diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dff68982698600f4d0e7e6577f4f60f8903b8324
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000001_tree_id.txt
@@ -0,0 +1,2 @@
+(((((((((((1_1025:0.00000000,1_2210:0.00000000):0.00000000,1_577:0.00000000):0.00337008,0_2445:0.00026392):0.00114750,0_703:0.00340150):0.02635533,(0_2612:0.00526519,1_578:0.00326081):0.03380717):0.00788706,(0_673:0.02471196,((1_1155:0.00000050,1_1969:0.00000050):0.00046683,(4_2137:0.00000050,4_2154:0.00000050):0.00074617):0.03187404):0.00619406):0.02887453,(((1_2165:0.00349121,((1_2205:-0.00203685,(1_2168:0.00128162,(1_2170:0.02169909,(1_1452:0.52640554,1_2004:0.03110246):0.06102341):0.11691813):0.00811785):0.01256939,(1_1351:0.00000000,(1_687:0.00000000,(1_564:0.00000000,1_166:0.00000000):0.00000000):0.00000000):0.00016443):0.00129351):0.02190863,1_598:0.02425093):0.06665167,((1_1346:-0.02082854,(3_1088:0.20261045,4_1936:-0.02437645):0.02449054):0.02442171,4_1295:-0.02098121):0.35285918):0.04109445):0.09456086,0_876:0.18610125):0.07857963,1_1451:0.18399885):0.18600090,3_1087:0.31742073):0.04899627,1_2171:0.24689482,1_2003:0.10455618);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c08b7c9dd6842219d5713b29ae33b27981df3017
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000002_tree_id.txt
@@ -0,0 +1,2 @@
+((((((3_751:0.00123687,((((2_1798:0.00000000,(2_1758:0.00000000,2_2156:0.00000000):0.00000000):0.00403270,((((1_1024:0.02079803,0_2281:-0.00002603):0.00002603,0_739:-0.00002603):0.00002603,0_1278:-0.00002603):0.00147652,4_1486:0.00040598):0.00161499):0.00138189,(0_1255:0.00212247,(0_1293:0.00000000,0_1288:0.00000000):0.00353253):0.02689702):0.00372999,(((3_304:-0.00001277,(3_2208:-0.00001277,(3_1284:-0.00001277,(0_2571:0.00000000,0_2297:0.00000000):0.02652277):0.00001277):0.00001277):0.00001277,1_1339:-0.00001277):0.00136415,3_1078:0.00997735):0.00200872):0.00217197):0.00526825,(4_974:0.00622306,(3_316:0.00000000,2_2179:0.00000000):0.00696494):0.01543675):0.00487737,3_1610:0.00804765):0.00139610,2_302:0.04967373):0.00882327,(2_604:0.00000000,2_609:0.00000000):0.00250577):0.00507023,4_1824:0.00000000,4_108:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ac836335d9ae074f1d8f991b3e12e1480264270
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000007_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1290:0.00250603,(4_565:0.16364407,4_1826:0.00900793):0.01933747):0.01820729,(((1_2016:-0.00009953,(1_993:-0.00009953,(((4_563:0.00000000,4_2145:0.00000000):0.00189142,3_1065:-0.00008342):0.00002009,(((0_1189:0.00131131,(3_972:0.11610363,3_1075:0.01017937):0.00153869):0.00056055,1_1244:-0.00011055):0.00011055,4_1201:-0.00011055):0.00007434):0.00005231):0.00009953):0.00009953,1_149:-0.00009953):0.00136053,3_1073:0.00138604):0.00224471):0.00276396,1_1336:0.00089900,3_1971:0.00272400);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..829e34fc0339978b5d9b967dad9d83b1f205e036
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000008_tree_id.txt
@@ -0,0 +1,2 @@
+(((((4_2104:0.00000000,(3_327:0.00000000,(3_80:0.00000000,(3_1350:0.00000000,(4_1300:0.00000000,(4_581:0.00000000,(3_2226:0.00000000,3_974:0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0.00000000,1_685:0.00000000):0.00098700,(4_971:0.00000000,(1_2166:0.09516164,4_1111:-0.00482164):0.00482164):0.00098700):0.15460173,1_1350:0.09274169):0.10759912,1_1449:0.05673154,1_2164:0.69997046);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6620ec4d4afc53f133d829973a02080484977052
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000009_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1450:0.21983549,((3_1349:-0.00000549,(4_2103:-0.00000549,(1_1352:-0.00000549,(4_582:-0.00000549,(3_328:-0.00000549,(1_686:-0.00000549,(4_1110:-0.00000549,(3_975:-0.00000549,((1_2167:0.11810349,4_1301:-0.00000549):0.00000549,3_2225:-0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549):0.00000549,4_972:-0.00000549):0.00000549,3_79:-0.00000549);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35d5c4ebfeec41e0112fef36d2cbd4b8f3c3a646
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000010_tree_id.txt
@@ -0,0 +1,2 @@
+((((((2_613:0.00000000,2_820:0.00000000):0.00000000,2_621:0.00000000):0.33667149,(((0_1070:0.00000000,0_491:0.00000000):0.51747797,0_99:-0.09934097):0.15045989,(0_490:0.02647741,0_1071:0.13421859):0.11184455):0.17754245):0.62525320,(1_815:0.16719453,1_432:0.26129447):0.06313377):0.52658948,3_1085:0.00513422):0.00500683,4_1294:-0.00262205,1_1344:0.00638105);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad00c24d1876af3d8b9e6cc8da8c5438acf460e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000011_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_584:0.01836466,3_1719:0.02965334):0.13164373,(((((3_323:0.00000000,3_1729:0.00000000):0.00000000,1_591:0.00000000):0.01062291,0_701:0.01093009):0.07869023,(1_2013:0.01805192,4_1942:0.04409708):0.13257427):0.06241858,(0_709:0.04496850,0_2314:0.07097450):0.03310580):0.03865239):0.02924489,4_1945:0.71690827):0.62638223,3_334:0.00684395,3_753:0.01135805);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..68655e92e77c68213c25f8ec5a6b269fdff5e110
