +1,20 @@
+>2_85
+MADIDLTAAPATPEAATGQLTPLASLGRAAAVFGDREAVVYGALRWDYAQFAAHVQSFAR
+ALRGRIEPGQTVAAILPNVPAMLAAHFAVPLAGGVLCALNPRLTPRELEYILEHAEARVV
+LADADVAEDVRGVVERIGTGAAVAEVVDPEAGHAQPDDGRLTYEALVAEGADGADLPWTV
+PDERLPITLNYTSGTTGRPKGVRYTHRSAQLTAVANVLSQEFDAQTRYLWTLPMFHCNGW
+TRPWSVTAAGGTHVCLRAVRQDPIWDAFEREGITHLCGAPIVAASIIEAERAHPVEQKIR
+MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELSRPDRAQVMARQ
+GVALPLVGEVAVVDMDMNPVPADGQTLGEVVMRGDGVMLGYFKNPEATEEAFRGGWFHSG
+DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVVAAHPAVADVAVVGVQDDRWGERP
+VAYVVFRSGVERPDDAALRAHCREHLAGFKVPDRFVPVEEMPRTATGKIRKNELRQG
+>3_56
+MDVTQDTLAPELAVARTEPLTPLAFLGRAAAVFGDREAVVYGDMRWSYAELAAHVQSLAR
+ALTARIEPGQTVAAILPNVPAMLAAHYAVPLAGGVLTALNPRLTPRELEYILEHAEARVV
+LADGDVAAEVRGVVEQIGTGAAVAEVVDAAAGHAAPDAGLLTYDALLAEGAEGEDLPWAV
+ADETAPITLNYTSGTTGRPKGVRYTHRSAHQTAVANVITQGYDGATRYLWTLPMFHCNGW
+TRPWAVTAAAGTHVCLRAVRMDPIWDALDDEGVTHLCGAPIVAAMIIESERAHPVDREIR
+MAAAGAAPPPSVIAALEGLNITPVHVYGLTETHGPFTICEPQPGWAELDRAARAQVMARQ
+GVAMPMVGQVAVVDMDMNPVPADGRTMGEVVMRGEGVMLGYYKNPEATAEAFRGGWFHSG
+DLGVMHPDGYIQLRDRAKDIIISGGENISSIEVEGVLHAHPAVTDVAVVGVSDERWGERP
+VAYLVLDPASGPLDVEALRAHCREHLAGFKVPDRFEVVEEMPRTATGKIRKNELRRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002244.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002244.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f8a0b2a94a9f7c204b9bc5fed8e534e507276fa5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002244.fa
@@ -0,0 +1,24 @@
+>2_108
+MNPTFSRRTGLRTLAAAVVAGTVTIQAPAVLARTAASTPAAGADGFRVLPYLMEPTATSM
+DLVWFSEREVPGTVVVSGPGLGDNHRGGRTRPAGTRVSTPEFQPLLAYTEKERAQSIKGL
+AQGSWLLGPASYKHRVSLTGLKAGKEYRYTVTQGGQRHTAAFRTADDGANWSDLRLIAFS
+DTETEPYGRIENREWELSMVTPYTEGSLPRPGEGSVWHQTFGSTTRYGQFTLKYPLTQDV
+ALRENIRHIDAAAPDLLLVAGDLGQGGGYQPGWDEFFRHFAGEHSDIASRVPLITSLGNW
+ETFAALNDGYGTAADRSPVVRSRNKYHAYFERTSAGTDRENPRFRGSYYRTDHGPLTILT
+LDSTNGVPDESVGAGLLSGAPFSGDDRNLTAATMPSDTQGSFTQAEYEAAFPTVFPGSTP
+ADADLPVLNPGHEQWAWTERQLADARAAGRIVIVEFHHAAYSVGVHGTPPNHEFPDDQSG
+VAMRVYTPLFEKYGVAVVISGHDEMFQRSWVDEDGDGVGFHSYDVGVAADGLRGEQYAKD
+ASGQWKPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGREAEMTL
+TPMYVFPILDDEYRLVRTERRAYDDVQTVRFDRRGVPKPRR
+>3_76
+MNPAFSRRTGLRALAAAVVTGTVATTAPAALAKTAQHAPAVPAGADGFRVLPYLMEPTAT
+SMDLVWFSERPVAGTVVVSGPGLGNNHGNGRTRPAGTRVSAPELQPLLAYTQKELTQTLT
+GLPQGSWLLGAENWKHRVSLAGLKPGKEYTYTVTQGGRRHTASFRTADDGRDWSDLRLIA
+FSDTETEPYGRIENREWELSQVTPYTEGSLPRPGEGSLWQQTFGSTVRYGAFTLKYPLTQ
+DVGLRENIAHIDAADPDLLLVAGDLGQGSAYQPGWDEFFRHVAGEHSDIASRVPLITALG
+NWETFAALNGGYGTPADRSPVVRSRNKYHAYFERTGAGTDRQNPRFRGSYYRTDHGPLTI
+ITLDSTNGVPDESVNGPLSGAPISGDDRGLTAATMPTDTQGSFTQAEYEAAFPKVFPGST
+PADADLPVFNPGHAQWAWAEEQLADARAKGQIILVEFHHVPLSIGEHGTPPNHAVPDDQS
+GVAMRVYAPLLEKHGVAVVISGHDEMFQRSWVDADGDGVGFHSYDVGVASDGLRGEKYAK
+NAAGEYEPVRFNTHMEWTANTHEPETWADVDGVRQLVDGGMHYGHLQIDLKRRGQSAEMT
+LTPMYVFPILDSQYRLVRTERRAYGDVQLIRFDRNGVPLPRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002247.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002247.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c6b93a0dba61151d250af113a72cb5ce9ee79b7e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002247.fa
@@ -0,0 +1,6 @@
+>2_214
+MTDEQDAVDGRAGVPSWRVIADRISAEHRAADDGPIDEVDPADFDLDEDCCLGGCCAKGI
+AYLDAVEQAAARRARRTRA
+>4_164
+MTDEQDAADGRAGVPSWRAIADRISAEHRAGDDGPIDEVDPADFDLDEDCCLGGCCAKGL
+AYLDAVERAAARRARRTRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002250.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002250.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1bfa18c74a2cae933ad086df182e455c6341299f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002250.fa
@@ -0,0 +1,18 @@
+>2_325
+MSAEEKNLPHGEESTTVGEMNDTVATGLPEEPRTEEGADAPQGARAENPQSDAAAGQCPV
+AHGGAALPHPTSGDANQQWWPNRLNLKILAKDQPVQSPHEADFDYPAAFEALDLAEVKET
+IAEVLTTSKDWWPADFGNYGPFMIRMAWHSAGTYRVTDGRGGAGEGQQRFAPLNSWPDNA
+SLDKARRLLWPVKKKYGQSLSWADLIVLAGNVAHEIMGMPTFGFSGGRIDAYEPADDVYW
+GPETEWTNGGAERYKGERDLDNPLAAVEMGLIYVNPEGPEGEPDPLKSAKDIHETFSRMG
+MDAEETVALIGGGHTFGKTHGAGPVEPHIGPEPEAADLEQMGLGWKNTYGQGKGRDTITS
+GLEVTWTYHPTRWDNEFFHILYAYEWELMESPAGAKQWRPVNGGGSDMVPESDFQGRREP
+RMLTSDLALRFDPVFGEISRRFKDDFAAFQDAYSRAWFKLTHRDMGPRPRHRGVEVPQEE
+LLWMDPVPAPESVPGDAEVKAVKDAVAQAGLSVTDVVKTAWAAASSFRSSDFRGGANGGR
+IRLEPQRSWEVNEPAVTGPVIDALEKIAQEAGVSFADTVVIAGNWAVEKAAADGGVQVTV
+PFTPGRGDATAEQTDVTSFGHLEPKVDGFRNWDPRGSKTFPAEFALVDRANLLGVSAPEM
+TVLVAGLRVLGAVHGDSQDGVWTDRVGVLSQDFLTAVTDIDTQWEKVAEGRYRGVTADGR
+ELTGTRNDLVFGSNPELRTLAEVYAADDAREKFVQDFVRAWAKVMDADRFDAK
+>3_266
+MHGKGASLPHPTSGDANQQWWPNRLNLKILAKEQQVINAHDADFDYPTAFAALDLDEVKK
+TIAEVLTTSKDWWPADVGNYGPFMIRMAWHSAGTYRSGDGRGGAGTGQPLTARPAADDGR
+PPHRVGARSAFPPGAGPCLQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002251.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002251.fa
new file mode 100644
index 0000000000000000000000000000000000000000..16d230b22f2a82c2813138d5707faf00be9ad284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002251.fa
@@ -0,0 +1,11 @@
+>2_328
+MQRIVPNIWCDGTADAAAEFYLRAFAGLPGTAHVRTDRYPTEGLLDFQRPLAGKTLTQEL
+DLAGHRFILVNAGDEFAPNPSISFFVNADPSRMDDPRGTLDALWAELTDGGRVLMDLGPY
+PHSEHYGWVEDRHGVSWQLMLTDPAGDPRPVIIPQLMFCGPAQNRAAEALDHYLAVFDDA
+TPGQRVTYGDMGHVPEGGPVEAGSIVFADARLRGEWVAAMDSAVAQDFTFTEGVSLMVQC
+RDQAEIDRLWEALSAVPEAEQCGWLKDRWGVSWQIVPEDMGELMERPGAFEALLGMKKLV
+IADF
+>3_460
+MSDAAAGAPQLISPFLWFHDGAEEALRYYVDVFPDSEIEEIQRYPDESLDPHYAGMAGKV
+ISAWVRLGGVRFGALDGGPAFTLSEAVSFVVACRDQEEIDRYWAALSHVPEAEQCGWCKD
+RFGVSWQIIPADMGRLLQSPAQIQAMMAMRKIEVAALEALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002260.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002260.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25911143c2a01af232cf20f16250448b865dd072
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002260.fa
@@ -0,0 +1,4 @@
+>2_455
+MTVAITRLDPVGADRAEPIALLTGSAWPFPVRPHVTRPVAKEAIEDGGRHHTLSGHQLPM
+>4_2136
+MDVTFTPLDPAGADRDALVALLTENAWPFHTRPRVTRPEAEKAVDDGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002262.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002262.fa
new file mode 100644
index 0000000000000000000000000000000000000000..144aead477170820382fea70bb92dcee867b72ce
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002262.fa
@@ -0,0 +1,7 @@
+>2_473
+MDEDQGKILATHRQELRRGTLVVACLLACRTPRYGYALLEHLADARLDAEANTLYPLLRR
+LEGQGLLQAEWNTDEPRPRKYYRTTPEGEAIVAELRGDWLRLTDSMTRLGKDPS
+>2_747
+MNEPTDRPPSGTAPEAWPSAWVRAALEPAILGSLAGGPLHGYGIAHALADHGFGRLRGGS
+LYPVLGRLEEAGHITARWAPGDAGPGRKDYELTDAGRAAYRDAVANWRRLGDALADLGAT
+PRLTAQEGTAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002265.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002265.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0218a18706477bb012bca2a9aaa7d08ad07c0cf0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002265.fa
@@ -0,0 +1,12 @@
+>2_492
+MTATPRPAARRFLEVDVFATGPLTGNPLAVVVDAEGLPAERMQALAAWTGFSETAFLLPP
+TDPEADYRVRIFTPREEFDFAGHPTLGSALAWLHAGGTPRTPGRLVQECGVGLVPVTVAD
+DGVLAFATPPLRRSGPLNEADVVRIAAGLGVEREAIVDHAWGENGPAWQLVRLTDADAVR
+ALRPRGHAELKVGVVGLEAAGAETACEVRAFAYGSEDPVTGSLNGALAQWLRGAGLVSPR
+YVAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTIAL
+>3_427
+MTESHAPFPDSSPARPRRFLEVDVFATGPLTGNPLAVVVDAEGLTDGQMQAVAAWTGFSE
+TTFLLPPTDPAADYRVRIFTPREEFDFAGHPTLGTALAWLHTGGTPRTPGRGGGSTALVQ
+ECGAGLVPVTLAGDGLLAFATPPLRRSGPLGEEDVRAIAAGLRIDRDAILDHGWGDNGPG
+WQLVRVADAEAVRALEPRGHEELKVGVVGLEPEGAETAYEVRAFAYGGEDPVTGSLNGAL
+AQWLRGAGLVPPRYAAAQGSQVGRRGRIHVHDDGARIWVGGRAAVLVDGTLTL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002271.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002271.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e0a071018bb40465f133e838165b67d74e60759e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002271.fa
@@ -0,0 +1,10 @@
+>2_540
+MSETIERAYPHAPTADDAPLDTAALAVCTTVLQQGAADLRRRFGPVLGEAVVDRQIEDSL
+EELRRSGVPRTHRESTAIHFAESRLLALAETTGVVEPSVPRVLFVCLQNAGRSQLAAALL
+AERAGDAVRVSSAGSRPTPEVHDDVAPVLSEIGADPAAAYPKPVTPELLAAADYVISLGC
+SDECRERTGVEVRDWPVGDPAEADWERLQEIVADIERRVDALWAEIQGRFAA
+>3_468
+MAEAHPAVAGTGPSPSTGPLPRIGEHVGILAHGAAELRRVFGPALGEETVDRIVEESAAG
+LSPAAADPAHRESIAVRFAHDRLASLADARGVTRSGVPHVLFVCVQNAGRSQLAAALLAE
+RAGDAVRVSSAGSQPAGRIHGNVQPVLTAHGADPARIFPKPITEEVLASADYVITMGCGD
+DCPVRLGQDARDWPVGDPAEVDWDRLQEIVADIEVRVDALWREISGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002277.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002277.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4420aee4fabb13f1eb5bd26daed6159e1bf8f1ef
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002277.fa
@@ -0,0 +1,8 @@
+>2_626
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYARE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQVFR
+AQVTLRPRSEGRGCEADLDWWESRLGALPAQMREWARS
+>3_2172
+MSGGAQSVSVRVHGDSILGQECLKSMMWPWSVERLGLPCVGLSWGVPGETFKVQGAYAQE
+PVRYEDLNFQEIGLVGEDFGRGRPAWPDRCFSLELFPEYSPEVAWLRLRVVEEAGAQEFR
+AQVTLRPRSQGRGCQADLDWWESRLGALPAQMREWARS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002287.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002287.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d1fdf8e3aadb5d95d107ded0a03a41263651f391
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002287.fa
@@ -0,0 +1,6 @@
+>2_833
+MALFRKTAAWGATAAGAVALAAAAMAATWTGPGYTVVNDHSNIFDYKGSIKTTSCVRQSD
+GTHLIGGYIRYVQGGRDTGRLWTPTATSCGQTVSRSTTFKDSLALNAPKTQFYYGLNKAP
+YGALSEPLGGN
+>3_771
+MGDSRCGQTVSCSTTFGDSLGLNAPRTYFNFDLNDVPYGALSEPVDGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002291.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002291.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cadd608d498d546d80f577d3bff8f8dddafdfb77
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002291.fa
@@ -0,0 +1,8 @@
+>2_888
+MSTRSSIPDAVDTDRTAGTIELLEPPREAVEWMASPAPATDLWWTATVCGEADPDWHRLE
+TTVAETIEVLVSWAQGHGLPLPYGAALRTYGNPPDLGLVA
+>4_1811
+MSAPGSITADGARGLATHRAPGAVELVEPPREAVEWMASSAPATDLWWTATVCGEEDPGW
+HRLESAAQIADLVHALTDPRDKLILEDEPPTRYAQIMLLGDGLFMVEIAKRFEGLGAYNW
+RIGRGRAADEAANDPQDLVQPLQELTAAETVEVLVSWAQGHGLPLPYGAALRTYGTPPDP
+GLGFDS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002297.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002297.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a859cb9f328c08374224fcd05ba34e094963499f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002297.fa
@@ -0,0 +1,22 @@
+>2_940
+MAQNTAGEGLLESIRQGYSFEDATVTLGAAVVDGQVHADAPVRLPLRMMNRHGLVAGATG
+TGKTKTLQMMAEQLSSAGVPVFLADVKGDLSGLAVAGEASEKLAERTTATGMPWQSQAYP
+VEFLALGGDGVGVPVRATVDAFGPVLLSRIMELNETQESSLQLMFHWADQRGLAMDDLAD
+LKAVVTHLTSDEGKADLKGLGGVATSTANVILREVTGLEAAGMAAFFGVPEFETAELLRV
+APDGRGVISCLELPTLAAKPQLFSTFMVWLLADLFAELPEAGDLDQPKLVFFLDEAHLLF
+DGASKAFLDAITTTVRLIRSKGVGLFFVTQTPQDLPAEVLGQLANRVQHALRAFTPQDAK
+ALKQTVQTFPTTEYDLAETLTSAKVGEAVVTVMDPEGAPTPVALTRMWSPQSAMEPAPEE
+AMRQIVGASALLPVYGTAQDRESASEVLSAQAAAAAPSTGGSARGSAAGAGDTRVADGHG
+GGTVVSGVDLGDIEALRREEEKATARARKEADKPSDFERAMGNFMKSAGTQLGREVVRSV
+LGTRGRRGGGLLGGLFRR
+>3_881
+MAENTALLDTLRAGYTFDDPTITLGAAVVDGEVHADVPVRLPLRMMNRHGLVAGATGTGK
+TKTLQMMAEQLSAAGVPVFLADVKGDLSGLATAGTASDTLTERTRATGMPWQAQAYPVEF
+YALGGDGVGVPVRATVDSFGPVLLSRIMELNETQESCLQLMFHWADQRDLPLDDLKDLKA
+VVVHLTSDEGKADLKGLGGVSTATANVILRKVTGLEASGMDQFFGVPEFETAELLRVAPD
+GRGVVSCLELPTLQSKPELFSTFMIWLLADLFAELPEAGDLDKPKLVFFLDEAHLLFDGA
+SRAFLEAITTTVRLIRSKGVGLFFITQTPKDVPGDVLAQLANRVQHALRAFTPEDAKALK
+ATVQTFPKTDYDLEEVLTGAKVGEAVVTVMDPDGAPTPVALTRMWSPQSTMGPTPEDAMK
+AAVAASPLMGQYGTAQERESAAEKLAAQAAAPQGETAVPATGESARDGGNVTVSGVDLGN
+IEEIRREEDARARRAQEKADKPSDFEKAMGNFMKSAGTQIGREVVRSVFGTRRRSGGGLL
+GGLFG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002300.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002300.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1ea81163f907d2ab4bb8e816d17a3db4e03c56f3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002300.fa
@@ -0,0 +1,13 @@
+>2_990
+MTDAGPQGPAVPVRTRRVAHPGRVTAVVLVVAALVAAAFLAGRFFQPPSTAADNEAAATP
+IDVWAHAEERVIDDGSSYVATVAAGRTRTVTVAADGPAVVLRQAAEVGEMVRPGDAAGEV
+SGVAYVFLPEPLALYRDLTEGDRGEDVASLQRALRQTGRWTATDGVFGDSTARALRETFR
+GAGSPLPEDEPVTVGWRQFIPVSDDGAVVTAAATYGATLTEDRPLLELQVSAPTIRFTAD
+VTQATALEKGQEVEVSGAFGSLHGTIAKIGEFAAAEGSERAGHPVTVAFDATAEDAPPVG
+QSVTVSTTAAEDVPAMLTVPQTAVRVEGASSYVVVQVPASAREGSASSAPAERRVPVTVE
+RTGGGYAAVSGDLAPGDRVKVS
+>3_934
+MLVLALLAASFVAGRFFQPPTTADPAAVARPIDVWAAVEQRAVDTTASFAGTVAAGKTRS
+VAVQAEGPAVVLRQTAKPGESVRPGDVAGEVSGVTYVFLAEPLALYRDLTEGDEGEDVAS
+LQRALQKAGHATDTDGVLDSGTARALRELFAEAGDPLPEDAPVTVSWHQFIPLGKDGAQV
+TAAAGVVSALYPAWVASRQRPADALRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002305.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002305.fa
new file mode 100644
index 0000000000000000000000000000000000000000..30d68a45af937d0c8a6dd21985614bf9d7b1c2b4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002305.fa
@@ -0,0 +1,15 @@
+>2_1187
+MVLGFGGSTVLILVVGLVYATAIRALPRTGGGVLFAVLSAGRIPGFIAGWSLALGYIGII
+AMNASAVSLIFRVTFPGLLSHGKLLEVAGWEVYLAEVLVSILFIWVFALLNMKGVEFSGR
+FQFWAVVTMLTCIAVLGVSAVYAFLTKNIELPAAVPSGQSPLTSVVVILAIAPWALSSKV
+PLVRAWAAILRSPDLMDNPPLHGAGVGPPAGCRGRRTRMGGGLHLSDSTGSIRRCATPGR
+R
+>2_1835
+MSHVTSSPPATGPGLKKTLSSLDAYAMGFGAMIGFGWVVLVGGWLKDAGTLGSIIAIVSG
+GLIMTVVALVYAELVAAIPKAGGEHHYLLRGMGARWSFLGSWGITGGYISIVAFEAVALP
+RTAAYIWPEIESIPLWNAFGSDVYLVWALVGAGAAVVITWINYIGVKLAGIVQTIVVATL
+LVIGALLVFGAGTGGSVANFEPLFTDARGLFTVMIVVPFLFVGFDVIPQSAEELNMPPRR
+MGVMIIVSVAAATLWYIMVILTNASSMPREQLVNADLVTADAMAALFHSPAMANVLLVGG
+MAGILTSWIALLMGAARLLYAMGVSGMLPRWFGHIHPKYRTPSNAVLFIGVLSIAAPFFG
+AGALGWFVDSGSPSIVFTYMMVCIVFLLLRRREPEMDRPFRAGGATAGRVLGVTGVILTA
+GLLSLYIPGMPASIAPMAYAFFGLWWLLGLVFLFRIPRGITPGEDAEERLLERLARR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002310.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002310.fa
new file mode 100644
index 0000000000000000000000000000000000000000..07a9004b977ec69adcb480e3c200287841f8e758
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002310.fa
@@ -0,0 +1,12 @@
+>2_1286
+MTVQKFPVFPAGTLEHVCKLIAELYTGNELTRIMSEIPLRDDLGEGNTKWRRLACAVSKN
+QAHTQSGNAVIALVSASMRPERTLDRADAARLTRDQLNQVLSLVGYRVRDDGRVARASRA
+RSTDEAEKRTEHLRGLLERGGAHREVLTYCRPELLRKDYYEAVFEAIKGLGSRLRQLTGV
+DGDGYALVEDAMAGSTPRIRLNALQTRTQRDEQRGVANLTKGLFSAFRNPAAHEPRIEWT
+LSEQDALDVLGTLSMIHRRLDMATVEAL
+>2_2160
+MQRAGLTPVTIIKNRGSANEERIEVQAQLQNSSLAMFAIEDPLFEGDHVEMPDPRGGQMV
+KVVRKLVQHPMPANMARAFGGSNGYAEVTWGESAAVRQAPVRRLELEGLHPEVVRVSSAL
+FADEQFDSAVTEAMKSLEIRVRRLAASTLSGAPLMQEAFRPKEPKLDVAVEEGRSGEDER
+EGFFHLFRGAMVGIRNPKAHELAHGDNPFEALEALALASMLHRRLDIAAGRLECADDSVT
+VLDQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002319.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002319.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e8e2de235a2105842c50dbd1650f3c1e4837c87
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002319.fa
@@ -0,0 +1,13 @@
+>2_2227
+MADAVQVCAFNSTYTASQGPAVPCSSSAREREDALLDALDVDPPGSWWSRAAELARPRTV
+VAGDPPREDWLAVPLRRDGPLATTGDLGRAAAVGLVIREDGPLWDEDLVRTLTPPPICPK
+VLEVRTPADWLRLVEAWPEAASKATAEILARHTGLDGRWLVPRWTAVAEQWDAVHLSIGA
+WARSAGVVQPVGEGSAWTMCAGWDPDATFWLTAQPTVASEQVLPTLTPAEALDGLAG
+>3_1267
+MKASVQDLLPGPRGRRLCLEAARMLSHRVADLVFWLGYELDPDRGISSLVMWPPGGGALE
+AGARPAVSIDQVAQALADLDLSGLTDGVVQAALVGSVMSARYWQEPDGEDVLAGHPDIHA