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000013_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_1715:0.00214371,((0_688:0.47567477,0_2441:0.29584323):0.36602046,((3_325:0.12568084,(4_864:0.02020567,2_1844:0.03139033):0.11514616):0.05253490,4_1490:0.31001335):0.11818860):0.08849507):0.04192191,0_2226:-0.02265507):0.03162807,0_2557:-0.02489720):0.08779720,0_2577:0.01641084,0_2440:0.16014216);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9684f6bb82d3b1dc8daef4be0213bd1c9a89fd73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000017_tree_id.txt
@@ -0,0 +1,2 @@
+(((((3_1225:0.01532611,4_1432:0.00921789):0.00776337,1_1505:0.01480302):0.36350839,(1_1604:0.00021408,(4_1534:0.00624150,3_1319:-0.00163650):0.00986642):0.37788074):0.14131429,1_1786:0.64645720):0.27642981,0_1211:0.22298879,2_1123:0.53626021);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9dc90bbbb803a3f6998c1b1d968de8cfc364f2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000018_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_2558:0.00000000,0_2442:0.00000000):0.00247070,(0_2225:0.00604717,0_2575:-0.00069917):0.01153047):0.01767701,3_1716:0.04967698):0.14093497,(3_326:0.12605278,4_1489:0.21603122):0.04749702):0.18790151,2_1843:0.01029236,4_865:0.06802764);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e0f048ac8fe647ce71a17203ccef8cb1e13c0d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000021_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2236:0.01392864,(((0_421:0.26787438,((4_562:1.16960650,0_1803:0.73325550):0.24232796,2_2381:0.91730269):0.78918974):0.07000540,2_375:0.16747856):0.17454073,4_2178:0.00856487):0.01108813,3_1940:0.01916036);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..113d4e973e7a46c3f25a0e1bf4475d1d0c7ae050
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000022_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_437:0.03141573,((2_423:0.81439658,2_633:1.16393842):0.37186589,2_1824:0.37487511):0.31832802):0.02772414,4_2110:-0.00321052):0.00991827,1_2177:-0.00407695):0.01843095,3_1890:0.02172467,0_495:0.11277233);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0e816106fe126bfc7d5695829d7b90b3b403513
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000023_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_2364:0.08977012,(4_512:0.01134396,3_242:0.00593104):0.07751757):0.05735580,2_2245:0.39459568):0.25160059,0_1186:1.04887880):0.37293559,3_231:0.01304829):0.00956661,4_501:0.00675058,1_501:0.00442542);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91d94659faec50ece4d08671dab2bf11fa1542aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000024_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_2323:0.33192837,2_2201:0.43306662):0.20798345,0_2322:0.54684660):0.08839560,(1_547:0.01019928,3_280:0.00689172):0.13442273):0.26639933,4_548:-0.01415217):0.27921589,3_279:0.00112167,1_546:0.02915833);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6f4f944215c370f786b904cecfa1548b7cc2dbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000025_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2215:0.00839211,(4_249:0.00334650,1_251:0.00048250):0.00863291):0.22004869,((0_572:1.45049530,2_507:1.26279670):0.25544114,2_68:0.41616340):0.28058851,0_100:0.18897131);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b643e8c442b8f3e98dcbf40387241edb7de3d07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000026_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_84:0.64215019,3_88:0.96025081):0.33458081,2_84:0.18483869):0.17312881,((4_236:0.01456513,0_115:0.01158787):0.01153969,3_2199:0.00155281):0.00141406,1_236:0.00111569);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0a8c71183b087f87e84a1e5cfbf50373ba02ad2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000031_tree_id.txt
@@ -0,0 +1,2 @@
+(((((1_1747:0.00762216,4_1669:0.00143484):0.02344403,3_1455:0.03247947):0.05811453,0_1047:0.27084322):0.05888703,2_983:0.14246872):0.16667328,0_2582:0.71102266,0_381:0.41369034);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ba1dccd7508bbdb2b1e306a8d228f8cb877814d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000032_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1671:0.00437206,0_1045:0.00580594):0.01823306,(2_981:0.15989219,(0_2584:0.73428844,0_382:0.21050756):0.07262231):0.08636306):0.04485594,3_1457:0.00000050,1_1749:0.00000050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cd21c68419a1c466f6609acefe367bd6d391128
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000033_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_606:0.00000000,4_575:0.00000000):0.02581813,(0_387:0.01433900,2_2146:0.01267200):0.01285637):0.86902513,2_434:1.31047688):0.14546663,0_1305:1.37118763,0_1228:0.94384438);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7b54492ad2955710fe642140bd6b724b0c688ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000034_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_631:0.00000000,2_2164:0.00000000):0.01171738,(0_396:0.03020512,2_311:0.02041888):0.00376613):0.00558413,4_1298:0.00511887):0.00439462,1_1349:0.00028712,3_1091:0.01393088);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a42962dc9970a729e9db972314d0e1e8b809440e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000035_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_632:-0.00373256,(2_312:0.08377256,2_2165:-0.00373256):0.00373256):0.00575