+ALEAVAAGVLGSAAARHWGSPRAAAQWVIDWRAFEDPAPVPRDARRVLAAWAREERRQEV
+RAAAEHPVDPTANFSGTWWSIPQGAVVSVGQIPTGLDLVEDDIGAEAATVIPVRGAGRTY
+EVRGPGDWIRLCRRFPLEVSASRRHDWYRVTGRSGRWVIPDWEQVASEWDAVHLTTLGYL
+SAATRALPVEAGVATVLAGWDPDTTVWLADAVRESEEPRQCWQRVSGDDGWARCVPVRDV
+GSEGPARGRGASPPVEG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002320.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002320.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1459ebd4c3c309510b7ad1cb7402d9e412af0513
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002320.fa
@@ -0,0 +1,6 @@
+>2_2273
+MTAFGIIWLIAVTLVSAVAVRGILRQSTGVHAADRNGSTSFLWFLVALAFLLTNLPSGID
+PFRAVGLHLGAAALLGFLLHVLTRGAPAARD
+>3_2135
+MTVIGIIWLSELTLVSGVAVRGLLLTHLPSGIDPFRAVGLHLGAAALSGFILHVLTRGSA
+SRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002326.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002326.fa
new file mode 100644
index 0000000000000000000000000000000000000000..acb41aa860d38f01c4beb073383f55068c9972ff
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002326.fa
@@ -0,0 +1,14 @@
+>2_2593
+MATLAEQVQGERMARVALSMIAEPNDPITGYVLARHGGVETLRLIESDDEVPGLARADTL
+MWRERLTARVTPGLLDQMAQAERHGFGTLIPADKEWPAGLNDLSDRAPYLLWTRGAVSFL
+MTALSDRATITGARAATAYGEQVAGELAAGLADEERVVVSGGAYGIEGAAHKSVLAASGQ
+TIAVLAGGLDRPYPAGHSELLNRIGDVGLLVSELPPGAAPTRHRFLARNRLLAALSGATV
+IPEAGPRSGSMTTVIAARELSRGVGAVPGPVTSVASAGPNELIKQGFASLVTQPSDVIDL
+LDADRTPDRTVTRPEVGREFGHRHPSPGTPGRSL
+>3_1734
+MSGVAGLGVDERRARVVLALLAEPDDPVTGGLLRRLGAVETLGLLDTDTTVPGLGRVDGQ
+VWRDRLTSQGRLDGLDQRLRVLEESGIVILIPGDAQWPRALDDLGERAPYVLFVRGAASF
+LARPMQDLVTVTGSRAASAYGEYVAAELAGDLANRERVLVAGGAYGVESAVHRAALAAGG
+DTIAVLAGGVDRPYPSGNRDLLDRVGDVGALVSELPPGSVPTRHRFLARSRLLGAMSAAT
+VVVEAGARSGAIGVAAEAHQLGRQVGAVPGPVTSVTSHGPHELLRAGHARLVTSAADVEE
+LTANRATHRPGLSADFTRHTAPAAGPPERSL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002328.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002328.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6835d604d0d7a7bc646bbf9e6ece202ceba44ef3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002328.fa
@@ -0,0 +1,10 @@
+>2_2616
+MSNTERDPKEQVCENGPGAAPTGQEESLREARFTDGLSAGVAEAAGDAGAVVEILEPREV
+PLGGPRAMPVQRTLPQRARSLIGAWCFLDFYGPDDVSATGGMDVPRHPHTGLATVSWLFE
+GRIDHADSAGNWATVRPGEVNLMNAGTGITHTEYSTDDTSGLHGAQLWYALPDAHRFSAP
+ALHSHRPEPVAGEGWTARVFLGDLLGESSPVPTYIPLTGAELRLEPGATARIAVPQDHEH
+GLLTVSGAVTLQGADVPAAHLGYVGTGTAELTVTAGEEPVIALLIGGEPLGEQIIMWWNF
+VGRSHEEVVRWRSAYQQEMGFEAPEDGSPLASAAARALRGGDGALGSPVQGALLDALVGT
+AYDDGRAFPQFGDFPPDPKPPIPAPPLPNTRMRLRG
+>3_2427
+MDALRGAAYDDGRAFPQFGDFPPDPKPPIRAPPLPHTRMRPRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002330.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002330.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b6284902211b2ba8b671c6c57b6d7126e0d83f5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002330.fa
@@ -0,0 +1,10 @@
+>3_42
+MAAVPDSLKLEGARFVGRSLRGARFIDSDLSHVRARGVMLDGADFDSPWLLDGEGSLVVN
+GVDVAPLVEVELNRRFPGRAQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSV
+EGEWSFSQTLRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYE
+QVLAVRSERLAQVREFLASVDDAGLDEERRHPWSPEYPETVRSCLHVILEEEWEHLRYAL
+RDLDALDDAAAQGR
+>3_1184
+MPALSAGACGTQRRAEDAEGLRGAWGAVEASWRQATDRASALPDGAVDVSVEGEWSFSQT
+LRHLVFATDAWLSRGIQGAEEPFHPLGQPRAGAEDDGVDLAFFASTPPPYEQVLAVRSER
+LAQVREFLESVDDAAAQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002331.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002331.fa
new file mode 100644
index 0000000000000000000000000000000000000000..58194e67dbaca66a5e622bd38575a9cb8cc2f494
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002331.fa
@@ -0,0 +1,12 @@
+>3_44
+MRLIALPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEE
+VAGEALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHSQGRYPLED
+TVSAFHQLVEDGKIRYWGVSNFDHRDLADLQDVPGSSGLATDQVLYNLSRRGPEYDLLPW
+CADHQLPVMAYSPIEQGRILHDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQ
+HVRDNATALDVELTRDDLDALDRAFPPPSGPRPLEML
+>4_1935
+MTLPSGESIPVLGQGTWGWGEDPGRRGDEVAALHAGLELGMTLVDTAEMYADGGAEEVVG
+EALAGRRDEAFVVSKVMPSHASRSGTIAACERSLKRLGTDRIDLYLLHWQGRYPLQDTVA
+AFHQLVEDGKIRYWGVSNFDHRALAELQDVPGSSGLATDQVLYNLSRRGPEYDLLPWCTD
+HQLPVMAYSPIEQGRILDDTTLNDVAARHSVSPAAAALAWVLRRDSLCTIPKASSPQHVR
+DNATALDVQLTREDLDALDRAFPPPSGPVKSF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002332.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002332.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ed72498557857e6b51b56259369bd04bfc94e12e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002332.fa
@@ -0,0 +1,18 @@
+>3_137
+MSTLRTHRRRAALGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV
+GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR
+CLQGVSAGMEWGGAALMSVEHAPAGRRGLFGSFTQVGSSAGMLLATGAFSLVKLVTTDEQ
+FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDVGTVSRAPVVELLRHHARPVLV
+TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLLSTPFWGAVSDRVGR
+ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFSEQFPVR
+VRYSGVNLGYQLGTVVGGGFAPFIAALLYEAGGHTPWLIAAYLTLLATLSLIATRFARDP
+VARPETDLVADDAAILAPQADGPAAVVPADRAPVTLETR
+>4_192
+MSTLRTHRRRAVLGSFIGTTIEWYDFYLYGLAAALVFNVQFFPGQTAFGATLASFATLAV
+GVVLRPLGGIVAGHFGDRVGRKALLVISLLLMGGASMLIGVLPTFAQAGWWAVAGLVLLR
+CLQGLSAGMEWGGAALMSVEHAPADRRGLFGSFTQVGSSAGMLLATGAFSLVKLATTDEQ
+FAAFGWRLPFLASGLLVVVGLAIRLGVEDSAEFRVHRDAGTVSRAPVVELLRHHARPVLV
+TAGLRLGQNGLYYLVTAYLVSYLVLRGADDGVLVSAIMVASAIGLVSTPFWGAVSDRVGR
+ARVSRVGYALTAVAGWVLFAVVDAGALAVLPLVVVLVINVAHDSVYGPQAAWFAEQFPVR
+VRYSGVNLGYQLGTVVGGGFAPFIAALLYEVGGHTPWLIAAYLTLLATLSLIASRFARDP
+VARPETDLVADDAAILAAQADGPAVDAAPGAAAVTARPDRAPVTLETR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002336.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002336.fa
new file mode 100644
index 0000000000000000000000000000000000000000..49d54d057cd15288899d32a0c3151868f8ab74d5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002336.fa
@@ -0,0 +1,8 @@
+>3_310
+MPEYDFETYPTTPDAMAKYLQEREAAGNPMTGEEALAYSDWSRERGRAIQAKIDARKTPE
+EREEFRRFAEEFERQCLEDEKRFAEEAAREAAEDAERAAQGKRPIKRERDIVTPKGFSGI
+GVTPRGW
+>3_330
+MTKYNFEAYPTEPESMAKYLHEREAAGKPITRAEGEAYIEWSLAKEQEITERKERMSPAE
+RAGHEGFQREEEPMGAIFDLEDARSEVEALVEAAEDAERAAAGKRPLKRERDIVTPEGFS
+GMGVTPRGW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002337.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002337.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d527ddbf3006931b7fbc5aece9e6dd5124762693
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002337.fa
@@ -0,0 +1,14 @@
+>3_313
+MGAPRELFAEHALRGEIVVLDYAAGRTRSGLPVRRHHVVVRAGDRLVHSFRWYVGAAREV
+FEVTLTFDEEWLPHRLWEPVAEAVRSARAPLAGEVDVPAVVPGAWDERPETVVVESGPGL
+DVAESLVEGLEVISASRKRWRSWSEADEVEQAVVRSMAPTLSARGGLRGRRTEVDVYAVL
+DEAVVVRRRWWGDQGTEIIEREVLRVPGRVAPWAMFVGMDVRAGWMREVSARRPVDAEAR
+SSDAEWEVIAGGERALGLLHGPRDVWAVSTGGGGLVAEWWQLPGEGLLGVFRDADSAQMM
+VGPVDGWTIYLLVLEAWLA
+>3_319
+MHPTVALRHFTEPADGNVASASFREAFLGGQEVVEGFLLLSYEAFFTGRGLPGRRHHVIG
+WEEDLVWHSVRWYVGSGAEIVELTLTAEAGADLEIWGGQCDRMIRNVVCQGAPEPASNLC
+WPEVPADVRAQDSWEVVTEQGLNPPWLESLRAGYDAVQEQAPWSAWAREPSLEQRRVLEQ
+ELPILSGVGERSGQGFRIEACLDGRGGAVVVVVPEGEGDGTNVRRGVRTVPVSLVVPVLL
+TWAGLRADWLRDEVMEAPGDVAPTEMAELWRGRRGADGVGSEASADWWRWWNQEGEVVAE
+WVQPLHRAPLAVFRDESRCVGVPVMPGVLYSVLQATVQEIAGSPHM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002346.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002346.fa
new file mode 100644
index 0000000000000000000000000000000000000000..df70da3b3a76938feaf992305c5aa18282898571
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002346.fa
@@ -0,0 +1,10 @@
+>3_620
+MSQLMGDAGGGPATPWSHLEFSTPEGPVLCHPTDPLPDLGTIMSVRTPRSHALSRHVPVQ
+TFSATNTDVVAVESGLEQELVLVLDRDPAQDRLVGQPLTVTWARQSGGTRRHTPDLLTLT
+HEGAVTVWDVRPEGRRDPKFWEAARCTRAVCEHNGWTYELFGGLPEVHAINLRWLSSYRH
+SMPWYADLRDTLERLACTNSATIGTLLGADDGSGELISAMWHWAWDGRLQLDLTRPLKTS
+TPVRWEPR
+>4_2159
+MLSLDRDGQVCLWDARPSRRQDEEFLEAARTTEACARLLGWDYRVHAGHGPAYEANLRWL
+SAFRALKPWYPEAEQRLGQLLAHGERSVQEVFAVDDGTGELISGLWHHVWAGRVETDLDS
+PLCGASILRWVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002350.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002350.fa
new file mode 100644
index 0000000000000000000000000000000000000000..112147ffa12cb6655e4d69f41009941f002bcf11
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002350.fa
@@ -0,0 +1,6 @@
+>3_651
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
+>4_1956
+MHAPFYSRAIPVHQIATITCGPDDGMNHGLLNWFVTGLATSPDGLRINNGGQAHIDMSTT
+EGLRSVVVVDDLSQTEQLICAVRTTCSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002353.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002353.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5326dab0638312bded3dd1503abdbe3d09e36d63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002353.fa
@@ -0,0 +1,13 @@
+>3_678
+MSRRSLASLATAAAFVVTAVLGGAGPAAAGTTYSAPLRTAVASLPVAAENNAGYDRAAQF
+GDWKDANRDCQNTRAEVLIAESKTTPKFTTARKCTVATGKWVSSWDLRTHTSASTVQIDH
+MVPVHEAWGSGARYWTKAKRVAFYNDLGDARSLNAQTSALNSAKQARGPEQWLPPKNQCQ
+YIADWTAVKIRWGLKADATEKAFLVKKAASCANTTLKVTRY
+>3_2127
+MLGCSGCLGLVALGLLLLSLLVGGFTGSPSPSAASQAPDGRSAAPSAPDAPGDPAGSAPA
+PAPTPDRAEAPVSDRAEAPAPAPAPASAPAPAPGDAGEAAPSSPAAEAPAADGTALAALQ
+SLPVKGRAPKTGYSREQFGPAWADVDRNGCDTRNDVLRRDLADVVLKAGTNGCVVLSGTL
+HGPYTGEVIAFQRGPGTSTAVQIDHVVSLSDAWQKGAQGLSAGRRAAFGNDPLNLLAVQG
+SVNQSKSDGDAATWLPPLRSARCPMVARQIAVKARYGLWVTPAERDAMARVLRECPGQGL
+PAEGGPVDPSPETAAEPTPQAPAPTVQAPAPAPAAPAGGADPSFSSCRKAKAAGYGPYVQ
+GVDPEYAWYRDGDGDGMNCE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002356.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002356.fa
new file mode 100644
index 0000000000000000000000000000000000000000..961d93334af07b4280021db867d93a1528a4219c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002356.fa
@@ -0,0 +1,11 @@
+>3_1163
+MDTRDDTELAPSATLGRRERAKAEKRARILAAARALFEERGFERTSMSEVARAADVAEGT
+VFQYAATKVELLMMVVDALWGAHERATTTPSLSAFAAPGAATAGGETADRIAELISPLVT
+AMWRWSELATWVAREILFGADMPHRRRVLDHVDRLEEEIAARLQDGRADASGAIGAARDG
+ATGTAGEEPGAAAAAGARLIVAGVLAELNRSRQRRIDGEDVDVVLRRLIDLVVAGAGAAR
+>3_2236
+MPVTLVSPRARGGEFATNVHMVDARPPLPSRSIDCAVVSHSRLAPESEPEPEPEPEPATP
+TRVPGLRERNKAAQRERILAAVRERLGRQGYRAMTTAQIAQDAGVAAGTVFTYAATKPEM
+LMMATHDRWKDSVPSALAGSLPEDRTEAVRALVDPIVATAVAEPENSAAIARELLFGQPG
+AHHDAVLVLVRRLEEAIARIIADGDPGPRERTAADLVVMGVVLELHRDRTEGGRVEGLEE
+RIERVIGLFID
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002359.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002359.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25a094456be6ae3a60ecc7c6c293e5612bfd05a8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002359.fa
@@ -0,0 +1,10 @@
+>3_1172
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIRKHNPNLSGTAESAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDAISTPEAVDY
+>4_1479
+MTDRSDPRLQDESRLDAVKRAVEDVAQDAPTLAKIALEAMIREHNPDLSGTADSAGRVGM
+RSGKVSELTAIARLKPGGAERLQRIFDLTRGNMDGAQRVSTLHDMRFVFFDDNTRILFAT
+AYDGDWDAYINDFATKIPELMDLLFQNVEGWPGIDSPTVKDFIADHQITASGWFVANPQV
+TVVDTRRLQRTEDAVNTFLDQMAGRTDLDEDTAAALKQLTDTISTPEAVDY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002362.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002362.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20d848f3b7625c61481368f5b3656175062acbeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002362.fa
@@ -0,0 +1,6 @@
+>3_1751
+MNIYPDFGAFGDNTTLHTVIGALLTFVLVTAVLTMLISGITWAIATANGNHTTATKARTG
+LLVALGTATLAGAGITWLNWLINLGDQL
+>3_1753
+MLDLMTSVLPTLPMMLPMEVDITPNDDGLPGIAQLRNIVAAVMTIGLILSVLALIISAIV
+WGFGANSSNPHLAGRGKVGVLVSCGAAIICGAAVTLINFFWNVGQSV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002363.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002363.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3250cf5262576ba7e1c16ed54ba4a58d0e484895
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002363.fa
@@ -0,0 +1,14 @@
+>3_1784
+MEGLERVGSVLGMMLQVCVNGARDIAEHPALSADPVRVAAECAEAVAAGADAVHVHPKDA
+HGQDSLQNPDVGRWVREVRARCAGVPVGVTTGAWALPSVEDRRQAIVGWQTLPDFASVNW
+HEPGADQIAATLLDRGIGVEAGIWHQEGLTAWLASPLRSRCLRVLIEVQDIPAEEVESEA
+LVLVQGVRRAEPAMPLLLHGEERSAWPALKLAGRLGLDTRAGLEDMVTFADGRPAPGNAE
+LITVASHLRGRSLEEEPTVMKPYSVPLAEARTAFLAALDAFEEGASSLDDLTLLGVSHVH
+GWSRLDCLVHVRLGLQEMLAGLAARTDDTPDVDAASYWTTYEPEKDPVPGILMTRRTASA
+YARPRNALEHLNQVSAGLRHAADTLIEESIAFQGHVLTAGDMLATWAVELAVHHHDLALP
+AGAPAPAPAAVHIGRLTAEALGSTSGARAGAEDDLAVMLAGFGRR
+>3_1829
+MSVAGEAERFAQQAHQFAEAASGLDDLALLDPSLCRGWSRLDLVVHVRLGLEEMAAGLGV
+RADDAPDHDDVTYWSSFAADEQDPVPGHMWLRRTASAYARPTDATAHLRDAAERACAASA
+LQDPRPVRFQGKVLSVMDFLRTWSVELALHLVQLDVGVVPSAAGLARRTLEALTGAPLPV
+RLTDHSALRVALGADPWPADEPGGGAYPLGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002364.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002364.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4aca42f69a1205f456ad4b6c3e1625368065550e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002364.fa
@@ -0,0 +1,16 @@
+>3_1842
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLGETLLVLGPQVATAFAGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+TECFNETLPEELNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+VRTWLVEHEGQQQSAATPARQTKTREAWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGEARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
+>4_866
+MAVEMGLWRADGDRLSRITPTAIGLESQLETYIESDPGMLDETLLILGRQVATAFGGFID
+LLALDETACVHVIELKRDRTPRDVTAQALDYGSWVSGLGRAEIQSIFEAYKPGVALEEAF
+AECFNETLPEEVNSAQTFTIVAASVDAATERIVRFLNEDFGVPINVVFFRHFADNGAKYL
+ARTWLVEHEGQQQSAATPARQTKTREVWNGSDWYVSFGEDSGTRQWSDGRKYGFVSGGGG
+KWFSQTLKNLPVGARVFVHIPKTGYVGVGTVTGVARRFDQLQVEVDGVDRLVKELPLSGS
+YAHEGDIEDVNAEWAVPVAWTHTVPRERAIWKNGMFANQNTAAKLRQKFTIEHVLEEFDI
+AD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002368.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002368.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e295435b614483368bb243da3e55913a868aa946
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002368.fa
@@ -0,0 +1,28 @@
+>3_2261
+MALHVGLYSPWNTTDPRAWSGVISPMAEALRDVFDVTVIPPVGQRDARGERIRTRLRGMT
+GRRSLPTHTMATARLRSAVLAHQLRRHTGAPLDALVTIAASTDVLSLPDDLPIVQVTDAT
+FPAIRGFYPLATGLGRRNEREGMRVEEAGAQATDRYLVASEWAALSLTDVVGVAPHRVTV
+APFGPGTPPPADARRREPGSSLRVLAVIADWERKRGDDIVAAVARAREFRDLTLTIVGRA
+PEGLPSWVNAPGVVDRARLAELYRGHDVLVDLALANAAGVVMTDALASGLPVIATHVGGV
+DTIVRDGKTGWLVQPSGAVDATARVLTTLDAAAVTRASAAALADARARLSWRAWAATADE
+VVRAAVAERRGQASPEAQRRRALMVTPILPSTGGQESAGEHLVNDIAQVIAERSELTMLS
+SDGPANRRALERGVAFAHRLLTSAPLRCDRLPRLLGVAPALNARTVEQVRGLVASADLVD
+LQWEESALLLGPLRRMNADARIVVTLHDVLSQRFARQRELQSSRLRKGVWAARQAAATML
+EAHIVREADAVVVLSQKDADLLPKRGRRARIHVVPPAITGPLRPLRDGTGAPFLLFVAYM
+ARWENEDAMHWFVTEILPRVRAEAPDVRVAVAGGGLRDHVVAELEANDVEVLGFVHDLEP
+LYEEASAVVVPLRYGAGVKFKVVDALVRGVPVVTTTVGNEGIHPADAAIVADEPAAFAEA
+VTAVLANLPCAERYARSRATDVAREFGPNRFRARLQEVYR
+>4_494
+MTPRIGLYSPWDLTDPRAWSGAAHQMAEALAAVADVEIVPPVQVDDAPLERARTRARGAR
+GRRSLPRHTMATARRRSQALSQALEARVGPSLDALVAIAGSTDVLRIPANLPLVQVTDAT
+FPAICGFYPMATGLGRRGEREGQRVEHASAVRTDRWAVASQWAADSLVADVGVPASAVRV
+APFGPGVTPTSAPRVRRPQRPMRVLAVIADWQRKRGDAVVDAVQQARRHADIELTIVGHA
+PDDLPIWVHLEGVVQSDRLSDIYADHDVLLDLASANAAGVVMTDALASGLPVIATRVGGV
+ASIVQDGRTGWLVDADRAAEQAANQLRLLGESGGADQVAAASKAAAEDAARRLTWRSWAA
+AVMESVEEAVAAHAATERRIVMISPLLPSAAHQETAGEKLVRQTVDTLTADGARVTLVST