931,0_397:0.01965469):0.01033281,(1_1353:0.13095931,4_1302:0.36028569):0.04558656,3_1092:0.00071144);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..51307e5f5a4df7d14c3921591c4296ff4c227ebd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000036_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_470:0.01530531,(2_417:0.00631569,4_2124:0.00430931):0.00174669):0.00470219,(0_475:0.13837944,1_2214:0.72640956):0.12850119):0.00616081,1_2192:0.00831700,3_1902:0.00431900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6005b8b00511b3fafa825bf11d03521e0c30e5f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000039_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1752:0.01924019,(1_2033:0.03951137,0_666:0.05828863):0.00386081):0.02766956,((4_1971:0.76443844,2_2050:0.70680156):0.15742419,2_583:0.29333481):0.28745206,2_582:0.33358244);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65011a404c4d7a5ca130c5a2d61432da3f4afe68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000040_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_645:1.81551912,4_1968:-0.17046712):0.19431437,0_676:-0.13629337):0.15651787,(3_1744:0.01053269,1_2028:0.01525831):0.03120325):0.30734975,0_1283:0.00842769,2_2185:0.03767031);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3389ad7268eba481f7af58b1b2649dcaa3c8c96e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000044_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_333:0.01479306,3_318:-0.00001406):0.00001456,1_155:-0.00001406):0.00001456,1_1026:-0.00001406):0.00631431,(4_975:-0.00002819,0_708:0.00841419):0.00002819,3_754:-0.00002819);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fd1d4e91a8a8a44ce41bc5dd1d49ba59ee55fa59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000046_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1665:0.00746079,(1_1944:0.01149893,4_1883:0.00327607):0.00149267):0.03924424,((4_165:0.39007030,4_166:0.81894370):0.57450385,2_756:0.06378426):0.02032753,0_818:0.03957108);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96a4f8722cd49d87d3102eab200cc1bbd7fe215f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000047_tree_id.txt
@@ -0,0 +1,2 @@
+(((((0_989:0.88923460,2_923:0.56510340):0.02650430,2_851:0.78702329):0.29923729,4_708:0.26459935):0.16959534,2_774:0.12521059):0.06452505,0_836:0.06745370,3_1646:0.20090630);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e46ec4f7757f68a49a56f692a47690770f8689bd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000049_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1003:0.05988475,(((1_1720:0.00569369,4_1649:0.00439331):0.00177587,3_1437:0.00726013):0.06023988,0_1078:0.07905762):0.00863038):0.66502275,1_806:0.44481738,1_807:0.13195263);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c91f53681168a43645a130f4e7989a8c12b54f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000050_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1359:0.00413422,3_1098:-0.00013422):0.00013422,(((1_164:1.17994078,2_2178:1.20931222):1.03587084,2_1370:-0.06368284):0.13228547,0_1459:0.00633928):0.05861997,4_1308:-0.00013422);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c6267194690a3b9bf3c99321dbe5a7f72d00773
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000051_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1678:0.66886616,3_862:-0.01859916):0.03596197,4_1084:-0.02181497):0.02542697,((0_1677:0.27866528,2_300:0.93003472):0.07313222,2_1575:0.46061678):0.38494822,1_1134:-0.01789897);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d601a31ad4dcb0a54ee385560d9a3299ee12a562
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000055_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_401:0.04619419,1_2200:0.03587081):0.00460275,4_2132:0.01101675):0.09859525,2_405:1.64472925):0.19826725,(4_2118:0.00688531,1_2185:-0.00064731):0.00196763,3_1898:0.01185187);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a16725b3075beed66a27b626c9fd163ced96baf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000058_tree_id.txt
@@ -0,0 +1,2 @@
+((((4_96:0.00278448,3_2065:-0.00001948):0.00085434,1_101:0.00192814):0.01772657,0_270:0.00792683):1.08985804,2_217:-1.01211388,0_31:1.72518988);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eca4118dcc18e6e1104e444db704409f56b84d21
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000060_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_278:0.01226176,(3_2251:0.00535373,4_284:0.00418227):0.00508912):0.05183981,0_58:0.05807560):0.03715005,1_1898:2.40110575,2_37:0.15497425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37a8449a25fbadcf1d88a900c4f10ef7f07d6887
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000065_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_136:0.01247692,4_193:0.01313708):0.10611384,0_185:0.15742458):0.38237198,0_84:0.78509765):0.15572245,2_123:1.16084463,0_83:0.85863137);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8e2cd9363e51a6e04b456511cc9a2fd2a7bf02a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000066_tree_id.txt
@@ -0,0 +1,2 @@
+((1_249:0.00275811,4_248:-0.00038611):0.01250307,((2_70:0.14359512,2_509:0.78097188):0.05206097,0_102:0.14411868):0.05953652,3_2214:0.00953305);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bedca3bd2275cd5e11e1c299631036178bb64235