+PGPANRRAILRGGVPDHRLLSPARRITGRAARLLDLAPVLSPADLAPVRGLLRTADVVDL
+QWEESGILLPALRLTAPGARTVVTLHDVLSQRFARQRDLQLRPARRAVWEARRRAALAVE
+RLVLAMADDVVVLSDKDAALLSSRGRARVHVVPPPIPGSLRPERRDLQPTAEPQLLFVGF
+MARWANEEGMHWFVTEVLPRIRAELPGARVAVAGGGHRDHVVEELENSEIEVLGFVEDLE
+ALYNAADIVVVPLLSGAGVKFKVVEALVRGVPVVTTSVGNEGIHPADAALVADDPQDFAD
+AVLDVARYPQIAESHARAHASAVAEEFGVAGFRQRIKEIYR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002391.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002391.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f728fd5023f60204a66b052a1eab319a3ee39203
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002391.fa
@@ -0,0 +1,3 @@
+>0_594
+MGKTVHRSASTGRFVKTSTAKRNPRTTTTETIPSPGGATRSVGRSAITGRFVTTSTVARH
+PGTTITQQVSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002392.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002392.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96b7fea26d4b789aacdf906a5928a9d1f2ba9792
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002392.fa
@@ -0,0 +1,3 @@
+>0_596
+MVSAEHGPSGSPYGEVLPGVGGNDSAQDPLVTWWLVLYGLSNLVRYHPAAWRATLDVDKS
+TLAVPLEQLVSFASEKVPDLLFEAFVDLGGGRQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002395.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002395.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8e919c1e68f557d5ddb4498ad762f33bad77c0c6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002395.fa
@@ -0,0 +1,13 @@
+>0_677
+MTARIAVVGSALTRSALVADPRLSVPAGHFLARVSMAGLGTPPVEDADLTGVASDFRREL
+VRRDVDRMLVADLVRLDPDAIVVDVADERFALDVLPSGAVVTVSPEYLESAPPQDGRRRV
+PSGDDEHFALWVAGWRTFLSTLDAVGLRERLILHHGGMAVRTADGTAARHEAAILAAARY
+ADRLADRAAQDLDPARVVRVDDAIRHAALADDGTADPLALAPAAAAALAAGVVAVLDGRD
+PWEVDGLVDVSPDAEPVEPAAPQAPAEPAAPEPSAEPAAPEPSAPYRDVVESDYANYGVD
+PVRWGSVEEFAASGFGPGLHILPLPDGNHLDLIIRGDLGGVGERESVVVFLTGAMSQRNS
+VAPPFFAGRRLSYELGIPWVAVSDPSMQLADDLLLGWYTGSPGSQAHATLLATLRALADG
+LGRDLLLVGGSGGGFAALRLNEELEGRSSVFAWNPQTDLLDYHPPTVRDYLRTLFPGKEL
+DPVAEREAVEARLAEEGIGHRVGTLDAGRRVVVFQNAGDHHVEGHLLPLVHRTPGMTGGP
+RRFATDAEHQVRIATWGAGHAALPAHVTARAVDAMRRGHSASTVATDIDALLAHERGDDS
+DGPDVLVTAEPGGLSRVDWAAFPGEADDGHACTLSRMHGEDVVDQVEHIGPPVVLPRLDD
+GEHWRLEAFDARGRRVHEIHVDGRGDPVLFGGTGGSARPRRARQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002396.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002396.fa
new file mode 100644
index 0000000000000000000000000000000000000000..357d4c20ff23f61c1a41a1c69963d9a16f6b6bc0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002396.fa
@@ -0,0 +1,7 @@
+>0_809
+MNRRALLLALLQVAVAAGILGWVVLLFGTGPFVAAVRVLTWPGVVGALVLGSIGVLVQAQ
+RWRLIARRHGIELGWRAAAERCWQAAFINSVLPGGLAGDVVRAAEQRPVGAGRRRDMVKR
+SLGVVAAERLAGTSVVFLAAGFALLAVRPGLGGLGLLVAAVAATAAWPWLRRLGVRDIGL
+VWGLSAVGWCSFAGLFLLACLAVSPDLPPAQIPYLAAVTLAGMSIPLNVAGWGPREGAAA
+LGFMAWGHAAQQGVEVSVAYGILALVSVLPGGLVLLVRTVQGSRRRRLGGGEIELGAHVI
+AQDEAAHGGGEGSGKSVGPVETNPGDPVSHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002401.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002401.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37b2b50b50e97b5a1edf5de69671b194989718f2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002401.fa
@@ -0,0 +1,8 @@
+>0_865
+MLREQLGGRAGLDAAQRLRTRVGEALGHAALEQRPLPQHDALPRRGRVGSPVAGRLGLGE
+RLTAGLPEGGEHVLAWPRPVQDGRLRDLVRHPEGLGHHARHHGVGLVLLTEGDGPCVDVA
+TLQQGEQGAGVLPAGEPQLHRAAGEHVLDPIHGRGEGGGRRLGPLLRRVVLRQRRAQARG
+DLPERGGAPHDLQRPVDRQSRDALERGDVLEAVPRVQVVGQVALVPAHARPVSGGQGERH
+QERPVGDVHVLRVLRPVETVESGHGGPRGHPVHVAFHHHGRVLTPYRAVVPETGADPADI
+PDQLIPHGMAAGDGPPVPLGSGKRGATSALEHEGDGRDGGLHDHRLLVVGRAHERCVTVS
+DRAQAAPGEVEGETPAGPTRDGEEELGHAGSPPSKAGSRSPTPSSSAIAETVRSAARPSP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002403.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002403.fa
new file mode 100644
index 0000000000000000000000000000000000000000..535e9702a3f25e38eddbe5049bb30dad29d98d91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002403.fa
@@ -0,0 +1,13 @@
+>0_868
+MSRPRGFRVLPRARARSAALAVTLGAGLVLTGCTAPDGVEEPREPPTVTASPAPPSAAPT
+ASGAAAPADPASASASTAELARAELYPCQGYGRVPRHNTVESNARDVYAWHVFEPVAVGD
+GHGDVDWDADPYEDEGWRLWLASLRWIGPSIEAAREGDEEAFAVAERLIADWAADHEQGW
+AEDHDDLEANTHRLNVLLCFRSVVLQREGGTVPEEYAWVDELIGRHADQNMARYSARHNH
+GSMENRGLLGAGCVLDRPKWMRHAMQRVEADLPYQIDEEGLSNEAAPHYAQFNYTLFHAI
+DTTSTACGVPSEAFEGRVEAMGEALPHMVDSTGSYWQYGDSAEYPVKPFTGISEGLRYAA
+TQGAEGVAPADRVRAFENGPVFGRSSWGTPEEGFRQAASWMLRSGTGTEKKAHRGDLLQF
+LYTARGRQVIEDGGHPGIVTDDWRPWGLGPTAHNVIHLPTLEEFPGDGAAERTSLTVSPD
+GSADGASARQALTAGGERGRSVLVLTEPDAAVVVDRTRIEDGRAGHVVESLWNLPTEFTA
+ERIAPDTVRAVESASGEATTLVQVRLDGASVGEDDLAIHRGRMDPEGHLHRGWHYPAEQV
+REEATQVAFRSAGPEAGLVSVLIPAGSEDEVGVEVEQHDDGTLTLVVRGAEGTARVGIDA
+DGTPTRLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002414.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002414.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5b2145eabccdd9a7ada205ad35d4b617194b9b9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002414.fa
@@ -0,0 +1,3 @@
+>0_1555
+MTFACGVAIAGLHVVNRRFITPMYDVVLNLAAFLAAVASSVLLGHVLPAVFAALAVLAWL
+ILAVRTVRARRAGHKSAGQRPAGAGL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002415.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002415.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e5faa5b2d043640eed16f314bf27c373cd4e05e4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002415.fa
@@ -0,0 +1,3 @@
+>0_1565
+MDTDTLDNTPRVWIGCLHCYNSGGLVGEWFDAVDAEEVTLTHVHRGAGGTAPVARSCGAS
+TTRICPCAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002416.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002416.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0883f9eccbdce20bdb66d92384d6dfb6fb6b84a0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002416.fa
@@ -0,0 +1,3 @@
+>0_1865
+MAEADRVAEGAADVGVTEDAAAVEETLPGDAEHPEMAVPRRAATTTAADNAARFFSMSIR
+MIRSLSENRLRGRGLRSRAPLSSGLILAGDARCVKHHIGQLG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002421.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002421.fa
new file mode 100644
index 0000000000000000000000000000000000000000..aed003c508f709ded5a4cf492ec35af62d199b4b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002421.fa
@@ -0,0 +1,3 @@
+>0_1899
+MNKHDETLAQLREFVAERDWARFHTPASLAKSISIEAAELLEHFQWTEDGADMAEVQDEL
+ADVLTYAFMFADHMGWDVDEIIQAKLVKTRVKHPVPTGGDEEATSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002430.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002430.fa
new file mode 100644
index 0000000000000000000000000000000000000000..11ee4957e0446e1cbc33aecaa4214c4765652e40
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002430.fa
@@ -0,0 +1,3 @@
+>1_11
+MVTLDTEHTIHLGAVALESPGTSTLTVYGKIVTTEAPGRPRVAWADVRVEDSELSTGGAF
+LPDARQARALADYFLRLADLMDVETGQG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002431.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002431.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4e27292944ebf3a53dbed36c67c692b7fec18c5e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002431.fa
@@ -0,0 +1,8 @@
+>1_12
+MIPSEEEVDWSEVTGSAHSSGPSGSTRETGPIGPTLDAVDGWLSRFIRTTTPEDIHLLTL
+WAAHTYVVEQTYTSPRLQIDSVMPGSGKTTCLEHLAHLARRPLSASTISSEALLPRVLES
+GIRTILIDEADRSLDMKNPIMAGVLATINTGYKRGGSRPVLVKDAEGNWTDREMSTFAPV
+ALAGNNPNLPDDTRSRCIRVLLMPDLDGTAEPSDWEDLEDDADRLQVQLSEAMDAARDAV
+AEARPELPPGCVARHREKWRPLARVAAVAGGRWPSIVERLILRDLQEHETEKEEGLMNRP
+LRVHLLFDLAEVWREGEAFVPTPELIARLAHVAPHRWGAESLKGLTPQGLGRMLMTGYKI
+ASDREPTGARRRGYTRQALEPAWRLFHIDLSDSDRTSPV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002432.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002432.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8038ae170665deb9e83494801d6d45c4c04c4166
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002432.fa
@@ -0,0 +1,4 @@
+>1_13
+MTLPQTRERRPHAVGAAPWKSYDGDETRIPTASAPEGLATPLFVADLLGRLAEAEHAPSC
+TCGDWGRALALVLALASEHECTAHPAIVESVARTFAGWDGADAAEDRSVTRFRVWHAAAR
+ADINEGMAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002433.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002433.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90c6329a480a772bcb618979162e1ef2cc2e3b5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002433.fa
@@ -0,0 +1,4 @@
+>1_15
+MSTPSRQGHFITVVCAHPRHRGERRWIVTRFMGTADGSPVDWIEIPGTSRAWRAERKHPS
+PDRNAAELGWVSDKPGHRFYYQHGQSRPLFELLNEYGEPRDVSAPIENRVILWCERCARA
+GRTPELRCPEPELWRLLDLLLAAGRESVTVRELIQARQQVRPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002437.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002437.fa
new file mode 100644
index 0000000000000000000000000000000000000000..69f5625e30a71a82c2ad97b92d46a5c5c495a61d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002437.fa
@@ -0,0 +1,4 @@
+>1_87
+MYTTVITPRVSETDGVGHINNTVLPAWFEAGRAELFRLFNPTDSFEDWPMIVKTYTVTFD
+REIRYGADVTVECAVSRIGGTSIRLAERIVQDGTVCATGEVVYVLVGGDRRPMAIPADLR
+RELERHLIEENHD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002440.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002440.fa
new file mode 100644
index 0000000000000000000000000000000000000000..19d5e49c2af0702d39a79e8ec60bff6588a89686
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002440.fa
@@ -0,0 +1,4 @@
+>1_252
+MTVEVNGKRVDVTLPTWGEALHTISGAAQRAGAGRRRPRGKRGAPVAAAVSTDALTAPMQ
+GTVVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATI
+ADAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002441.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002441.fa
new file mode 100644
index 0000000000000000000000000000000000000000..06b9cd89ad8315fa61279ad9a8505c200f6eba18
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002441.fa
@@ -0,0 +1,3 @@
+>1_338
+MRTGSVSSTSNGGTSRIALNNGKTYNATNGLAVPANGSVGRTDGTCRLGLDRTEACGTTG
+QSPYSVAGSTGASSTAVTAISLYRSITVSGYGTTVVYLNATGVGTNLSVSAAPLI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002443.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002443.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f89904c80231eada8fa5881aef6d9d8a176d0ee3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002443.fa
@@ -0,0 +1,5 @@
+>1_346
+MVLELRGEPDRTGLRFFRLKSHTACMETKPNATRTVLPPADLEEMLDLSRFLGALTQPAA
+LLGPDGQTVPLPLEAFNVLREVVEAMQVGKAITVAPVDQMLTTQEAANFLGISRPTLVKL
+LEGGELAHELTSGGRHRRVRLQDVVQYQEAKRRDRRAALEDLTGSASEAGLYDEDADRYR
+QALRQARRDLGRQAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002444.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002444.fa
new file mode 100644
index 0000000000000000000000000000000000000000..759f3eefda7c42008056dbc96f813a901d583d42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002444.fa
@@ -0,0 +1,3 @@
+>1_347
+MARFSAVLDACVLVPIAQADTLLYMAEAGLYRPLWSERILEETIRALETIHPDMRETGAA
+RRRAAVMNQAFDDACV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002445.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002445.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e2923b03cc859191120cf6cab7984d9c64d076a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002445.fa
@@ -0,0 +1,3 @@
+>1_348
+MVAAAVQGRADLIVTANLKDFPAEVLGRFNLQAQDPDEFFMNQLDLDPAQVMRSVQVQAA
+ATRNPPLTVAAVLASLERCGAGMFAEAARGQTWRL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002446.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002446.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c098c7e0bdb03cbab3e1f62611fb4aa83a8f72bd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002446.fa
@@ -0,0 +1,3 @@
+>1_349
+MLLWGGEAKTPLTAGWLAVPVLGERPFIAHERLWWDADRDAQVTQTPMPDRGPNFDERPA
+AALSMALKQRPQEGQA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002454.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002454.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a3aa03d42632864933416c80ed3c42d19ee4d867
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002454.fa
@@ -0,0 +1,10 @@
+>1_1285
+MGQKQKTKSFQLGEIPSSSDAWWNLFNFAAEAQWEIPGVSLESFANPESIFLRSAAEISL
+NQPTRLRLEHGGFHFAVRLADNSSVPIDIDADIIPNEYILSSYEYEYSTKNFTYRGYKAQ
+RTSPADLTVILGHELTIDLKEVGSDNGKCDIKYPLSRYLAHRVRDLELYIDILEYGFLTI
+GSYGIQVDTTAVSDVHIQEDKEYLETLRNLLQNIEYFGGNAEKVLVDSINDDQVRAIQAA
+VESSRSHQRPPGYRGSTGRVRFGVGDKSLELFVYARDDEGQIDVTNLFGDDNGFWLASTE
+TVDGGESSRLVTPYEFIDDEDLVGLININLSSISRHYERIKGYDGVEQIADSMIIRLWRV
+AVKQEDRREEFRSAALSLALWVSCAYVNSTQRLRYLTNIHLLRFWANGFAWSDDSQRLAC
+RRLQQDVMRANLSDISLYHVCLTFLLGSEVDLGDTIQGLNENEMKQLQSWPVWDLIGEAY
+PKLTAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002459.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002459.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c1baa52b311c448fe19e3c378e700292878d996c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002459.fa
@@ -0,0 +1,2 @@
+>1_1649
+MVRGIFWVSHSKEAIMALLRKTAAWGAAAVGAVARVQYGALSEPIGGN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002468.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002468.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f5fa5ffd8909fc9f4e15e561df2f79d4482066c4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002468.fa
@@ -0,0 +1,5 @@
+>1_1976
+MDTVTTTTPARQRLLDAVARLFYAEGMVATGIDTITAEAGVARKRLYNNFASKQDLMLAY
+IRGRHEEWLELFQDRLDRAGSPRERVLAVFDAYLDHAEAAYAHGFRGCGLLNAAEFRAGS
+AGREAVREHKEQVEAILTDHLTEAGCADPAGTAEHFSFLLEGAMSRAGLEGRSDRLLRAR
+RIAETLLDAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002475.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002475.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ea8687cb2d9e589fbbb979ce216482247c03cbcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002475.fa
@@ -0,0 +1,6 @@
+>1_2162
+MPAPKVHLPLETRCSTYFVDEAGAKGSQGEYFVTAAVKTDDPDRVLRGFEAVRQESNYTN
+ADELKFGRVNKGSLPVLRRVIDDAVGAGARFGIFVLDKRHFDPWVDVEQWEGHLFATERL
+LRGMTTRRELGVALLDHISVPKEVSYGAELLARINGRMGNRRFLTAVSLDSKTCPGLQIA
+DIVASSAYHYRRGVEEMGQTQYLQQQSPKAQLARHVAETIGLGDFSDHKSDIASVRTSHP
+QSLTELRDGVASLVSEEP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002477.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002477.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f59b666e9213743b53fac8f525ca8a0137b1e846
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002477.fa
@@ -0,0 +1,8 @@
+>1_2164
+MSTTKTAPAYTTAEDIRAQVHAHAEEERRDASAHGAMLNLMQKIGDGREDPEPDLDAAYE
+QARISGDWEEYERIFRAHDDWADRSAKRARMANNLRSRAIPNPERRRTLKGDAGRLTLAY
+LAGALPSILDAAQRLTLHGVPSTAEAAMTADPRTRGRYLEAAAVVDAYRALRRAQAAAVT
+DINATASDSFGGPSKVSSQSVLTIGQFRDALHLDATWLSNRRNAIGQLRSSATRAHLRRY
+VPGIVEFLDDAPAELFGPITADGFPAECTTVPARAQWLATWSTRLDFWVPEFEDLQQLQH
+LYGAAINPGHWQDRKGLVLANTYEGESAADNAERLALVNLDYRRPDWDTPQSEPTAEDLD
+ATTANRAALPREQHPGLRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002482.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002482.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7e7f15b610f32ee2aa2dff5dbe5c63c6a41e0e91
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002482.fa
@@ -0,0 +1,3 @@
+>1_2173
+MPGFGPYGGQNYVMTDMKKGRPATDGAAPTTKLATPILLDPETMLEGVLVLVVAHTEAGE
+TRYRRRVFYTVAAAQRAADRAVERGHAASVTLCRLAPVTTLAGGWKA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002484.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002484.fa
new file mode 100644
index 0000000000000000000000000000000000000000..155e893d2e0bdaabd171004bd60521db751ad03c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002484.fa
@@ -0,0 +1,5 @@
+>2_6
+MGRRLASAWALPALLVLSEPGRLPLVLALGVAVAAVLATRAVGAGAEEVGRSPELERLLP
+IGRDAAWSVHTVAPALVLVPWGAGLGLVLALGTHGVGPSLGPVVLCGALAGVGLAGAVVR
+TATPDPVDWGAVMQPAQTTRAAGPLVRDAVRGADAAVLAVAPLALTPLLSAVPLGFAGVA
+GVVALIAWGIGRHVRPAG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002485.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002485.fa
new file mode 100644
index 0000000000000000000000000000000000000000..90cfbffe3fc8f050c390135811cc6a4f8ae8b1e6
--- /dev/null
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@@ -0,0 +1,3 @@
+>2_29
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002486.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002486.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ae289f5356b5e881b994707528cb30496f143881
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@@ -0,0 +1,2 @@
+>2_32
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002491.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002491.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b3c31f2e94a0b7e9fe9b08111f209893aa451ed
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@@ -0,0 +1,3 @@
+>2_40
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002495.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002495.fa
new file mode 100644
index 0000000000000000000000000000000000000000..04f8d11268bc70f9fce2aa70803ce0811e278110
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@@ -0,0 +1,7 @@
+>2_76
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002498.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002498.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9e2f6d2b32a7a474521b49b859a395561bd6d8cb
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@@ -0,0 +1,6 @@
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+PRGDVAAVMAICGAATVHLLSLFVFVGLLGTWLVSVLPADLMLVVGTYILPAVLGAVFVQ
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+DDDVELHY
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002509.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002509.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c46a5a1039f759603913738d6ec2f8f4bfb1fc0
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@@ -0,0 +1,3 @@
+>2_168
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002510.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002510.fa
new file mode 100644
index 0000000000000000000000000000000000000000..581ea66626e72dca0bf69e271fc3304ec0e5ece6
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@@ -0,0 +1,3 @@
+>2_169
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002511.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002511.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ccea3180a6735a71650bc5515d87838745c5e7cb
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@@ -0,0 +1,6 @@
+>2_170
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+EALRADPLLVEPPHGLWEKVAAAIEAEGDLAATPATVADLDAHRSRRRGGAGARWWVPAA
+AAVAGLLVGGGAVWLNLQPSEAPETGPVAEPQVIGDAEMDPVAATGTTASAKMTREPDGS
+LELTVDVPEVPDAAAGYYEVWLRDADASRLISLGTISSTSTTLRVPEGIDFSRYPVVDVS
+HEHFDGDPTHSGTTLWAGAMTERS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002513.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002513.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1b0305677c71ee8d946946f1961d1116029bae56
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@@ -0,0 +1,3 @@
+>2_216
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002529.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002529.fa
new file mode 100644
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@@ -0,0 +1,3 @@
+>2_393
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002532.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002532.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0482ac00d0e9d23516a4b555d90706c41db5c995
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@@ -0,0 +1,3 @@
+>2_438
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002543.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002543.fa
new file mode 100644
index 0000000000000000000000000000000000000000..91c0678fe05f30ebdf8548b1cf977943203cc9de
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@@ -0,0 +1,4 @@
+>2_465
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+P
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002551.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002551.fa
new file mode 100644
index 0000000000000000000000000000000000000000..17f2c8785e2494ceb50e035adfa43b799b369560
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@@ -0,0 +1,2 @@
+>2_480
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002552.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002552.fa
new file mode 100644
index 0000000000000000000000000000000000000000..989c36901def55b5840ee12a3e2de163a9ba8891
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@@ -0,0 +1,7 @@
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+WTVSFPALRAAEEAGELPRAGVTSDYKSANVVIAEDGPVIVDPDNGGWEPRLFDLAMAVV
+LLHNDTDSAPGRMMTAAEWEAFHAAYARHVTLTDRERALWPAALDHMLWEEGTWALEDND
+DDAYAQPRQGGYLRDLATMPVERYRLPGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002558.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002558.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b34a037864b3f46941cdd4821d43512185e41874
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002558.fa
@@ -0,0 +1,5 @@
+>2_504
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+RGDEHARYYAALLGAEVTAGGEVTDPALQAPTLWWQGSAGEGSASETPLPAPEVEQRWHL
+DVWVAPEEAPARLRAVLDAGGRLVSDAAAPSFWVVEDVEGNRSCICTSQDRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002559.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002559.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d21a19e238070425aa74deb8dac6facb12436442
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002559.fa
@@ -0,0 +1,2 @@
+>2_506
+MDTQETQDLPAFTFLAADPADGDAEGAVEDTDAAFCRLDGSC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002561.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002561.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05f205449b4817c60626d00feb48dcee98fb187a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002561.fa
@@ -0,0 +1,3 @@
+>2_537
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002562.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002562.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cd632ee3c3872a03f9d1790388b1a93b3a4e0833
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@@ -0,0 +1,4 @@
+>2_546
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+PRFAGIATGGLGRADFDAAALTDGRPRLLTQAVSPHLWEMRQKDGAVRCDGVEFLSRHGD
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002577.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002577.fa
new file mode 100644
index 0000000000000000000000000000000000000000..77984bf8e6e0b3fdfbd989e514e4bf91c2cda555
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@@ -0,0 +1,5 @@
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+DVLGLHRLQGETLVDNVASQRVLAACGFKHYGTAPDYLRIDGRWRAHELFQRINPGWRPR
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002578.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002578.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a21f33b7d449845374dfaf9b42d47f19a36551c2
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@@ -0,0 +1,2 @@
+>2_689
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002582.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002582.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ebbb857ef11845c910ed3bfc5be9c1444402f0b6
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@@ -0,0 +1,4 @@
+>2_699
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diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002586.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002586.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6053181427b27cfb23bb408c11d12440b1092a8b
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+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002586.fa
@@ -0,0 +1,3 @@
+>2_729
+MKVREGGRVVNAVVLLATGVNGDGHREVLGLRVATSETGAAWNEFFADLVARGLAGVRLV
+TSDAHTRDCARRLPRTCPARPGSAAAPTTQRI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002591.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002591.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f8cd7a1ffdbd6f4579f45b19a62d291fd4bfd02
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@@ -0,0 +1,7 @@
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+ADAEATARAMVLEYRTGMPEDPPSTGPDGFPLLDPPWLMMTVMLPPADDDGALAPVVHLA
+TGTGVTPAPDLVSRLEADLRDARPGTEHTGALEALVRTAVEHSTPSEQVRAAAAEDSLFA
+DRPAWQWALVGALLLALAAVVATALRRRRRRADPARDAHAADPARFAHAGEDPALRLRAL
+TELLALAADAPGARALPQARDATAAVVEHTLALDALAPGSRQGRPDAFRRSVRPELEDRV
+GRAGATLRVLVAAGRDARPAVRFPDAVLEAAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002598.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002598.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5e65a6adca9fea3f70b37648ac250f9348d020a1
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@@ -0,0 +1,9 @@
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+QAARRGEGFETTWTGGGMAGELRGEEDHLTEDTAHLEQESARAARTRHGRPDPPVALAAV
+PLLIVILVNLALSRWILPTLDFGYLAEEQWGATTLTSVIGLWSVFVALVTAVAFVLLVNL
+RRVRVLVEDLHQGAKDAVLPVFSTASEVGFGAVIASLPAYALVRDALLGVSSNPLVTASL
+ATTSLAGITASASGGLSIALETLGADMLASAQAAGISPEALHRVASIASGGLDTLPHSGA
+VITLLLITGMSHRESYKDVAMVTVVGPLLATALVVVAAAAL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002602.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002602.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e61357c94fe7630815553b5f9087d569b5851f38
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002602.fa
@@ -0,0 +1,12 @@
+>2_801
+MTTETAGDFRLQTPEEIEAVVAVLGDAGMLGENARIAYLGLLDPPRGAERAAVSRDRRFR
+VFVLDVAGGLPVEAVVSATRRELLSSRELDSTVDGEFPVMEEEFAVVEEVLAQDPRWQEA
+MRARGIPVEEVRVAPLSAGVFEYEEERGHRILRGLAFHQQHEADSPWAHPIDGIVGYVDV
+TAKEVTQVIDLGAMPVPQEHGNYTDPELTGDLRTTQKPIEITQPEGPSFTVDGGNHVEWE
+RWSLDIGFDMREGLVLQNIAFDDPHTSRRRTILDRASIAEMVVHYGDPSPIRSWQNYFDT
+GEYLVGQWANSLELGCDCLGDITYLSPWVVNNAGEPRQIKNGICMHEEDWSILSKHTEMW
+TGISYTRRNRRLVISFFTTIGNYDYGFYWYLYLDGTIGFEAKATGIVFTSAVPEGSTDFA
+SEIAPGLGAPFHQHLFSARLDFALDDGTCRVLEEDGVRLPFSEENPRGNAFTRRRTVLAT
+EQQAQRDADMAVGRTWVVESSEHTNRLGAPVGYKLHPEGLPTLMAAEGSSIHRRATFASK
+ALWVSQYHEDERYPTGDFPNQHGGGAGLPEWTAADRNVDGEDLVVWHTFGLTHFPRVEDW
+PIMPVDQVGFRLRPEGFFDRSPVLDVPGPRKGACHSGGAPGAGDGGSDDACGCGH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002604.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002604.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ca8779311c981aabac329856bf1d144a3d710299
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002604.fa
@@ -0,0 +1,7 @@
+>2_803
+MFRRTVGDHAEWKELISRSFVPLESEPLRPSRSFSGRLDVSEFGGIGLTTLAAGPHAVHR
+TERLAAAGGGGMFKVSLQLSGRGLLLQDGREVLLEPGRLAIYDTSQPYTLSFDRDFTSHV
+LMFPHTALGIAPGQAAQVTATALDEGHRLGPAVSAFLTQAADAMPVLDPATGGRLAHNVV
+DLVGTLVADLLGLPPRPAEGARPAPAEGTDDARGRQRAAVLRHIDEHLADPALSPASIAA
+AHFMSVRSLHLLFEGTGETVAATIRRRRLERCRDELGDPGNAGRPVAVVGARWGFADPAH
+FSRAFRARFGVTPGGYRRQAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002607.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002607.fa
new file mode 100644
index 0000000000000000000000000000000000000000..880cde2081162907166503d054b778fdd4c1e209
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002607.fa
@@ -0,0 +1,4 @@
+>2_855
+MNLLHGLDGMDRRLLELLRQDARRTNASLAEELGIAASTCLARLKALRASGAVRGFTVDV
+DPAALGHGLVALISVRIRPGARHRMEELFDRLRGLSGVQQVFFLGGEDDFLLHVAVADSE
+EVSRFVLKNLSADPAVAATRTSLVFRHEGGERPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002611.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002611.fa
new file mode 100644
index 0000000000000000000000000000000000000000..53a37d24318d0031c154d5d6321cbfd76dc06f42
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002611.fa
@@ -0,0 +1,6 @@
+>2_912
+MGGRGSRGRGPEGDRASLAWLWALVAGAALTQTALNLARPVTSYRLLALDAPEAAVGWAT
+AAYALLPLLGALWMGRATDRLPSAVPLVAAGALTMGAGGAGLALATSAPAVYAASAVLGV
+GHLAFTIAGQAAIARRAGPGLLDAGFGWFTAAFSAGQMAGPLIAGPLLADGATAEATALA
+LWASAGIAAAGMLPVLLVPGARPRPGERDGTVEPDARSGDAAETAHASAPRGGETADAAA
+SPGEATTPEPAAGRHGGGRASRASCGCRAWPRSCSPGWRCWPWWTSSPRSCRWWGNTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002613.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002613.fa
new file mode 100644
index 0000000000000000000000000000000000000000..25bd04ec4d007eea8aebedf28a7d0244a470cd83
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002613.fa
@@ -0,0 +1,5 @@
+>2_964
+MASQDWMDKDFYATLGVSKDASEADVKKAYRKLARTHHPDQNPGDEAAEKKFKEISEAYA
+VLSDPQERQEYDAIRAMGGGARFSAPGGAGGGGFEDVFGGMFGGGGGPRTTQSGPDLSDL
+FGGMFGGAARQTGGFGPGGFGDAGYARRAPRRARTAPPPPRSPSAARSRAPRCPCALRTA
+RRSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002614.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002614.fa
new file mode 100644
index 0000000000000000000000000000000000000000..236f8674e05a5a1b4c7e785667e5e4d633e6f5e8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002614.fa
@@ -0,0 +1,5 @@
+>2_979
+MDTARDFVSGLPEALQGLGVFLVSFIPWVEGEGAALIGVLVGVSPWLAIPVAVVGNVLAV
+AALVYAVGGTREAVLRRRRSAVAAGVGPVDADLHDDVAPPAADARMRERFERWGVPGVSM
+LGPWVFLPGHVAGPAMVGLGATKGYVMLWQVVSIVVYTVFTGLLAAGLIGWAARAGVEAS
+LPGAF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002619.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002619.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c7ec0e188b99e49f2fefc934103582efc8736594
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002619.fa
@@ -0,0 +1,10 @@
+>2_1036
+MRFAREAWHAAISWPSILLAVVLTALTLHGVSEAASDPGVNGWDVAVVQVSNLQLVPLVI
+AVVWAPVFLARHRALQREDELLRRGSWRKAVAAVVISDAAIIIGALTLSTAAVLAVSASL
+GLDGGWSDRVVGIVSSGGLDSEVSAAAAAAWVGQWHGAPWLFLAIQTAWTAAGLLAWAAL
+HAALMIGIGPRTAAAVVISGALWGVLSGAGLLVGRPFPDMSAWTNSLWAVSNPPSVAVTV
+ALWTLAGVGVVGAAAARDGVREDGRLRLTFPHLAVSLALSVVLLYSWYGAGTEGGTGLAD
+VAFGGQYSSLLGHLLGALPAVVMAGLLAVQLSDLEGGGAEQILLRHGAPHRWVGGLLGRF
+LVGSVAMTGLLVGTFAAADFLWHSEGTTRSAGEWTLLAAAYVSFCCLLGVIALVLFWVRG
+HVQEWIFVVLAILVLGYPTLFPPSPANPLVPYSLEPGTPFTATPLVASLSLLALFVLGLG
+VLLSRLPAPRSS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002620.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002620.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b5eb39551141b89ddf8970404ea0420c376bcd34
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002620.fa
@@ -0,0 +1,4 @@
+>2_1054
+MLLVAEAEGRPLGVAAWAAPGQAVAQRRRSLLAAPALLRAAWPHRAALRVLGERGPRVDQ
+ALEARHAAEPHWYLGLLTVAPDAQVGGVGSALVRAGLARADADGLPACLECDRHLEAYYA
+RFGFARTHTVEIDDGAPAHLGMGRPAGG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002621.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002621.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7a94965683f594396ecc2e828e38c3ec9d72b627
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002621.fa
@@ -0,0 +1,5 @@
+>2_1185
+MTRFQWQPGGGDRHALEREGPFKVLFVCTANICRSAYADVTSRARGIQGVEFGSAGTRAL
+VEHPIDPPMAAEVHAAGDPSQHVARQLTRDLLEKADLVLAMGPDHRRWILDAWPQHGRKV