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000067_tree_id.txt
@@ -0,0 +1,2 @@
+(4_241:0.00346887,((0_111:0.02766164,(2_2414:0.33228438,2_79:0.08046962):0.06964269):0.03121270,1_241:0.00680102):0.00579598,3_2204:0.00627913);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f815f5f404823c780c7d987a97f567a72f2afa01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000068_tree_id.txt
@@ -0,0 +1,2 @@
+((((4_1892:0.00544775,1_1953:0.00658725):0.00188362,3_1674:0.00615238):0.05153512,2_747:0.02090362):0.12500038,0_807:0.06069962,0_120:1.37125538);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1d93e688928b4b06fb38a55b64b367dadb5f49a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000069_tree_id.txt
@@ -0,0 +1,2 @@
+((1_227:0.00582243,(3_2191:0.00185525,4_228:0.00135175):0.00552860):0.04819149,(3_90:0.41198038,2_91:0.15001562):0.08036185,0_126:0.02842895);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59cbca33b40c91cc4bc7676c2b18a92618a59780
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000072_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1072:0.00724640,4_1022:-0.00042040):0.00042040,((0_153:2.03961412,2_1636:0.10579087):0.08437458,0_1744:0.04286542):0.02328605,3_800:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8d49c6eb5361324f4d832af4670a2e77ac620df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000073_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_2156:0.52650587,2_307:0.72564913):0.60167566,0_157:0.04740756):0.15668744,1_208:-0.00000000):0.00000000,3_2152:0.00000000,4_208:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92265bce59ba7cb952012b52672d6c7d653fcd9c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000080_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_317:0.03592237,0_191:1.90909163):0.06457935,2_259:0.12408396):0.11241423,4_54:0.02107557):0.01065043,1_59:0.00728648,3_2023:0.02848752);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8676a88a366388e206f98cd09f4de882bd3b15ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000081_tree_id.txt
@@ -0,0 +1,2 @@
+(1_72:0.00000000,(3_2036:0.00795127,((0_2287:1.34913975,2_244:0.14167525):0.25774774,0_302:0.01884497):0.00309078):0.00241173,4_66:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92c822d394d1285d62b89c4c362d341950be1f3a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000084_tree_id.txt
@@ -0,0 +1,2 @@
+(1_49:0.01309531,((2_279:0.18316219,(2_270:0.04642919,0_331:0.01886881):0.10450031):0.10272481,3_2013:0.01009569):0.04873081,4_44:0.01313569);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..04850ca9f4e68deb695eb7e3e69c1738897b6183
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000085_tree_id.txt
@@ -0,0 +1,2 @@
+(1_45:0.00000021,(((2_1473:0.31915438,0_1578:0.15227962):0.36810510,0_339:0.10271446):0.09883727,3_2009:0.00175419):0.00250281,4_40:0.00919579);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..358ba1a4044cdc20fddfe179f805541a161f5a48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000086_tree_id.txt
@@ -0,0 +1,2 @@
+((0_355:0.40449971,1_22:0.00328129):0.01738548,((0_354:0.24056787,2_338:0.43686212):0.08569158,3_1991:0.01884131):0.00733491,4_22:0.01099227);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffe6aed0f6a5c746ae5b1db1cd07740bc15a308f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000087_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_355:0.00375637,4_580:0.00745362):0.00211225,2_2136:0.04231225):0.00502325,0_376:0.00909975):0.15216025,1_601:0.11164837,0_395:0.13646063);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5494fd970e4287f2de229ae55f8a9b28c54f2d4c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000091_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1946:0.00560969,(4_2184:0.00549603,1_2242:0.00226797):0.00086950):0.03322888,(2_369:0.06960375,0_721:0.49235125):0.03909647,0_416:0.03501343);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18a162d0696fc26a1e4a09444dcb051892273c70
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000095_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1068:0.85842637,2_469:0.41506062):0.07065275,(0_725:0.20549737,0_542:0.22077262):0.02002725):0.18450200,1_2009:0.00753475,4_1938:0.00941525);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b7f245efd3efc7e283ae07e45052d38387189e24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000097_tree_id.txt
@@ -0,0 +1,2 @@
+((((3_1838:0.00000050,1_2113:0.00000050):-0.00000000,4_2059:0.00000050):0.12777250,0_560:0.08344900):0.06457550,2_488:0.07951750,1_579:1.63863050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b58879a27a6710de6a1b897a54856b33416d7a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000100_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_530:0.00000000,3_264:0.00000000):0.00000000,4_533:0.00000000):0.16302875,0_2339:0.14467925):0.67440575,0_622:1.36968725,2_2222:-0.45122725);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88a4016b3854d7110bb35c57b75d787e2a2ae698
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000102_tree_id.txt
@@ -0,0 +1,2 @@
+((0_663:0.04625276,(0_1470:3.11273725,2_578:0.16577875):0.05846438):0.02811238,(3_1755:0.00000000,1_2037:0.00000000):0.00429658,4_1978:0.00060442);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01e105670a722681eba84babffb7f0a67b9d8089