+LLLGQAARIMSDLPADLELDRLVAHLWARRSTDPSDEVQDPYRRGPEAMAIAARQIDAAM
+DVIAPTLEHVAQR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002624.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002624.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ac6c25cd01ee1e92787b19929a316ba55ed2101b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002624.fa
@@ -0,0 +1,7 @@
+>2_1197
+MRILLSSVGRRPYLVRWFRDALAANGVEGTVLAADVDPDAPSRPFADGFVSAPKVVDPGY
+ESWLRQTLVDHDVDLAVSINDFELSTWATLPEDPAWAPLVRLDAGTQRLVEDKFATSQAL
+LEAGVTSPVTWLGSTPPSTEDAAGPFVTKGRYGSASRGLRFVDRAGLPGALEEASGEVTT
+RQGVPALQQDAVPPAELIVIQERIDGVEYGLDVVCDLEGRYAGVLARRKITMRSGETDRA
+VSVDAAPFESIARGIAEAIPHPGTIDVDVFVDASGDIYVIDINPRFGGGYPFSHMAGARV
+PECYVAWALGRKAGAEWLRCRPDVVAGKFVEITATSEGGTGADA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002627.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002627.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0ef9851cbe00233441a7d7ff8282c943fd091ef9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002627.fa
@@ -0,0 +1,6 @@
+>2_1249
+MEFSRVGLTDMPRTLVHYTNAPAFMSILEGHALWASSIGYMNDSQEYHYLYVQARHFLEI
+GYGALRHYGDAHPEDLETFINGVGWPYANSPSVYVIALSTDDDDLNLWRAYTAPGEGYCI
+SFDSQKIRELAEKSGWRLAQVEYGASCIPVLEDLWVRAFTKVEEGESSQEVLTWVNSRLA
+EIAPFYKHESFASEREWRLVKVQANFDQEDLRFRPGVSFIVPFVVFDFGAPDQHSIVQVR
+CGPGPNQKLAFDSMDWMVDKIGWNPSRGVSNAPFRPW
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002630.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002630.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0fd1d8736eb16671602c32768cab0af07fd14048
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002630.fa
@@ -0,0 +1,5 @@
+>2_1264
+MPLATPTLDTERLRLRPFTEADGDALFALMTDAEVLRYWDSPPWKDRGSVERFMAGNVRA
+AEEGTGARVAVECRSDGAFLGWCTFNSWDPDFRSASLGFCFTRDSWGQGYATEAARALLQ
+WAYSTLDLNRVQAECDTRNPASARVLEKLGFRLEGTLREDCIVDGVVSDSWVYGLLRRDW
+QMHGASAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002633.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002633.fa
new file mode 100644
index 0000000000000000000000000000000000000000..48322b76f33c01d9d6f91fa1e90eef83fb618ef4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002633.fa
@@ -0,0 +1,6 @@
+>2_1280
+MESPLTPHPIGATLLPRLPGAVPVLLEFEDVQLGGYAWWRERQAPAILLLHGWGEDASTM
+APVAHQVLERGRHAVSISLRGWHGSTGVDDYGLSASLDISRVLAWIRRQPDVAGIVLVGF
+SMGGLMAALAAADQPAGALDGVVLVNAPAELRSFARDTAFGGARRYLEKTLQPRQWQDSS
+PLNHADRLSHPLLVVVGTEDTMTPPDQGRRLADAAPASALFEVAGMGHHPTHGEWAQILE
+AADTQFDLRRGLPSPAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002635.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002635.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d6076c6b941d4af4bd8ab113e30305a85e2aea6f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002635.fa
@@ -0,0 +1,8 @@
+>2_1282
+MNIAWTRRPRARVVCVGVVLAVLLTGCGASRGDGSTPSSSSAPPGTPTLGEGSSSGDQDT
+LAYVDRALDVLDTGLYASGERWERARAQVQEAARTARSPRDLDSVLRYATGVAGGKHSSF
+APGADPDVRGGRSTSSASESPRMNVALPTVTTTDGVSTLSLPALPVASDDPQASEYAMVL
+ADGIDAAAPATCGWVVDVQGNLGGNMWPMLSGVSALLPEGPVMFFRDRAGEDTAVTVQED
+GAGTEGMTFVSVGPRTQRDGAPIAVLQDRSTSSSGEAVLAAFRGLPNARSFGQSSSGYGS
+GNATHVLPDGSRITLTAAEFVDRGGEVLGDRPVDPDVPIRRDGGGGTDAAQAAARIWLQE
+RGCP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002643.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002643.fa
new file mode 100644
index 0000000000000000000000000000000000000000..475be38c13ad36acf8f10e27ac9c48471c66c529
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002643.fa
@@ -0,0 +1,8 @@
+>2_1316
+MTFHVAVDARSPRMSHCSCSSPRIGVSWVSSPGGVLALVGAHVQGEHVERRAAGDPAVDA
+GGLEAGAAAQGRGVGDGHVLLPRAAGAGGQRVHVTDLGVARVFEDLARPPVVGRLVVVPL
+GDDGDVRVQGAEVVVHHVVAVAAAELVQRLGDLGRLLRDEVAPGGLAGHLEGLRDGVVRV
+DRVAGVQEEVGLRGVHRRVAAHAADLRVDAVALPRGVRGPHEGLGGGGLPAEPRAGRRGE
+AGHGRLAQAAGLVLERVRHLEAGAGGQRVREDLRGVVGGPVDPAGVQGQPASEAAAQHLP
+VLVDRAQRGVQARTAGRARPQHGRVRGDVAGGDAGRQRQTGRGQATGGVAGRTGGGGVGE
+GGGGEHGGGRRGEHRTAGGGVGQGCGGLLHGARVGHAGEGHVASG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002646.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002646.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5ea4976ed8c0fe1a0f3f9d7a24bd5199a1cb9e82
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002646.fa
@@ -0,0 +1,7 @@
+>2_1332
+MSTGRPLRASVWRHAVDVLRPAATPARPAVVRLGVGAFAAWNGHRRRDLVRGLHRQDPRR
+FEPVGVVKVLKRPLPPRVADGLFDAAQAVNALATLGVAHRVTGPLNAALQLWTLSYRNSW
+GMLYHNDNMLLMHQMVLGVSPSADALSVDAAVAGRGLAPAVLERRYGGVLPMVNAATCVV
+YLISGVAKVRSELGVKWAGGDVLRGQIAIDGLRKELLGSEMPAAGRALYRQEHLFTLMAT
+VALAVELGAPLSLVDRRLGRAFAVAAWGMHVGIRVIMGIKFTYNTSGVSYLGYFPVGPAL
+PR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002647.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002647.fa
new file mode 100644
index 0000000000000000000000000000000000000000..139c620505f5f48e43649fabca4d03f6618ec79b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002647.fa
@@ -0,0 +1,12 @@
+>2_1404
+MDPGPRLARAAPPLGPVPAAAHRRAGRAAHPPGRAGVLRTAHPADHAGPLRLPLRAGPGR
+GPPRPEPGAGHVRPDLRHGRPEHGRARHPDAARPRGRLRHHHPPPLPPGAAAGLGVRLRG
+HDLLDRPGPRRDPGGSAGGRRLRPRRLRRQRGPARRLRRHAARPRLRCPGGAPAGRRLRP
+LPRLRPLRRAGVPRLRAAGAARVRRRVPAGQRARVLVGLAARGAARAAGRPGRRVHLRRQ
+PGRAHAGARRGRDGPPGHLVQPDGGQHPGPDRPARAALPDAAAVRLGRLPRAAHPADHRA
+DGRGRALRLPRRLRPRQPPLHRAALPPGRPLPGHARRPARDHPVRRRRRHPGPRGDRHAR
+ARPRRRSHRPAAGGPDRRARLPGADGPGSPGRLRGVRGPAPHRAHPAQPGEQRDRARRGP
+ARGRARGRRRRGRQPGRGGPRHRHEPRGGAARVRPVLARRPLAQAHHGRLRARPGDRHRG
+HPPARRTARGLGRAGGGLHLHGDPAAAAARDRPGRRGARADRPVGAAHAPAVQHRGPSVR
+RGPHPARAAGPRRRRVRRRRPRRRGGDGRRRRARGGRGAASAARHAEQALLPPSRLLGTP
+AAQGDDGGRSGRDPGEDDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002651.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002651.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6837fb9ae18e2d7c16f746e9607f0165b241b19a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002651.fa
@@ -0,0 +1,9 @@
+>2_1466
+MADENVPVPVWTLATEAVAVPDLVGDADMTPERLADLRTALATFAQAPIATLEMHPIERR
+RDTAGGIMLHASSPLAQQLSQLVTQTARSAPAKVDIAASGEVLYRMVVPAKVASQVSKGL
+VKPMASKAVSGGVYSALRDSTGIVSKATFVPVAGTGATTGAAATAGVGIAGAGALTVAAP
+LVLMAVAVGASAYADHQRQKAIERITDLLEQLHDDKLEHERNRLDGCRDAIDKATSVLLD
+QGKIGQSLGLDSASHEISTAIAAVRTRLKKWQDALDELPEGPVELATLTEAFPGITNENG
+AFSAHLETARLALALKRRVLVLQAVEHAQLDGTGNPFNSFLSELRSDEQRLNDLEASING
+VLLRLASLELKRPGGLLKKVHYAPSDVDKLLTAAYRLRGLSSGVDAAGNHADVVIEIERG
+HDGSVVVFPAAAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002659.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002659.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8038f823bdc531f19bf437b9160a4c064047d833
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002659.fa
@@ -0,0 +1,3 @@
+>2_1543
+MPSHRNARDAPMTRRAWRLRIVLASTAFGGAAGALALRTQLPPAWLLAAAVVAVVLGVVA
+LPDPALQSPAAAVLAAAVASAVHGVLSLSTTPTPQPVPDVVRPGPSTG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002660.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002660.fa
new file mode 100644
index 0000000000000000000000000000000000000000..88ff2bc8eda800404ac52668155d57c4bcb14b8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002660.fa
@@ -0,0 +1,12 @@
+>2_1556
+MAGRSRAAGASAFRASSSSASSAASEGVPAGDVVVGGVGGVGRSGLGGVGDLGRGVRGRL
+RRLVRPVDDGLDLGGGRGIGVDTGRALVRGILSGAGLVRGGQAALRVHGGEAARGLVLAG
+LAVGVLAGDEVGEGVVGLHVRAHALAAAHPQDLQQVGVPVRPRGGGARRGDGLRGVGRDL
+ALVVLGLQRGVGGGAGLGAGEHVPGLGLGEDAGPRVPGLQVAAGRAEGPQGGRLLAGGQA
+GQSRHGETGGHGPAALLAAPGVPLQGGAVHADLGEAVAGEEAEGAGPAVLDDVRVEVRTA
+DPDLHGLGLLGHPAALSQHRVAVGADAGERVAALPGHLLHGGAGADALLDLTGERGSASW
+VAAAFTDSWSVSAAGEAAAGAASSSSASAAGCGVCVGGWLGVDARGQGQLLVRTGGAGGV
+LARAGRVIVVRRFLARGRVLLGGLVHLRQVVPGGGCGGGVVVARPLGVLEHEAAQVGGQG
+QRVLGAVGIQQAQGVAVLGGSGQSQLCHGGGPSHVVFSSPGARTPGRAFPDPSGRAARRT
+PTGARRDPRVRRRRDGRSSFGRAGAMVHNLRATAQAGPVCSGHGPVPSLPGTGPGAVPHQ
+RSVRTPWPPTTTPLGRTRKS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002663.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002663.fa
new file mode 100644
index 0000000000000000000000000000000000000000..3278e091315bc222f90a7bdaf1e3a43e982ea724
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002663.fa
@@ -0,0 +1,3 @@
+>2_1694
+MPGAGGDGGRQDVPPGGGLGVLESLGQAGDAVRSDADAERGEDLHEGLVRDGLGRAVLAD
+VVRLHAVRAGESAQQRAGFQGHRVLHAVVSGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002682.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002682.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b50230eef9ee36d22425ae46d0f158268af7507e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002682.fa
@@ -0,0 +1,3 @@
+>2_1899
+MSTPLIEDLLPSAPGSGVYDVEVRGGVVHESVWLDEAGFWRSADDVLVMPAQIERFAVVD
+GPDVIRWVRDTDHRWSSIVERDLEAGPAVAGGVVTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002688.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002688.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0101fe475427d500a8940dcfe02509c061048974
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002688.fa
@@ -0,0 +1,3 @@
+>2_1905
+MSTRQSHPLVFARPGGKPLSRPYPVVSYTDATSLKTAVALAARHYFPALRSVFVDLAGPW
+RQCRGRAYIVAPSHPPVDLEFHPAATRPQAPEATQEGLLP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002689.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002689.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9ffbcdc98831141263257d587de92f8c8655cf8d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002689.fa
@@ -0,0 +1,3 @@
+>2_1907
+MRALVTDGLGATSVEESGEWPCRRADPDAWFSTNPYRQAEAAQACHQCPAQELCLRAALD
+LEGSTGKSYRFGVWGGHTPEDRARIARARRRLVRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002694.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002694.fa
new file mode 100644
index 0000000000000000000000000000000000000000..102ce4a5728c67774ab0e5d6488876847f2d2e45
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002694.fa
@@ -0,0 +1,3 @@
+>2_1912
+MSARRPRTYPAGSPERAVADAVAAVYAEADLKLEALQLDLLEPRPDGTRWTPQQVQARRI
+TEALDALRDGFQEFGRGITAVAAAASKAVAALSAALTTTTRDDYTLAGPSKGAAS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002704.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002704.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e90712aa2f2d416fcf241ea26b801a24d07772f0
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002704.fa
@@ -0,0 +1,10 @@
+>2_1922
+MSVNPRYLLTPPADDVDETHADGAIALAAGYGLVLDDWQQQAVRAWLRCGPDGRFLASTW
+GLSAARQNGKNAALEAVELYLMTVLGWKIIHTSHKLGSARKAFKRLTKFFGRFKGDPSAP
+YPELSALIQEFRRTNSQEAIELTNGGLIELSARTSGGARGTSYDLLVVDEAQEYEELEQE
+ALEPTISASAHGQPIVIYLGTPPKTIGERGEPFIRVRSKAVSGQMERTAWVEYGASLEID
+RMTDVELQAAVRDDHHVRDANPAVGARVTWETVNGERGRWSARTFARERLNCFPLPRTSS
+EKAIEEDVWAARHDPDPDPHARLAAVGLDMDPARTKVTITMAYWAEAGVHVEVAAAAPYA
+DAGVASLVAWLWERCKARVPVVIDSFSPARAIEVHLLQKRMKVRVLSAREWADACMGLYD
+AVSAGAVTHFDQTQLSLAVLAATKAPVGTQGAWRMQWPKDDVDRAPAVAGVCAHFGAMKF
+GRRPREGAASQKQTGHSFV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002711.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002711.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f6bcc7565739a0d3ce456abf3cb15c5033d9641
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002711.fa
@@ -0,0 +1,4 @@
+>2_1929
+MSGFATVQDLEERWPGITTGAVTRAETLIEDAELLIEGDYPAVGEWVASGLLRADVVTFV
+VCRMVKRALGPDADDAPGGQFESMSRTTGPFLTTLNFREPAGDGEELFLRRAERNLLTAH
+LRARARAGRAFTIQPGAGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002714.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002714.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b74be65839a0cf1cf706addf0b59948afc94d54f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002714.fa
@@ -0,0 +1,4 @@
+>2_1932
+MQGQRFPQPREVLRELTDGREFAGHVVTTVFQEQADAYGAHDPVPQLLVFETSVVEGFLD
+RVTQVQLALYAEGPSAALQVLEAILAEVCGVGITTSAGYIDSISVVQGATEAPYTERLNR
+GSALLQVVSRPI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002715.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002715.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eb778c969dafbc2c436bb1c94a55e59cec5f99d1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002715.fa
@@ -0,0 +1,5 @@
+>2_1933
+MVTFHELQTQSDERKLVRKIQKAVALIAPRNVDLPESLFAGAGQLVNLKEEGWLPLGIVT
+PDGYEFTRDVETEDIDGLGYASPVRTDVTRVPRAITTTLIESGRKHVQEMLYGTDLSTVT
+QDPVTGEVVFDEPDMPANREYRLLLLGKDGPADEEWVLGKGYGTVSLTAGGGATWGQEGA
+VSTEVTLSVYADDELGTPVRHYMGGTGALKYKDVLGYTAGTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002717.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002717.fa
new file mode 100644
index 0000000000000000000000000000000000000000..75dd83ec38799e9b04712760cc05735001a725d7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002717.fa
@@ -0,0 +1,3 @@
+>2_1935
+MATQKKTDSPKVHASLAKLRKESPAAAEPFQIALEDSHVITFPDPFAMDVDAAERMFALP
+DTQVKAALREWLSEEDFTALFRVKRSLRDLMLISQAAQAHFEATYGPVGEDSASRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002721.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002721.fa
new file mode 100644
index 0000000000000000000000000000000000000000..bdc331d79b16db39059976987a7a5414207f9fd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002721.fa
@@ -0,0 +1,8 @@
+>2_1939
+MTDQLHLIDAPEWGPAAVDLLAGSRDVEWIYELVHARTNRFIRTLRGVRNFRFENNLHAT
+IRSGGSCIWQGAEDIDWMEHRLRAHQRISHRGQSLQWTVGTFIVESPTRVLTDKTRGAQD
+LQLFDAMYRLDVQTSTVSEWVAHKGSNIIGTVRHLLDRQGIKHALEDSDAVFASQMSWEA
+GTTYLRMVNDMLAAANFTAVYADPQGVLRAGPARAATSRGVAWTFRDDSTAMRYAPEVTH
+NRDTYSIPNEVVLIARSDDPDTLPMSASARDTSSPYGTMRRGMVITKVEEVDAASQAILQ
+ARADLRLKEVQRPASTFTFQHLPLPLEMSQVVRFVRTRHDVDVLAVVEKTGFDDGTGLAE
+TTVREVVS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002723.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002723.fa
new file mode 100644
index 0000000000000000000000000000000000000000..80cd06ce8e11746d2afc584156b0db33bbcdc8c1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002723.fa
@@ -0,0 +1,12 @@
+>2_1941
+MHTYAARVIADQATGRPLAGVRVAVEDAETGAPVQPCRDGQPVTLVTGAHGLITEWQTED
+TTRRVALTAGPVRLTQWCEELQGTAADAVSLMDDRLADAASAVSQAATIRDGLEPRVQTV
+EARQTALESAEGFGPSTPEDGTTASYLSQATSLTAKAATVMFSRGTATVSDRYAPSLQAL
+VDEARPGDTVLVSRAWSLAEPLTISTPLRLRTLDAGEIYAPDRTKDGVVVTSDDVELAAR
+IRGAGATTAGAQRLVRVAGASLASPVRRFALTGSTITDAARDGVQLEWCDDWTIEDCDLS
+HLAYSAITTLSASRGVVRKSRVANVLQPTGFVNSYGFTASRRTDQPLSTHPRSSQIRVDD
+LTVDGVPKWEGIDTHAGENITIRDSTVRNCRVGIALVPGVDASGVDDIAPKGIRVINNDI
+DSGVSDGTRGIGIQAVGALNADGTMREALTGTIEGNTIRGHGTDGTATSGAIMTQATSGL
+SVRGNTIVEPAMNGVIATTRNEGLRVEGNTVVDAWTDKLGYTSVLRVTSHNNSIRLTGND
+AVRGSRTAAVVHGRGLYVSSSLSGVSVRAEGNDFTSASLPMVDGGLSYAREGATKLSFHP
+TAEPVTRPTLRGAATDELTARALVNQLRTALIGYGLAN
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002729.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002729.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f81be3c3d45fc8b21ebdc4e5d30c8a5412c62e56
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002729.fa
@@ -0,0 +1,3 @@
+>2_1947
+MQTRRTPIIDTLTLWTGSVQAALAAGAGAAILSDLPGWVAFSLAVGLFVVGMVQAGLRWA
+AQNATVPVGDVVEVREGSDVVAGPANDQVAEGAFVRELGRSPRHRVAD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002737.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002737.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e99b244e32668ccc32499e25a39945359838c022
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002737.fa
@@ -0,0 +1,3 @@
+>2_2051
+MASIEPRRNGDGVVTSYRVVWRDLGAKRSQAVASLEQAQQWKAVLEAAGHDTGACQLVCV
+SGVVTGRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002740.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002740.fa
new file mode 100644
index 0000000000000000000000000000000000000000..801650bf0bd840d45805aee955fe7d5bc5800bb8
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002740.fa
@@ -0,0 +1,3 @@
+>2_2058
+MPDRERGTGLSVRDHLVLQLWGRRWRHGAARDRAAVELVGLRPTELALRVAVLAEEHAAI
+AAYPVVPRRAREARQTRHRVVGGRAASAAEVVAGGS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002742.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002742.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7814570670eadbfd6a927411cebccb0fff34eb43
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002742.fa
@@ -0,0 +1,3 @@
+>2_2147
+MPASNLAPAHSDTLTVLEAAREYESFSPEYLRAQIRKGLLPAEKGRRGYLIRRADLDSHP
+GPAPGRPSDRDRLEAFARALVAQAPRFTEEQRQQIVIALEPYADGST
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002747.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002747.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7adaffe9443dbae910c14c25294c9d1b81f7fb5a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002747.fa
@@ -0,0 +1,7 @@
+>2_2162
+MEPSATAPETVSTAAVCSRDERPPKKGHPPVEPLPPHEPMAPERDQELQAVLAWLQARPI
+QDELTEAVLQSVHYILDGASTGRVYLHDPEVDSDERSAVGVNLQYRVLHVLGLPKEAPLD
+TTIEGIPVDIKCTTGTGYGWMIPPEAQCELCLLVKIDAEHDRFAAYLMRTHRVWLNEGGN
+QDKKRTITAAARKQYAVQLFEGEWAPLPRNPLRDLTSDQRELVLNLHPDRQRGQETRIKA
+MFSYLPSTVVPRHVLETIGAGRTDPARRARAIRSQLRAEHGLILLCGKWKPERDAARSAG
+FDLTGRDWVAVPEADVDPHQLDLVLAQRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002757.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002757.fa
new file mode 100644
index 0000000000000000000000000000000000000000..33300ac40eb1b354b66d5cfe8d9e520ffe23cbae
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002757.fa
@@ -0,0 +1,3 @@
+>2_2198
+MTAEQAREAGHQVKVASKPVATIAAMPRPKIEEDAHGVIEVVVDAATDLVLGARPHCVEA
+QGLVNLVALAMRADVMASALRDGIWTHPSATEALNEVLGELG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002758.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002758.fa
new file mode 100644
index 0000000000000000000000000000000000000000..136a99008ddff4b84046e9602353d177f4a48547
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002758.fa
@@ -0,0 +1,4 @@
+>2_2217
+MSRTSDPVQPSRPRPVLLLALAVGAVLVYALQGLVPLLMDGEVPRPDELLAPPSPVVLGG
+PIAWAAALAALVLPRGRAHPLATTAVGTLAYVAGLALGAFVEIGPGTGGWNWGWESVVAI
+LLVTGVWVPALVAAAALAWLARPRRTPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002767.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002767.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9a1d5c123308c4b2bbcd4e32206da60317eab01a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002767.fa
@@ -0,0 +1,5 @@
+>2_2352
+MRSTRPGMFSVIIPTLQKSPELREVVRRCAAHPAVAEVLVVNNAPEPLGWTEPKMRVLQQ
+SENIYVNPAWNLGAREARGDLLAIVNDDVLFEPEVLDECRKVLRRGLFAVIGPGEACFEA
+APRGRIGHQVAPFFSFKGRFGTFMAMRREDYVEIPEQLRIWGGDDWLLMQQRRPNAVLTN
+TRFVTDMGTTSSSPEFRALRERELTVARRVLNPLYRSRWWHRPIEYLDRLRRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002779.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002779.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0990e56f18ae51837a30f41f95f89b83ba02833
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002779.fa
@@ -0,0 +1,5 @@
+>2_2526
+MIVTTEIRRRPARRGPDLGDVLMAAPFALWGAATLALQFNRGHRFIRALDPTGLIVPDWR
+FFAPRPASHEYHLLYRDARPDGTMSGWNEIDLGADRRLRHIVWAPHRRLEKGLFDATTEL
+MRVITDVRDPAVVRMSAAYLALLTVVTHSASHQDGAVRTQFMLVRAAAHEPDVIPSIDYI
+SDWHRLEGEH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002781.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002781.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f42575ba5178de0d593e1a7fd5e8ffc641aae93
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002781.fa
@@ -0,0 +1,6 @@
+>2_2528
+MFTLIDAATNTIRPMTAKQPLDREVDGAATAGRLTAVGALVGSLEELSRREDGGDRSLFS
+WPVRQTALRAFRRRSLAPLWSLIEPRRYPILLAGRVLCAGVVLLAPDTSRVRGPALVGLT
+VSGLLKSYRNSYGSDGSDQLSFITFASLATAHLPGLTAGQRAVPLHFVGFQSVLSYTVAG
+VAKLLSTQWRDGSAIEGIFRTRTYGDAGFYRMIKDRPAAARALSWTVIVAETMTPIVLVL
+PPAGRRAVLGLAGLFHLGNARYMGLNRFFWAFTGTYPLVDRSARSIRRVLGLVEGRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002791.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002791.fa
new file mode 100644
index 0000000000000000000000000000000000000000..816fc60d8eb456f622a0614f72abe9023de868cd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002791.fa
@@ -0,0 +1,2 @@
+>2_2595
+MHDPHDRTRPLRVGSLFSGYGGLDLAVEHALDGETIWFSENNEHVSRIFAHH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002792.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002792.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e973e0a2c4fb3551b096e3343c913b4cf73e4bf9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002792.fa
@@ -0,0 +1,7 @@
+>2_2596
+MGKRAGLAPGTRSGLWSYMAAAIDALQPQLVVIENVRGLLSSPAVRAPLEEDDDAQSNPD
+HATPGDAALREVEPDPWGLGDLAARPLRAVGAVLGDLADLRYDTQWIGLPASLVGAPHPR
+LRVFILARSRGTVQDAARHGLDSWRRVTGTGEGEAGDDRALASDHRPRAKRAGWLAEQEQ
+RTRDAVVPDRGHLRRWGRYARAIARWEHVTGRIAPALLDRTSGPRPSPEFVEWLMGLPSG
+WITDPIHQLTANQQIAALGNGVLPLQALSAMRVGALVQADAASLAGVQHPMVSRGCTVSQ
+EEEGEDEKAGESA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002795.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002795.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a775a62b9034a35ff0b565c905559bc37971e9a4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002795.fa
@@ -0,0 +1,3 @@
+>2_2600
+MRFTAGLIVLVSLLVAEFLWPESRFIAFALSAGLVVAALTGSCLMGRILSRMPWNKVTAS
+PTARSAIASIPVATQEL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002799.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002799.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0a28fa94125adb5977866deff003249eed8b21e5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002799.fa
@@ -0,0 +1,5 @@
+>2_2605
+MGSMTSPTTRSRQGIGESFRLAVQALRGWTGRQVLAAIAASAVVAVVIGVATVLIPNPLF
+GRDIPPVWWNYPVWLVTSVLSGMLVATYIRPYRAAADEQQANAVSEDGAATDAADEAQAR
+RSSRMGMAGGILAWFAVGCPVCNKLALLALGYSGAITWFTPVQPFLALGALILTGVALVW
+RLRGQVACPVRPEPVAAVR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002802.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002802.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0c5bf4240f2eaf6a2329ab169b0229fff6cc9773
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002802.fa
@@ -0,0 +1,5 @@
+>2_2609
+MRTIGLLHGMSSVATVDYYRRINDRVNELRGGHERAELVLSSVNFGVIERCVRAEAWDEA
+GQYLAGKARGLQRAGADFIACGSNTMHRVAPVIEAAITVPFLHIADVVATTATDIGVTRL
+GLLGTAPTMEQDFYRRRLERAGFTVLPPEPVDRTTVDQIIFDELTRHVFRPESRETYIRV
+MTDLHAAGAEAIVLGCTEIILLVGPDDVPGLPLLDSTTLHVEAIVQTAMSRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002803.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002803.fa
new file mode 100644
index 0000000000000000000000000000000000000000..db653c85cf1d8b7bd217e88058d4aabba25da13b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002803.fa
@@ -0,0 +1,2 @@
+>2_2613
+MTHANAPLTPTGRLRMVHRHLHDGIPQAHVAAEFRVSRPTVATWGSSPS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002814.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002814.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37d5407e3128c9775dfb631f9f7cad05de964377
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002814.fa
@@ -0,0 +1,4 @@
+>3_132
+MNNLTPAEVVGAYFQNLADGNVEQAMSALDPNIEWHQPGENRFAGVHRGPEAVGALIGGM
+MEVSQGTFAVAPAGPLMTNGDVVAAPVRFTGRRDGEVLDQDGIDLLTVTDGRISQVRLFS
+SDGPAEDRFWGQS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002818.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002818.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1db40c63a8419350b55f9ecdd2a9e70057ceb34c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002818.fa
@@ -0,0 +1,5 @@
+>3_192
+MYLPRVRAPHTKTLPTLALVASITAALATGCSANTSQDAPASSAPAPTATASASSLSPDE
+AARSLASLESEAAQAKVDAAQRNFDAAVASASARALEYSQSKAAGQDLGQVTLETLDIGD
+TRPEWARPIKDVKAVGTDGIYVTYSETLTTAQAVEVATSIARRLAMFSVDSLNRVTLSDA
+SGTEHVVDITRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002819.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002819.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4cbd0816f4e147fbdec2cf8b431fb6ca21f1c0a1
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002819.fa
@@ -0,0 +1,5 @@
+>3_193
+MTTAQTITANLTAARHAYYAAVQTARTYQDPDLTPEALTRQRQDREAAARTAYAQELRPI
+REDYERAARLNAKALAKVPAPTGSTADVWRRVEMRLGAGATLDQIVATADVPTLQAVREW
+APTYLAVNGGDPAAAPALGDRLERATLARYATVTKDADMAAALAEAPTLAGLAVTLDDAE
+AEAQGIPGAGGLNGAVAAALAVQAAGSTTVDPDTTA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002821.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002821.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c7600a624477e527a6da9f3a2d56d043f05e461
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002821.fa
@@ -0,0 +1,3 @@
+>3_196
+MTRTHPAENQHASGRYLDTTARDAEDLAAVADAAAKDADAMARIAADIVAQHAEDLAGIT
+ATTADDSQAHT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002822.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002822.fa
new file mode 100644
index 0000000000000000000000000000000000000000..686b48502bfdb3834861f1aebca32becb400d671
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002822.fa
@@ -0,0 +1,3 @@
+>3_197
+MVTTATRHHRRTPAGTLRTAAPFFAVLAARHGIPAPDAPTPARTPTTAPRATQDTRPAQD
+HLPNLEGHQ
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002824.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002824.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d4928943c377e89df587754e98a80bc4bed28d3f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002824.fa
@@ -0,0 +1,3 @@
+>3_199
+MSAPDRYRLDPAVLDVEARTPAAGARLPSGWVRAATAAARAMGEPFTPARLRAALPEPVH
+PAHFGAVVRHLHAARVIRPAGLALERSPDGSARPVRVWEAVPEDAQDPAEDTATPAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002828.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002828.fa
new file mode 100644
index 0000000000000000000000000000000000000000..ba9742b9646825fa701967f215ea039577fdb266
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002828.fa
@@ -0,0 +1,5 @@
+>3_214
+MRLPESLDDIEAYADALSSEVADLGDYVLVGDSFGANIALALGARQPEGLSGLVLSGGFA
+ANPITSPAWKAAMRLMGRLRGPAYRQMVLRAHAHRLASPHDTEGQVPWSESQSRQLFLDH
+TPATSFGARVTAVLNADYTDELDRIQVPTLILTPSHDTLIGDDAARVLRDGIPHARERVL
+ERTGHMFRFTHPETYSQAVAEFLADESL
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002837.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002837.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9f0551bd9b835053d15df7416e92f84bcd9d1eee
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002837.fa
@@ -0,0 +1,3 @@
+>3_297
+MPVISTLRRVGAAVTAAAALTTLGAGAASAADYKLPYPSGESYRVTQGNFGNYSHTGAYN
+QYA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002845.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002845.fa
new file mode 100644
index 0000000000000000000000000000000000000000..456426deacc7f0226536f655038360922071ceeb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002845.fa
@@ -0,0 +1,3 @@
+>3_324
+MGFSLEMTDINVFQKANTESAVSGEELMQEIENLRTGVEALKETFKGQGATSYNNFMVAV
+NDAQNQLAEALGKINVGQADVFQAYVTQEDEQVSTNEPAVSEAQSFSFPR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002847.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002847.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4edcee18317e493fdb848eb4d3122639f6f0e85a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002847.fa
@@ -0,0 +1,9 @@
+>3_326
+MATKYSRVTLLGERRHADVLLPSDTPVGVLMPQILSLLAEQPGREPAVRALYRDTGAQLA
+PETTLGLAGVLDGETLRVAATTTAPDAPIVYDLHDTVAAQTDARGRWGKRARLTVLGLVA
+VFLGWWAAVQLTVGLPDEASALARLGIGAGLLLASLGVSVWSRRRAVALTLLGAGAVIAL
+NGHWWLMAVRAMPLAPAVLIGLCGGVALLLLAAQVSGQRRPLVLAAGVLAVLTGAWAAGP
+TAAGWLIGERTASVPVTVGALTAVVALLVLSVLAQAAVSHAGLAGLDDQESAGARLLRTD
+VAAAVATAHRSMVLGVLLCAASIAVSFWWISDDIVQPAFSVPFSAVLTIAVWLRAQAFPL
+TLQRAPLLLTAAWGLWCTVRLTSTAFPALAVPLLVALAVIAVLLVALQVVTVPPHVQARA
+RRLSTTLETLAVVALIPLLVGYVGLYAAMLETF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002852.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002852.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b4913fbb1a09318fca235ac4aaa58a9a127e4ccc
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002852.fa
@@ -0,0 +1,12 @@
+>3_337
+MARTFPNSAPTRDNQSLAGLYDMDFAPNEGAVRGEFTMLRNAQTAARIMEHAGLADLIAT
+WQAEDGQGNRPGPKPWLTEVNVLALLLLLALSRRAPLFQEVGEVLIEASDETLAALGIDP
+ARRTYSEKAAYHRAYHSYRRLLPLIDPEPAPLYRRLTVQECDEVKAAWVLEENAVKRERA
+HTMANALLYGTWMLLPRQVRRAYKGDIAMDATFVKSPAYNGNTKPKSSASEVVHYRSSDP
+FAGWYKRDGNHAGPNELPASRAKYQRTQDYVGWGREAHTAVSYGKDVPGIVLAVSLDTPS
+ARLPENALRMVEHLKRNNMPVGHVVTDRAYLPGTKPAELARPLRARGYRLVFDYRAEEHG
+MGQTASHGGAIQVEGRWYCPSMPAPLVNATKDHMLRKESDPEYIDEATYRTRIEQRKQYE
+LHLKERPDAEGVARYACPAVGPSATVSCPRRKEHPKAADKPKGRIMLPLLVKPAPQVCEQ
+QSMKISPLTGEKYAQEYPYKSEKWREHYTGGRQMVESLNASLKNGAHMPIDDTQMRPRRG
+FAAQIVSLAVMVAATNTRKIIAWLHEQVGVTSLSSAPVKRARRRERTAGFTRADEFGPAY
+SPPGGLPPERRETA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002854.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002854.fa
new file mode 100644
index 0000000000000000000000000000000000000000..82c328346a535d604c88dce4fd6d91efc5f99ed6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002854.fa
@@ -0,0 +1,3 @@
+>3_355
+MIAAFASRKEHPSLPFWPMLFENHVIRFVGSDDVPAPSKAAAVREVTVAAAHLVIPVAEV
+LPLGETARAHDLGDAGPGGRVLVDACR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002858.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002858.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9b271be2e555eed86fc1612aad052bad055a6688
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002858.fa
@@ -0,0 +1,4 @@
+>3_407
+MREFGETRGDAMRALAARDVAPGVVGYADGEPVAWCSISPRPQIPRLEASQLMPRTDDVD
+VWSVICSGHRRQGHTTRLLEAAVAFAREHGAPAVEAHPVDNRPDGGGAASGTDAPDRIDT
+TMAFAGTWSMFDRAGFEVVGETAAKGSGRPRLVMRRDC
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002860.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002860.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a9c027142f3d4b269961db6abfe518f18a307f09
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002860.fa
@@ -0,0 +1,6 @@
+>3_421
+MSKNPQTVTDVAATGAISRVELTWTPLPWEPLIDHYRVYALPTSGRGGTPDETHLVGKTV
+YPRFVHHGLDPAGEAFRYVVVAVSDAGRRGRPSSAVVGESQRSVTATGRELARIGEFDGK
+SLELRFAPAQYGQIPKAYPKAVIDYVQGVDTPAEAWPYLLPGPGDAWAGRKAYRARWTVT
+LDAAPQREVDLALWFVDTTRLGGRLDVAVNGQSVRSVELAKGATRGSREGDATLPGSTLL
+RSYHEFTLPTGALAAGENVVEFTLAEGGWVAWDALGLYERAR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002864.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002864.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a334fb337ac301918150473a14a8264de1754f47
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002864.fa
@@ -0,0 +1,5 @@
+>3_436
+MATALLPPNSPSHPLRRAPGGRPALAPVRIVAAFLAAVLVVGGGLALIPVTADLPVTRAF
+NDWNTGAVGVLSNALYQALEPAFAVVLALAVASLVALRRGDLALGVRLGLAVALAWLPVG
+AVKLLVHRPRPAAAALPHPTAVPAVDWTFPSGHVAFVAAMAFMLVLASRTSGQRAARAVL
+GVVAVAVMVATVLVLGVHYPTDVLASLAWVLLAGPLMWQLAGLVAGPLRRLTDRRGAHRA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002868.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002868.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6351f6f93aa32a9e9c91b48549026c55f8314518
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002868.fa
@@ -0,0 +1,6 @@
+>3_496
+MDPRTRTRRPLLPLTTAALALALGLTGCTGGPQEAASSAAASETTSAAGDVVRGGAEIDA