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000103_tree_id.txt
@@ -0,0 +1,2 @@
+(0_667:0.02323945,(((1_2032:0.12695662,3_1751:0.24614738):0.28487316,2_538:0.90740507):0.20161618,3_1750:0.39764675):0.19146225,2_584:0.04518255);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..870e9dfd8f018640beb65a56504aff04c581adf0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000104_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_602:0.29466787,(4_1957:0.01980263,0_687:0.01871937):0.00170629):0.00361488,2_598:0.00572419):0.00510684,3_1733:0.02426825,1_2018:0.00763775);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcd6bc12f93a0af17a606b16ed4d0366dd7c431c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000105_tree_id.txt
@@ -0,0 +1,2 @@
+(0_722:0.17876833,((0_723:0.18700690,(1_2011:0.03939325,4_1940:0.02406075):0.14816145):0.61369909,0_718:0.49408598):0.13921852,2_471:0.15315267);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb400bc9709ba5d30d18e6a6836fc62951d4fe71
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000106_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1479:0.01354806,(1_1771:0.00865681,4_1693:0.02019619):0.00378644):0.15365194,0_1017:0.11437556):0.16171044,0_726:0.48833744,0_2284:1.52574456);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aede10c34ff2f65a2d4974e24c3d9b498e63e1be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000109_tree_id.txt
@@ -0,0 +1,2 @@
+((2_732:0.29889721,(1_1968:0.33353800,(4_1906:-0.01767737,0_771:0.34486937):0.12469038):0.07257050):0.08599729,1_1970:0.20198750,3_1688:-0.01166750);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000110_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000110_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..406668e56a11a8a89318d437a2b8517c9b2d9fd5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000110_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1677:0.01653606,(1_1957:0.00861506,((0_785:0.03646581,3_83:1.12642419):0.01229844,2_744:0.03623756):0.01766494):0.00151844,4_1895:0.00826094);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000114_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000114_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1685d814bd3d1c416070ac0ebb0625e955aadc0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000114_tree_id.txt
@@ -0,0 +1,2 @@
+(0_863:0.10301380,(((1_1914:0.09782337,2_799:0.08448463):0.44573764,1_1915:0.07809454):0.02242979,4_1841:0.00165599):0.00685351,3_1619:0.00277120);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99b90a259191b91244439f1f00845b94b3b7ba46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000116_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1500:0.01421431,(4_1714:0.01335269,1_1793:0.00120731):0.01337069):0.08074119,(0_1037:1.45413644,2_938:0.19297756):0.08160369,0_995:0.09983881);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000117_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000117_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82a82492468a23d45843d8a37a2a82dded3b9643
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000117_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ca95852d98bf3da03827eab9fa44e2f4bdbf89d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000118_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9e9eb60c183aae832cbefef88d807f17253d9f20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000129_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1158:-0.00083231,(0_1248:0.00074256,2_763:2.94686444):0.00535781):0.01772931,4_1497:0.01294894):0.00993206,1_1570:0.00159981,3_1286:0.00262219);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1dae2021cbe836a4d0e36463aa222def0115d7c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000130_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16924578c08f7ae1a1dfc4db52b460a2d5b0c24f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000132_tree_id.txt
@@ -0,0 +1,2 @@
+((((4_1458:0.00705462,3_1252:0.01074037):0.00493500,1_1531:0.00549600):0.00599000,0_1312:0.01205700):0.74381100,1_2190:0.06248450,2_439:0.14381950);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000134_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000134_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5795ccd4b093683d0f2fe7c6f78704d74547d9e5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000134_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1248:0.03124669,0_1315:-0.00864969):0.26975231,((4_1455:0.00712669,2_1210:0.00741931):0.00312781,1_1528:0.00093419):0.11817906,3_1249:0.20623269);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4bbe867e2ddda7cca8cd2f9c2d0c079cefde740
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000135_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1454:0.00033269,3_1247:0.00243331):0.00201631,(1_1527:0.00503269,(2_1730:2.02178006,0_1317:0.01123194):0.02710481):0.00311981,2_1211:0.00387419);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de2d874c71f2428e9e4457e1caadce429f3e5b33
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000136_tree_id.txt
@@ -0,0 +1,2 @@
+((((0_2521:0.28197600,2_1224:0.11629600):0.04387141,0_1330:0.09711531):0.09435374,4_1442:0.01244116):0.00429334,1_1515:0.00008964,3_1235:0.00352636);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..304231db9e13fc2085d6e323e1d3d584cb25aa20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000138_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1243:0.08982962,2_1272:1.82395038):0.04181391,0_1351:0.03972657):0.04340667,(1_1495:0.00145993,4_1422:0.00242707):0.00446074,3_1215:0.00168778);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0d36a62e1839d08f4647f8f1ccd7ce99137a4791
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000139_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_272:3.33823850,2_1253:0.10160450):0.03709559,0_1361:0.12836767):0.05152436,1_1485:0.02178710):0.00928940,4_1412:0.01618684,3_1205:0.04247016);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bca21996263d3bb373e54ad457554e326824f587
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000140_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1139:0.07830388,(4_1347:0.01262062,1_1398:0.02095638):0.04385663):0.01756688,0_1423:0.08935537):0.06798013,2_1738:2.07476275,2_1327:0.11894525);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5ba98a211e7a4fba651af4eff41a090f23305d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000142_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_274:0.55146250,0_1471:0.61606750):0.65005565,3_1967:1.27542760):0.34712129,4_106:-0.42290489):1.03222071,2_677:0.30923137,2_333:0.20729263);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e146c97fa15dfd4b39f26bd1f99b6aef4f40b8f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000144_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1293:0.00979600,(3_1022:0.00000000,4_1247:0.00000000):0.00337400):0.04411250,(2_1385:2.21555425,2_1417:0.01157075):0.24049350,0_1521:0.05244750);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e0ee55e7f445cb26ea2f35f5dcc2f6a46065ca2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000145_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1016:0.00125400,(4_1241:0.00000000,1_1286:0.00000000):0.00186900):0.06020175,0_1527:0.02307175):0.15596275,2_1423:0.08080900,2_121:1.74033000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74ae643a686188a2a80ef654ef7757bd216152cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000147_tree_id.txt
@@ -0,0 +1,2 @@
+((((1_1224:0.00000000,3_952:0.00000000):0.00000000,4_1181:0.00000000):0.04556150,0_1585:0.03217350):0.01239650,2_1480:0.07201000,4_1823:3.04938300);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc80117f9885d4f28453cfd9bcaaf6340cb7a1af
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000148_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1056:0.00000000,((2_1602:0.13354575,(2_528:1.91593650,0_1709:0.01363650):0.04902225):0.05343625,1_1106:0.00606400):0.01080500,3_834:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8f8080183457a7ffa11013b4ae08e8c4946ba01
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000154_tree_id.txt
@@ -0,0 +1,2 @@
+(1_971:0.00000000,(0_1841:0.37223750,(4_914:-0.01953970,(2_1727:0.80865188,0_1840:0.61457212):0.10873278):0.04889320):0.02342550,3_694:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3217959e8355adfcde982300d2c6308e9aea3a1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000155_tree_id.txt
@@ -0,0 +1,2 @@
+(4_875:0.00348525,(((2_1830:0.14851650,2_691:1.42047250):0.06373932,0_1882:0.07845764):0.05731556,1_929:0.01553661):0.00953689,3_651:0.00302275);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d436924e7374d6a0dfa180fabbafcd55a1c65df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000157_tree_id.txt
@@ -0,0 +1,2 @@
+((1_824:0.01032000,(3_555:0.00000000,4_783:0.00000000):0.00761300):0.20511250,(0_2034:-0.29456700,1_167:1.35620900):0.39129700,2_1928:0.44712050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9810c7ca5edf81796923a08b512f1f2a8f1e0c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000159_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_720:0.19035728,0_2133:0.47393172):0.15403713,3_460:0.03254465):0.04943525,(1_721:0.24459100,2_2027:0.91734800):0.16219672,4_685:0.01053005);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d49c009bdd99f28cadaa67b02af41192126b191
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000160_tree_id.txt
@@ -0,0 +1,2 @@
+(1_705:0.00550922,((0_2172:0.17876790,(2_2047:0.36522875,2_328:2.50642225):0.24849270):0.15471198,3_445:0.01706464):0.00998886,4_669:0.00286778);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..738d9a39e698ba855837217ca2b07c44728e8545
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000164_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2293:0.18683579,(1_586:0.13885244,(3_1721:0.20649983,2_1166:1.83428617):0.05785398):0.03246256):0.11027621,4_1948:0.00000000,3_311:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..976d7778afd8bc290d0f1e5ae5728e2d8600a9cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000165_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2230:0.49947350,(0_2346:0.32474400,0_2347:0.29526900):0.10283450):0.12939350,(4_527:0.00985112,3_258:0.00895888):0.00207375,1_524:0.00547575);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3a16025a1d8c90a832da50f883a7952f62a746e7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000167_tree_id.txt