+PESAEPLSNARAAAEGDDRAASARASHEAAASSEATAVPRHAVVTLPAALFETGGGGTTF
+DAWARTTDAWQADGSDPRMPDLGGWDPKTEPVVAEAVLPADQDSLRNPGVLTVPVSGPGV
+THRLVLLCEYTSPRRDEETAGVDVVAGETHAAIASSLGCTPIDVRHTVRPEHIVDGAVRY
+EFQVAPLEAGRLAVLQGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002881.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002881.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7d70dd7b4a97d117741038dfa7df6f1e4746cbcd
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002881.fa
@@ -0,0 +1,4 @@
+>3_606
+MGDGVEDPESQREAIRAEASRIHESAVFSAQGQFEAAKRWRLVHWGLAVLAAGLSSGTAV
+FTFADGAQAWSAVLAVLAAISTTVLASARPDRLAERAQVAGTGYTTLRNDVRRFHGITVP
+QGDPQDLAGELDALADRAAALDQSADPVPRWAYERARKNIEHDGGQAFEADV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002885.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002885.fa
new file mode 100644
index 0000000000000000000000000000000000000000..087816c5cac85032797576a3f04d46db9c4c7245
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002885.fa
@@ -0,0 +1,6 @@
+>3_622
+MAVGLDALDADQRQFVEAHVKGGRVVADHSWGQTDTVVLEVVAGPCRVIVKAGGPSNGHI
+AREIRGHREWAAPWRATGSAARMIAADERARVLITTYLEGQLVEGTPAQDDPGIYEQAGR
+LSAVFHDQYATADPTWNARLRDRTLRFLSMPHRIHPRIAEQVRQEVAGWPVGGATVVPTH
+GDWQPRNWLDDHGVLRVIDLGRADLRTPEEDFVRLGRQDFLRNPELEAAVVAGYGRDPRD
+PDMWRRTNVAEAVGTAAWAFKVRDEDFEALGHAHLGRLYPE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002886.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002886.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b186ed3b8f6f40c4eda3359ded5dd1687288afb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002886.fa
@@ -0,0 +1,4 @@
+>3_629
+MKQRQEPADHAIGRSRGGLSTKIHHLCDGNMRPLVMLLGPGQGGDAPMFGPVMNALRVPR
+TGRGRPRTTPVRALADKTYSSRAIRELLRRKGVQAVIPERADQITNRARRGAQGGRPVSY
+DPEAYKRRNVAERSFNVFKQWRALATRYDKLALTYHGGVVLRAITIWLKALGDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002893.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002893.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e67b2d05f39512b80e846b72f48e3e8a69d56e3d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002893.fa
@@ -0,0 +1,8 @@
+>3_664
+MRDRRLFRELERPGLIVSNLTPNWFASIMGTGIVAVAAASLPLQFPGLRTAATVVWAIAA
+VLLVALTIATVLHWVRYRSTAAKHHLNPVISHFYGAPPMAFLTVGAGTILLGKDWIGLPA
+AVTVDWVLWTIGTIGGLLTAVLVPYLAFTRHENTPESAFGGWLMPIVPPMVSASTGALLL
+PYAPAGQARETLLWSCYGFFGLSLITSLVVITLIWNRLAQHKVGAAGMVPTLWIVLGPVG
+QSITAVNLLASNAPAVVDASTAHALLVVALVYGFAMLGFALLWTVIALAITIRTAREHLL
+FSLTWWSFTFPVGTCVTGLNGLALHSGLTVVAVLAVVYYVGLVAAWITVAVRTFHGSVIR
+GTLLAPPQPA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002898.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002898.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1921a72e49214a0bbb2bdc3c015778c63415343f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002898.fa
@@ -0,0 +1,3 @@
+>3_675
+MVLACSASFRWIRASIRPGAIQFISERITVDKSGTFPVDGLMLGILAAFAEFERRRIKER
+QAEGIELAKARGKYVQAPKLSDTDVEQARVMIQMGIPRPKWRARSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002905.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002905.fa
new file mode 100644
index 0000000000000000000000000000000000000000..464c94c1a45f416671600c1651265b02f588e357
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002905.fa
@@ -0,0 +1,3 @@
+>3_699
+MSSCCSTNETNPAVENGGRENLLGGGADDMTTCPVMVGTPVSKKTAEAAGLYRDFEDERY
+YFCCAGCGPAFDSDPAKYAANMA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002914.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002914.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f7ba11f4d798bd1fff1168e84ab20355a877892a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002914.fa
@@ -0,0 +1,3 @@
+>3_804
+MAPGGVGGGLTGRRGVRAVPHASDRVRAPQDLHEVDGQAYDVVFHPGGPGREGAVAAGGP
+PPVRPGLTVPPAILDR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002918.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002918.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fb7b41fce92cd3e747dd1f3955d202bfb3daadd4
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002918.fa
@@ -0,0 +1,3 @@
+>3_852
+MHRTTITAPTSSRRHRSAGVAVGLAVVGLVMTACSAGKAQEPRPTTSAHVQAQGEGASRR
+SRKWREPGRWSTT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002922.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002922.fa
new file mode 100644
index 0000000000000000000000000000000000000000..cafcd226f16b8f00ea6d3b384c9817f308fdd905
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002922.fa
@@ -0,0 +1,4 @@
+>3_897
+MGVGKTTAVTALSDVSVAGTDVRRSTLAFTEPAQDGKTTTTVGIDYGEWTDPEGRRIALL
+GTPGQVRFSSARDSVTARRARLVLWVFGQRPDAAFEIGRWLELLGDESVWGRTVASLALT
+PGRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002924.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002924.fa
new file mode 100644
index 0000000000000000000000000000000000000000..21e12aea33db5b90187401eff17a838aed4576bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002924.fa
@@ -0,0 +1,9 @@
+>3_907
+MPSHPRLRLTAGLAALALALTACGGAEQQPAAGSPAPASSSSSAAASTSPSSTASASSDE
+ADEASSSAASASESSAAASSSLGASTSAGAPSPTDGSGSWSPSAAGTPSAAGSSSASAPR
+STWSPAAPTAKPSAAPVHAAAPVEADLGGPTTGVAPADTPVAVSSTAPVVEKADPVHVAP
+AHPAAPSASQAPSTTQAPSASSSAATRTPSASASASASSAPAATAPAHTAPVPHAGVDCR
+AVKCIALTFDDGPGRSTARLLDILSAERVPATFYLVGHSAEINPSLVKRMTAEGHQVGNH
+SYDHPNLTTLSPAQIASQITRSDAAIRAAGGRPSTVRAPYGALNESVLSTFGGLPAAGNV
+TWTVDTRDWEHRNPAKTLAAVQQGATPGGIVLMHDIHATSVDAVPAVIAYLRSQGYTFVT
+VDTITGGVTPGTTVRRGMHP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002928.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002928.fa
new file mode 100644
index 0000000000000000000000000000000000000000..eab34e16b33ad0d6835103ef3157e319cec74987
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002928.fa
@@ -0,0 +1,9 @@
+>3_924
+METRVISLFARRVFRDRTVWVLPVTAFAAASALTLAVAGGVHFFWTLPGEIGGFYKVLSG
+IALALLVLPLAALAGAAARLLARRRDDRLSSLRLLGASTATLTGLAVAEATILAAAGAVL
+GVVGWAALIPVIGLLPFAGGTIGVGAQWIGVPGVLAVLAGLTLIAGLSALTGLRRIAITP
+LGVRTRQNAQSVHWVRLLVFGALVVVGQLLIAVSKGAADVGLAISAVLVALAVPLLALHL
+LGPWVLSLGAKWRLRRARTPESLVAARTVLDAPRLAWQQVGSLAVTTYVGVMAGAGLGLA
+SEGEATLTHPEDLMVMQDLRTGVLLTLLISFLLAACSVALNQSAQVVDRADLHRGLAYGG
+MPVRRIHAMRRASVMLALGTVMTVSIGAAVITGGPLIGASALYAPLSLLVIVASLVGGVL
+LVRGGVDVTAPALRRSVALA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002932.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002932.fa
new file mode 100644
index 0000000000000000000000000000000000000000..9affea179db151f0de00e53fb4ab68c06df25a5d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002932.fa
@@ -0,0 +1,5 @@
+>3_973
+MLLLIFGPPAVGKMTVGRAVAAASDFRLFHNHMTIEPLLEVFGHGTEPFNVLTDEFRIRV
+IEEAARAGVDLAFTLVWDVTDPDDAEYVARCVAAAGDDAAFVELRADLATRLERNRTEER
+LLHKPSKRNLEWSDGNVREMEATWTMTTADGPGAAEVLLGAHPHLGLQTDDLTAEETAER
+ILAWLADVRG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002934.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002934.fa
new file mode 100644
index 0000000000000000000000000000000000000000..6cf95da4d22bde8553d6e19579c40435876b8e6d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002934.fa
@@ -0,0 +1,8 @@
+>3_1007
+MRSASRRTLIAGLGATAALALTGASAAPALAAGTATATATMDVYLRATPSWTAGRLLVVP
+RGAAVSVTGVVSSGWQQVGYAGQTGWIVPDYLTPVAAVAVTDLTSVATCLRSTPSWSGGQ
+LAYLAAGTGVARTGATSGSWAQVTTGGRTGWLHTGCLTPVVERTVAVVARPVTRLNSTFA
+YGAQSSAYHVWAEGIDWSRPTGVLWYLDGDYTNPAWSRVMNLTGAEMTSIAAEANRRNLV
+CVAVNTPDVYRADVGYSWWYDRPSTAPYFRAFADWFNRTYGMDAGRQWLMGYSGGAQMIT
+GSIMAQQQSTWGFSGGGAIIVGGGGRPWTYDEVGMGSTYKQMSATWVVGSLDVAGATVPA
+TWSALDSARGGQAYFAAQGFVNTAYTELAQVAHRYVLADVMQAPLEAAGVARLR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002939.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002939.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8b9f9d9bd4813cd861fc6c7a2556a9361e6ff33a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002939.fa
@@ -0,0 +1,6 @@
+>3_1155
+MSTTTTAPGRLFGYARREFVRNVRMIEGSFFIVVLPVALYLMFGALSDWGDLPVGHGNAS
+AYTMTGMAVYGAVMATTSIAGSAAVERQSGWGRQLSLTALTPGAYLAGKCLVALAMAALP
+VLAVLAAGALTGAELDGPLRWLTTGALALVSSLPFALFGLAAALLFRSEAAVSAASGILV
+VFGFLGNLFVPLSGIMLDIGRFTPVYGAGALARWPQMEGERAPMGTEPAAADPLWLPIVN
+LLAWTAVFAVVCLLASRSRTARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002942.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002942.fa
new file mode 100644
index 0000000000000000000000000000000000000000..a96da5705a5a8c4a745901103a37279a6aad645f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002942.fa
@@ -0,0 +1,8 @@
+>3_1188
+MTGTDDVAPTRSPEVAVIGGGIVGLSTAYALREQGVPVRLYEAGLPGAGQSAGESRIFRH
+AHDDPRLVAFARESRGVWDEWAEHFDVELVSSDGVVALGDSALARLRVLDEVGGVEAHEI
+DAAELAQRMPLLAGYSGPAVLDESGGAIRTRAAITALAGALGDAVTTAEVISIDPRADGT
+VEVRSVTDRAVYSKVVVCAGRETARLARTVGLSLPVRLAAHVRLTFDVKDAAPARVACLQ
+DSSGVFGEVGVYATPLPGNSSYSVGLSDTVGVRDDGTFIDPAAIRSLDERAREYVTRALP
+GLHPEPRDFLHCWVTDLPWSEDGVAVWEAGSVLFVAGHNLFKQAPALGRALARAATGGGL
+AADLTPAARLGEALR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002947.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002947.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e219ba642b47cf63710e6d7eccdc30cece85b462
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002947.fa
@@ -0,0 +1,6 @@
+>3_1200
+MDAAQLPAFLTSGTVEDLMADAAAPAWGTRAFVEQVMGGPVSVHVRAEDPRRADIAAAVR
+RVWDLLHRIDAVLSPWRTDSDLLRMRRGELDAAAAHPWLAEVRALTDESERVTGGLFTTD
+LPAPDGSRGWDPTGLVKGWAGDLAAQVLAGVPGISYAVNAAGDVRVGVTPGGPRDPWEVG
+VEDPARPGQMAVVVSLVEGALATSGTAARGAHVMDPRVVVDGHPAPATPQLTSVSVLGPT
+LTWADAWATASLLDPGALAAAGPAWAAYRVVSRTV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002951.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002951.fa
new file mode 100644
index 0000000000000000000000000000000000000000..b0caf7f68f2e1eda4851f9d42b4da38744a64d8c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002951.fa
@@ -0,0 +1,5 @@
+>3_1289
+MLVDAGLIGALLAIGTLARAVFTPLQTLIIPASVIAGILGLALGPNGAGWLPFSDQVGTY
+GSIVIVFVFVCLALTDDFDVRKIGRPVGSFAAYGVLIYASQVAIGALAALLILHPLFHTP
+DSFGLLLFAGWAGGFGSAAAVGAARGQRPRVCRPDLHPRGPAHGRARPGRRVPRDRPPHL
+LRRLRGVPGLPGGHRRHVRRRRLRPG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002956.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002956.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c6d587146e17598c20ff7be6db8ddc400baa8e2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002956.fa
@@ -0,0 +1,3 @@
+>3_1493
+MSLVKGAQMKLKAVGVSVKPGGEVEELVIGGTVSTRGEGIDAVEIDGVVKQARVGGVEAH
+GADARRVRVGDDATCPAGLEAFRD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002962.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002962.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2f6dee6c70df1320f411822803a79eaa82972421
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002962.fa
@@ -0,0 +1,4 @@
+>3_1711
+MHDSLRPTRSFVALLRNPRIRRALGALLTGSEVAASDRGALKAAESVGLTRADDDDTPVL
+QEAFLADAVAALDRALGPLAVLDGGRIRVGDLPHGEVDAAVGAVVERVLSPGERVPEATL
+NDRLALFVVDVAFFRRHAYDLGLVDRELDGSAYWRR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002963.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002963.fa
new file mode 100644
index 0000000000000000000000000000000000000000..059c3a16561885cbebf562fa00d75b839a1adee7
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002963.fa
@@ -0,0 +1,3 @@
+>3_1716
+MSGSWPERAGRPRRSPNEQDGRATLLAVLDYRDNGTAVSLTRAFTVPTFRGQGHAPTLTA
+GAVQDIAECGGAAGGTHVVPMCWYVAQWFDEHPERQAMLARV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002966.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002966.fa
new file mode 100644
index 0000000000000000000000000000000000000000..37e2cfef462cb44148ceb57b998747bccbd5cb7c
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002966.fa
@@ -0,0 +1,5 @@
+>3_1737
+MVLSVLADDAAVREVFLDSPALEVMNQGSVHVNLATISPSLASEAAGRHTGAGVGYVAAP
+MFGGVPVAQAGRLNIVTAGQTEVVERVRPYLDAFSAALWPVGEDPAQANVLKVAGQILIA
+SAIQAMSEAVSVVERSGGDVNRAVEVFTSTITPGPVYSMYGAMIAESRYEPARFTPILGR
+KDVDLARSQAAAEGLRLPFGDLLSGLLREALAAGHESRDWAVLGEMQRHRNGGEGA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002967.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002967.fa
new file mode 100644
index 0000000000000000000000000000000000000000..1fd14af564b0173cc1b8f45b87b97c737e925bd9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002967.fa
@@ -0,0 +1,7 @@
+>3_1739
+MMRGGEGEKGLGGRAGVEVVPREVLHPARGVANLHGNQIITVGDHMRGEQGDGESVANQP
+EDEIHGHRFESHVSLKIGGLKCQVRLSSTCGATGEINEPFAGDLLKSHVGPPRQPMRSRK
+HCNQTLTGELLGRHLRWWGALGQAQESGIKAAGMNVSQELLATPSAQGDADLRVRLVIAR
+QERRHIDRGHGGDHSEAERATNISRGGRSLGNRTVGRSQTLASGLDKHHTRRSGLHSPRR
+AGKQLDSDLSFQRLDLMTERRLHHKAAFRGPSEAPLLSDRDHVSQLLQFHRPMMHLHPSS
+PKYAARSLTVSGE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002972.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002972.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c897d342b9faa17648c16faf431493f1ddd9434d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002972.fa
@@ -0,0 +1,6 @@
+>3_1745
+MTHTTTPTTGTAAETGRGSSATPSTPHPDRADFRTSEGLRALLEHLAEHGWRNNPQAKEL
+LEFAAERFAPLARKHGLDVWEAASAAFDVMRTPAARKAADPWAVVTHAVRITCIYEERAQ
+GLMCSVHQARRAHISAHHDPERFSDRETPLYEYHPAFHLTDLHHREDAEPSEDVGASVQA
+AVADATGLFALLGWPEASARAGVDHVTNALARIGSRRGTYEALRRDKHARALLDLPAPAW
+TCLLRVLLGHPEPAYATTTAGRGILLRLLLGETLADLLGDDALVASIVRATPGRGRVRS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002973.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002973.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2bc967598b7fffcee7950fa09484e189ab830e63
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002973.fa
@@ -0,0 +1,7 @@
+>3_1746
+MSTPGHIELDRAVDSLHVGRRHRADLGDIDALAASIERDGLLQPLTVSPDGVLICGARRL
+AAIKQLGWRTVNVWVRSGISDRLGHLLAEQDDNVLHKPLTALEAAALYRELKSLMAEDAA
+RRKAATQFRSDNQPGTHGPGKFPEPSGATGEAREQAAGMIPGGASYKTLDKIGYLEHAAT
+DETLPEHVRAAAQRGLEQIDAGSPVHPIYETIRNHTANPDAGDEALHQAAADALARVQSA
+GRPKPAPAKKPNSTPESGPVQYPVRAFVVTWTELDQWWTHYDPAVLAVELTDEHVATFLR
+VIEHTIAFADALQAALTNHDDTTTASGTVTESDDGHAGGRPQLRAV
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002975.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002975.fa
new file mode 100644
index 0000000000000000000000000000000000000000..4c92e3fd8b41816aadd12ceac673981b6198b27d
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002975.fa
@@ -0,0 +1,6 @@
+>3_1752
+MSPADRLNEGPDRPRALALLNAVLEREGFHAFYAEDNHCYLRHMGTQSVTVLAANPHRPF
+SKAEQERRKLLAAYLDSCSEDDLIEKILLPMFRQLGYHRITAAGHKDKSLEYGKDVWMRY
+TLPTQHVLYFGLQAKKGKLDASGVTKAGNANMAEIHNQALMMLAHEIFDPEVNRRVLVDH
+AFIVAGGEITKSARNWLGNALDASKRSQIMFLDRDDILNLYVVSTLPLPDEAQPSSPPNP
+WLKTDEPPF
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002977.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002977.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5321fdbdc9a8de9c795bfdfbed43e53064bc2153
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002977.fa
@@ -0,0 +1,6 @@
+>3_1756
+MYNLLIGLTRGEVGADRLLEHTADDVREYLAPEVGQVRIERLLNLPTLLMPETGFDDEPQ
+IARVGHVTNVNKSRYGYTFSFVPNPAIAPIPSPRIEAAAGVLDITDWEFHRTHWAVKDVD
+LYRVLDQELSARVKPKVFQFPTSEPFDPDLVAVMMPFSPAFSAVYESLKEGIEAAGMRCL
+RADDIWERDHILDDVLSLIWRARVVIADLSEKNPNVFYETGIAHTLGRDTILVAQSMSDI
+PFDLQGIRALKYLNNGEGRAALSRGITSRLNTITTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002985.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002985.fa
new file mode 100644
index 0000000000000000000000000000000000000000..d000742f56d0520ab8694a2c44191f5dd2ffe176
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002985.fa
@@ -0,0 +1,5 @@
+>3_1772
+MTTPHESHRPDPDEELLRAVLAEEEAALTEEHGRRDPISPAARTRLRGGTAGAPVPQDRP
+SVEDVYGPVDRPSVGLPGDATADGSVTGAPGAASVPAAGDGSPEVFIGADAETPADVQAG
+RRGARPQRPGPGAAAHRAGHRGAAGRRGVVPVGPPPLARDHGDREHRPVGRPPVGRRGDA
+RRGRDLGGRGAIALTR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002986.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002986.fa
new file mode 100644
index 0000000000000000000000000000000000000000..734ca126debfc4c0f76bb323264ee8d8edb4bb73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002986.fa
@@ -0,0 +1,3 @@
+>3_1788
+MAGRTDGVEPDEIELGAVLSALADPHRRRVIHDLVNDADGSERSCTSFGLDLSKSTRSHH
+FKVLREAGLVHQVDRGNRSEVTLRRRDLDARFPGLLDLIGSDSGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002988.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002988.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5c473b3667607cfa379bf0f96b8f57bcd94f3f73
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002988.fa
@@ -0,0 +1,6 @@
+>3_1794
+MTSNATDQPHVILVPGYWLGAWAWDDVVPALKEHGLDVEAVTPPGLDEQDLNRKNATLQE
+QVNALQALVEQAGGDVVLVGHSGANAAVSTVTDRIPQLLRRVIWVDSGPMTDGAAFAPEL
+PQDIEELPLPDFDTLGQQASLEGLSDGQLKTFRARAVPEPAGVARASVSLNNDRRYGVPT
+TLICCSLPSSQVLELAQARHPMFAAVNDLIDVQFIDLPTGHWPMWSRPEDLGKAIATAAL
+AS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002989.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002989.fa
new file mode 100644
index 0000000000000000000000000000000000000000..05a905defceca23cf443fa6d1d6fe7dc900064df
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002989.fa
@@ -0,0 +1,3 @@
+>3_1795
+MTDQRVLRIDFVSAAGEHTRRDVEPILFAGTRGSWYLIGWCRLRGAVRWFSLDRIRKATL
+TRHPCSGHTVDEIGTPPDTAASVALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002993.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002993.fa
new file mode 100644
index 0000000000000000000000000000000000000000..7c488456765f1ac35e70238d8f315bdeb334a015
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002993.fa
@@ -0,0 +1,4 @@
+>3_1862
+MRRIDRIAGGRQAHLRIAPAALHHPRTRRDFRWITWILTAELVIGAAAVGIAVWLTVQGH
+PVAMSAWMRAVVVLGMTATLFYFFYFALRAAAGWRWAYQRLRLFAQVFPVITLVLAAVPG
+LYPVWMVTEQIVFSLLMIGVGDILTSDHMREAYRHPDRPVPRFE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002997.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002997.fa
new file mode 100644
index 0000000000000000000000000000000000000000..0adce7a7975115fa681cfbbced41ec4e21626ee6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0002997.fa
@@ -0,0 +1,7 @@
+>3_1931
+MTDSTLLFDAAVTGDRGAVRSSAEALAAVLAADPGDPDAWAALPAAQWAAEQTALTGYAE
+LFNTALPAALALRVAAGSGGRLPEGVAGAWAARLDPTLDAERRAGIDAALADAVAGERER
+RGVPTPEPFEDEPRTVFPRGFMAALTRLRSAALPVPPLYTAALRVVEAPVDEPAEPRPAR
+PLGELLDALVALEDLEWRRPATEKQIATLEQRTGVTLPADYRAFLERANGSKDREFEGAH
+EVARDAKEPPVYSHGTGEFVILDCAPGPEGTAGKVLSYGEGETRVTHPDFRAWLQDHVED
+LED
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003000.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003000.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a44fd2e4fb767f6e4561dcfe7fb9295ca8eb284
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003000.fa
@@ -0,0 +1,10 @@
+>3_1934
+MASSLESRADESDPPRRRPDGMNGLISRHQTAEMTCANAINALYGGTRYVQVSADGSAPP
+AGSEAYGMSREMLNSASGAGETPWGMPAVWDKPWYLDVADAVVDFGSGVWESLKGTVTGL
+LAMVNPFDWETFSATWKGIGTLAVDLAVTATPVGLLVSDERRAQSGQRLVQVGEAVLNVE
+MWKENPAKAAGMLTGDLATALVPGGAAVKGASVAAKSGKAASVLGKAARAADTVKELGTA
+AKFKVAFKAEDLVRGLSDKKFAVTDALHSKASAFAYRHPQVGAMASTMRTVWEFDVNKAA
+KVFSDGMLAKVPAVGVLADGGVMWVKSGESFSSVLRRAVDEGVSPVRSGGGGLPAGVVEG
+KGTMVMRPSPKWDLSTAEGRASYEAFVGKVDQYKQFVSSPERLGFTKPDARTIKRSDFMK
+DPDYALGRVTDLRGNQAPALLKGVEDDILRRLEDEMTRHNAAKGSRGEIADWHELPQYTQ
+ERAVRAAMKGFDLDHARDLQLGGRDAHENLQWLEKSANRSAGFAGAASSG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003001.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003001.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c92873f9ae0ff1bfb8649201cf69624e6209f501
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003001.fa
@@ -0,0 +1,3 @@
+>3_1965
+MRGGVFAEIAPREVTDEVCPPVNCLSAWETEVGRFVGFRHEGDAEYWHVVLGDEARRNDR
+VLVDFSGGKYDRDQVRHAVDVLFHDRDWT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003004.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003004.fa
new file mode 100644
index 0000000000000000000000000000000000000000..5f4310e46ac0279bcf7eaa8a32da600be20ad4bb
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003004.fa
@@ -0,0 +1,5 @@
+>3_2028
+MDAAFGPRVRFLGLQGSRARGEASATSDIDAVLVLDALTPRDVDAYRELLDGLPHRELAC
+GFLSGRDELLTWDAADLVQFVHDTTPIRGSLAELLPRLDAAAVARAVTAGAGNVYHGAVH
+TLVHTRSPETIAGLAKAAAFVVQARHLQRTGTHVRRQTDLLDVVDPADRDVLALALAVRG
+GAAVDVDRDGRLLFGWAQRVLVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003005.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003005.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e93af794db60ae845d0c2dc29ee92e0a2fe1b7b2
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003005.fa
@@ -0,0 +1,9 @@
+>3_2029
+MEAALFRETLIGDAGLIGGLLLVAVVLRAKVRVLQWLLLPAPVIAGLLGFLLGPQVAGAW
+GLRVGAWEFTGLPFSPYVGSYTTLLIAVVFACLALSQSFSFRKATGPLAGFTGYGVLMSA
+GQVVAGMLLVLLVLGPVMGSSDAIGMVLFASWSGGFGTSAALGDVFADAGRPEITSIAFT
+SATVGMLSGIVGGVILAKIGSSRGHTRAFSTQAAFTPSLRTGVLEHDDRPVAARHTMSGS
+SIETLTLHMALVGAVVALGWLFMTTTGEVLDDFALPLFASAFLAGLLARWVVVRSGASRV
+MEPQTLKALSGAASDVLIVCGIVSIEPAFVADHLAELAVVFALGLAFCLFLGLVVAPRYL
+GESWFEKQIFTWGWATGSVATGIALLRIVDPDLESGTVEDFGYAYLPLIPVEGAAVAIAP
+LLIVAGAPWSVVAIWGVIAVVGAVVMVRQGGPDPRRTTTAARA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003011.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003011.fa
new file mode 100644
index 0000000000000000000000000000000000000000..85e2d6b66edf93bd7df1f9fe00716b75a7828cb3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003011.fa
@@ -0,0 +1,3 @@
+>3_2160
+MVEGIVYRYRTGIAWRDLPEVFGPWQTVWTWHYRMASDGTWDRVLAKLTAAADAAGLVDW
+SLSVDSTIARAHQHATNTTRLTGGWIELQESAGRAA
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003012.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003012.fa
new file mode 100644
index 0000000000000000000000000000000000000000..f9ca354b56568bc58976158b8bdee00537520f4a
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003012.fa
@@ -0,0 +1,4 @@
+>3_2161
+MFLPLMGQLRVGRDRGRPRTRPNAVRADKAYSSRAIRGHLRSRGIKAVIPEPDDQKGHRR
+RRGSRGGRPIGLDAIDYKNRNVIERQYCHLKQWRGLATRYDKHAIVYRAAVVLNAVIAWA
+KTLSDTP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003013.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003013.fa
new file mode 100644
index 0000000000000000000000000000000000000000..96add5d7246d3faa3a106742cd3787fe5c1242a3
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003013.fa
@@ -0,0 +1,5 @@
+>3_2166
+MLSKPAANSWSESNSASLHQTQGASLQREKERLGQAIAAAKGRLAEASEAAESGARRLLT
+KNGEDLELAVEEALSALGFEVTLMDSDGVAKLEDLRVSTSSGTWTALVEVKGYSKAGKSN
+DFQKFARYSSEYSRQTNMQPDAYWYVVNAYMGQPPAARPGPFESVQDHVQTFSEEGGLVI
+PTAELFRLVRSVEAGVLTTGAAQASLTSQRGLYSTDSLTHEASDGGTAE
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003015.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003015.fa
new file mode 100644
index 0000000000000000000000000000000000000000..fafebcfa6346261446f31bd6506822a72a3c244e
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003015.fa
@@ -0,0 +1,2 @@
+>3_2176
+MHTLDQLTAQRPPHARTPMNSSSARPDVM
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003017.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003017.fa
new file mode 100644
index 0000000000000000000000000000000000000000..73f3f2c11db3a7db457f26c7829cdb7092cbd18b
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003017.fa
@@ -0,0 +1,6 @@
+>3_2186
+MDVSGIPTHDGLDDAFASVGMTIPRDTPSGESITKPRRMRTAFETADSNGLKATRRLISA
+LVDELRHRDVFQHPAPEIVAAVQAVRQLITEGGATLTTDGFITTAVAFPTVDAGQRETVD
+RLIARLRRNDQDPASILGTAKDLLEATSKHVLHERAPQQRQKDMPNIVYEAMEALDLSTK
+PSSINGPSAGAIAQLHQLIARTAQAVTASRNDGGDGHGHLNPTGVSPELAEYVRVVTLAA
+TKFLLDNAT
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003020.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003020.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8d02973e9890ec7edcf5bc56bf799cb0518d5186
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003020.fa
@@ -0,0 +1,2 @@
+>3_2202
+MFDPEAIESARERLDAKQIAPEERAGQTPDVG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003035.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003035.fa
new file mode 100644
index 0000000000000000000000000000000000000000..e85efde37832f5d6a95ca697a2cc7cb9cca1100f
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003035.fa
@@ -0,0 +1,4 @@
+>4_107
+MDFWSTIWDAIWWFFTIFVFVAYLIALFSIISDLFRDRELSGVYKAIWLLFLIFLPFLTA
+LVYLIFRGRGMGDRAERQTREAKATADDYIRTVAGGPASEIAQAKQLLDSGTISEAEFQS
+LKQSALDGSR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003038.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003038.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2425b957cf3539ccfac087831c89a67ba0423803
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003038.fa
@@ -0,0 +1,7 @@
+>4_113
+MMSAEGPKRRELFRWWEWALIALAVISIPAGPGALIFLMPVLPRIVLLIRKHRYFNSEEF
+QEKKAEIRAFVAEHNELKEYIDEIRARGSFSLGESSTGQHAHLAYSENTSRHNYIRDRNV
+ATLGAPNVHNCSLQVVRKAQMDPIRYLMKYFHINAEEDRLAEVEEMGSSLAQLEEALSNL
+QNREASITEAIQPPSFIQKHFLDEFMEQVGVEISPITIPYEIYTFEYVSAGGNSSERTNV
+VLNSQALDALIDTMSARIKFRKSAAGQRALMTSKLRHHIKDRDNFTCQNCGVSTYAEPHL
+LLEVDHIIPVSRGGLTTEENLQALCWKCNRSKSNKI
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003043.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003043.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8472349113374ded19ca1559915c2364e5029443
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003043.fa
@@ -0,0 +1,3 @@
+>4_162
+MLLYRWSRAEPVIRAELSLPSRMDRGDVVAWKERILLPEISLDQFDLSDFDVIAEDDVYF
+GISQTS
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003047.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003047.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2d537c9f69d349f83492dbc9f19733815cd93935
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003047.fa
@@ -0,0 +1,5 @@
+>4_858
+MKSVLHTRTAIAAALLLGLTACGDTASPAEEDAPAAAGSSTASAPAGAEEETEADEPEQQ
+AGGTAGTREDPLPLGTPIEGEDWVVTVNEVTPDATDAVMAANQFNDAPAEGTQYLLADVT
+VEYTGDESEMIMLGTGFAFVTATGETIDAGDAFAVGPEELDTAQELYNGGTAQGNVVLQV
+PEGADGLLRVTTGMFGGEKTFVALD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003048.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003048.fa
new file mode 100644
index 0000000000000000000000000000000000000000..2a45e7f22f2721aa691de2177030a3c025d5f7ac
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003048.fa
@@ -0,0 +1,3 @@
+>4_970
+MALDIRTHLRARGIKAVIPEPADQQGHRRRRGARGGRPIGLDAAAYKGRNVIERQYAHLK
+QWRGLATRYDKYAIIYRAAVVLNAVIAWSKRLSDMP
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003053.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003053.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c3f6be85c9c56633708c30ed831cf160a4b46069
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003053.fa
@@ -0,0 +1,9 @@
+>4_1491
+MSEGLALKCLAALLGSDAAHANLKYFRANPGIAVSELGPDAKDINSIAEQTEADGLFIIE
+DVAICVEVKAKSISSHARRGHVQRLSADLRETVGSATEQALRLENHIRTNHGLWLENREW
+LDLSEIREIRSVTVYLDDFGPLSTALDELVRAKVVGSDRFPWLVTLHDLIVIAEVIDRPA
+EFLLYLRRRTESEVSLKFSAVDELDLFMLFLSGGLWVEPDPDRVSEEFLGVAPPTVKERR
+RYQESAVPTRVMTQTDELDAWVYFNEGASDVEAEKPSFGVLPGIARIVDFLQDGRKPGWF
+RFSADLLNLDEESQESLGDMVEHLVSITRQDGLHHNSIMAFAGSWGYPTLFMGSKPRKMS
+IQEASTRLAAYGCAKKHQIRSDRALMVVFDEEQRIRSIRYDNSPPVENRELDGFVAEMGL
+IPPSVMGRPIPPSARRTTVRLNPSRKRKKRGKRGR
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003056.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003056.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c8bc982adb33d61b133c9aff596332dbd33c6fe5
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003056.fa
@@ -0,0 +1,10 @@
+>4_1739
+MLILSSRMRPKEQFEGYAFVGTDYVHGPAGMTAYRARTGRTVGPGEDGCYVVARRAGRLF
+GRRFEVGTDASGLGRLFLYRSGDDWALGSSYSGLVEHLRTEGMTLTPRLGRLRPFALRQT
+LTMQLSIFQTPFDEIRLLPVGTVVVIRGSVLSLERAPELQPLEYEAALQEYLDVWRGRTR
+ALLADPRVTFTADLSGGVDSRTVFAFLLESGLFRTDSDRFWLHSGVNQKEDLAVAKGIAE
+AHGLTVNGPKPPTRTLVSGSRAYRHWRENSLGVYTPVYMSSTFQNPFEVHAHGGGGGTIK
+QYYRHAEPLRLLEPFKEKMPAADFALWQEEMATTQEQLKQTAPGVVPSIQHYLEFRNRFH
+FGHIPKARPLFMPLNSKYAIRALTSLPQDVRRRFYFDVMESLAPGLKDVDYDNARKAPTA
+QELESLLVLPASDRLAAGTAYGDDTVETADPDDPLSAGFQRWLQDIDRAAARPEVRRFIM
+GRAMARTDRTVEALRALGKPFHSHSGHSVALSHLLMVDFTLGD
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003063.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003063.fa
new file mode 100644
index 0000000000000000000000000000000000000000..93d888620c47e2754cf21cf2eff43fea7516dff6
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003063.fa
@@ -0,0 +1,3 @@
+>4_2122
+MAKHLLETDGQVCPFPLVEANQAMQQIPSGDELVIDFDCTQATDSLPRWAAENGHEVTDF
+VKRGAAEWTITVKKG
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003065.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003065.fa
new file mode 100644
index 0000000000000000000000000000000000000000..20b15ee64bd6403243ab7825bdfd61bb1d677ac9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/Sequences_ids/OG0003065.fa
@@ -0,0 +1,6 @@
+>4_2149
+MTTPSGAPDVSADPEVRLLTARLNRARTHYLDFAELWAAYLEGRPHSIAREILTDGTVTI
+RLDRVAPIPAELSILLGEFLYEMRAALDNCLYAAAVIASGQNPPPGAERLEWPIRTDQTQ
+WKSQANRYKHLPAELTEALEAIQPYNAELPAWNCLAILHGLARFDRHRRPWPLALFLVKT
+QLQVRPDVVEPLDVACNRVIHPGEKLATLRLSPGHVLSPTNFDFHVEFDVDLADIEPSEG
+PEGLHVRPWGSLAHRLQSVHRAVTEYCDDLLLLAASCRKH
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/SimpleTest.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/SimpleTest.fa
new file mode 100644
index 0000000000000000000000000000000000000000..c0fe89cfc25f45694a7b5bcc4810f31006cd24d9
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/SimpleTest.fa
@@ -0,0 +1,4 @@
+>a
+A
+>b
+A
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8212909ce82d41e5b0fca1f922a0f44eac5a8121
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa
@@ -0,0 +1,8 @@
+>A
+MSKVIELKGIYAKYNKKSDYILEDLNLNVESGEFIAIIGPSGVGKSTLFKVIVNALEISKGSVRLFGQNI
+>B
+MLKLLSKFPLKVKLMALFAVILSTLHPFLSILIPTVTRQLITYLANSNINSEVSVYIFKSSWIIGSFSYA
+>C
+MQITVKDLVHTFLAKTPYELNAIDNINVTIKQGEFVGVIGQTGSGKTTFIEHLNALLLPSAGSVEWVFEN
+>D
+MIKVTDLMFKYPSAQANAIEKLNLEIESGKYVAILGHNGSGKSTFSKLLVALYKPADGKIELDGTTISKE
\ No newline at end of file
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa.output.txt b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa.output.txt
new file mode 100644
index 0000000000000000000000000000000000000000..485ff985b807ced95e8661209b7fef3cd8f0a556
--- /dev/null
+++ b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/Species0.fa.output.txt
@@ -0,0 +1 @@
+(B:2.789646230,C:3.934614000,(A:0.000000007,D:4.374925289)0.926:3.758208506);
diff --git a/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd
new file mode 100644
index 0000000000000000000000000000000000000000..ba6d89f3f3a0b51535c60cabbf49be309e60dafd
Binary files /dev/null and b/Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/WorkingDirectory/dependencies/diamondDBSpecies0.dmnd differ