@@ -0,0 +1,2 @@
+(3_157:0.00144544,(4_430:0.00279306,((2_2324:0.04906444,0_2453:0.04054856):0.01640494,2_666:0.87925356):0.02777794):0.00024344,1_427:-0.00022944);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db14f87724fb8330b09e400a4ed28775fccfaaa7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000168_tree_id.txt
@@ -0,0 +1,2 @@
+((((2_2349:0.05456069,0_2479:0.42698531):0.11230669,1_402:-0.00902969):0.05000619,4_405:-0.01355869):0.03622469,0_2478:0.45422019,3_132:-0.01751519);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b7f2651194e78a5584950f2af697bf5f0a25365
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000170_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c261b108ed42e4523f1f2e7e23cb87e384db0e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000172_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddc36eb711c19f6cf133d871eceda17d9e437e8c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000173_tree_id.txt
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+(3_1269:0.00000000,(((2_257:1.62756150,2_1785:0.97894150):0.90228200,2_1177:0.01864650):0.01701000,1_1547:0.00583425):0.00845575,4_1474:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f9c2a870f9037531ea771e6c375ec18b19cfa49
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000174_tree_id.txt
@@ -0,0 +1,2 @@
+(4_324:0.00573612,(1_317:0.01147663,(0_0:0.09484212,2_1:0.15409288):0.03200088):0.00121638,3_42:0.00630288);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b8a67d3821cefb718f5c780ffdf50c929894dc2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000175_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b8d1c0f4d409d300d311bcd7cc9e3c47f124708
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000179_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c41d0c26ebc3f2a7d2ef3c73381719aeaffa955
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000180_tree_id.txt
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+(3_33:0.00000000,((0_10:0.03022717,2_6:0.10265383):0.02118805,4_316:-0.00010436):0.00341036,1_309:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c0d8304ec187608fa0c45a062013982ba3ef168
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000181_tree_id.txt
@@ -0,0 +1,2 @@
+((1_308:0.00000000,3_32:0.00000000):0.00000000,(0_11:0.12641050,2_7:0.60008250):0.08837250,4_315:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a3917d5ce7487e4b34bab68c03b262705fa0c34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000182_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_314:0.00000000,3_31:0.00000000):0.00000000,1_307:0.00000000):0.03189550,2_8:0.06519050,0_12:0.00916150);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c96181d7bd03825eb590bb5ee790bc9d954d5166
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000184_tree_id.txt
@@ -0,0 +1,2 @@
+((1_305:0.00392625,(3_29:0.00277900,4_312:-0.00037500):0.01603475):0.04318225,2_10:0.21782525,0_14:0.06697875);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2e23568391fc7f63a4200f8355af6619f03fe72
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000185_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_310:0.00105784,3_27:0.00967616):0.00373992,1_303:0.01874493):0.06027417,0_16:0.04472667,2_12:0.25704033);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39f7bfb9d522bc578cb38c96812e96c55c0721f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000186_tree_id.txt
@@ -0,0 +1,2 @@
+((1_302:0.00544271,(3_26:0.00000000,4_309:0.00000000):0.02094429):0.08425074,0_17:0.08439650,2_13:0.54465550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf9b8656a377b0c924503012f5faedd232aae3c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000188_tree_id.txt
@@ -0,0 +1,2 @@
+(4_307:0.00000000,((0_19:0.04203850,2_15:0.14680850):0.02563566,1_300:0.01255347):0.00657653,3_24:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1a5d259c6acf8c18864bca436bfeaac4439ffb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000189_tree_id.txt
@@ -0,0 +1,2 @@
+((3_23:0.00279158,(1_299:0.01603203,4_306:0.00991297):0.00355341):0.11121537,0_20:0.17779717,2_16:0.28593783);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0eb660a548b7faf40b7ee5e267823a2fdaeb9ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000190_tree_id.txt
@@ -0,0 +1,2 @@
+(3_22:0.00757323,((2_17:0.29854650,0_21:0.07310050):0.07160280,4_305:0.00463789):0.00474161,1_298:0.01114777);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e6ba5a8ef8485dee6f9523a2fddd21eb177c70e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000192_tree_id.txt
@@ -0,0 +1,2 @@
+(4_302:0.00116730,(1_295:0.01102668,(0_24:0.12450267,2_20:0.21894733):0.10676456):0.01113832,3_19:0.00001470);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f397f0cf11045394b21b88f285e3a2a8725df20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000193_tree_id.txt
@@ -0,0 +1,2 @@
+((3_18:0.00421262,4_301:0.00048638):0.00421882,(0_25:0.04788400,2_21:0.41160100):0.03030821,1_294:0.01065303);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..977fc299d5d4f608df06bdfe28655c1ad938f9db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000196_tree_id.txt
@@ -0,0 +1,2 @@
+(4_297:0.00913737,((0_46:0.15922962,2_24:0.28822338):0.07038513,1_290:0.01727487):0.00981913,3_7:0.00826163);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99a9f3452b41b9e45257bfffb5b125c85d97b139
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000197_tree_id.txt
@@ -0,0 +1,2 @@
+((3_6:0.00046202,(1_289:0.00063545,4_296:0.00525455):0.00279012):0.03378682,0_47:0.03550867,2_25:0.15305733);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7601b55e98aa2529861b367b54560bf9aa11d959
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000198_tree_id.txt
@@ -0,0 +1,2 @@
+((4_295:0.00492825,(3_5:0.00534700,1_288:0.00135300):0.00072225):0.03015925,2_26:0.13447875,0_48:0.05238025);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c5a227734442510c6f4c506f75a1d3820b3ad30
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000199_tree_id.txt
@@ -0,0 +1,2 @@
+(2_27:0.30979888,((4_294:0.01423933,3_4:0.02824567):0.07411509,0_49:0.14922126):0.05931774,1_287:0.16512912);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2fdc5585340a24d8df146d20f0e895a2c1824f0f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000201_tree_id.txt
@@ -0,0 +1,2 @@
+(4_291:0.00520050,(1_284:-0.00151850,(2_31:0.19500975,0_52:0.02039725):0.01734650):0.00781150,3_1:0.00036250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c332fbc7dfdb3e7dc181c9ee07fcf3f406b8102
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000205_tree_id.txt
@@ -0,0 +1,2 @@
+((0_56:0.15221925,2_35:0.41801375):0.10246875,(4_286:0.00000000,3_2253:0.00000000):0.01258525,1_280:0.01449875);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..168ce9c11b9b17729c64173e7970563febe8e12d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000207_tree_id.txt
@@ -0,0 +1,2 @@
+(4_281:0.00277351,((0_60:0.55289000,2_40:0.13237300):0.14587453,1_275:0.04320159):0.03031991,3_2248:0.00281449);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05cbd2cf87ab872d5403ce6f0faa8a2f80aa5c84
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000209_tree_id.txt
@@ -0,0 +1,2 @@
+((4_271:0.02178612,(1_272:0.02879812,3_2238:0.01418388):0.01362238):0.31899787,0_63:0.40458037,2_49:0.68620162);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d8e0074cb4ca8d21c2acc86c0d4f9cdf9c4b5b5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000211_tree_id.txt
@@ -0,0 +1,2 @@
+(2_51:0.07739538,((0_66:0.00296538,1_269:-0.00021438):0.00021437,4_268:-0.00021437):0.00021438,3_2235:-0.00021437);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..103d5fd4105fccb0e0649a261581141546a22bf2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000215_tree_id.txt
@@ -0,0 +1,2 @@
+((0_253:0.03027973,(3_2080:0.00000000,4_121:0.00000000):0.01105027):0.85303624,0_80:0.57140400,2_126:0.56293900);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02ef7ab5cf2d7427e7a6a4c7b78181c579f1e77e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000218_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34b421c9316d7ba3426fb94daf19c7f47188b379
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000222_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e15e58e7abd71ba9e540758793efac131553fc6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000225_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..329c9e45e13209d0d899aa0b434b978d2de7bbd9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000226_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2212:0.00169869,((2_72:0.14138783,0_104:0.03789617):0.03238002,1_247:0.00194757):0.00103343,4_246:0.00359631);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e5570af9c6009a1dec51d07b29a46e8c14d33eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000228_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2205:0.00401025,(1_242:0.00346775,(0_110:0.07983850,2_78:0.37343450):0.07063575):0.00567075,4_242:-0.00011125);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff802bf8a4c9208910b22fdd29f9f45c167727a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000231_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2200:0.00026613,1_237:0.00235987):0.00436137,(2_83:0.35206483,0_114:0.39628117):0.02325476,4_237:0.00147058);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0efef59a841c03b6616e567cdbca4858e0897132
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000232_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2198:0.00294300,1_235:0.00675200):0.00927148,(0_116:0.11642767,2_85:0.58952233):0.11202344,4_235:0.00473793);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..760b2d5b0a0db846eaeef878a236a1587dafb508
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000234_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_87:0.57881050,0_122:0.23006850):0.18146500,1_231:0.03831750):0.02175100,3_2195:0.02538175,4_232:0.00516825);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a10462f2aed320362a5caa70c399cfcdc71153e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000235_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2194:0.00000000,4_231:0.00000000):0.00267921,(0_123:0.05038783,2_88:0.48227317):0.05595276,1_230:0.00539179);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b23a6738f8b8473131bc07faa6af94ef8fae68e6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000241_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1506:0.00564948,((0_1240:0.01810567,0_134:1.30570933):0.05248887,3_1292:0.00803860):0.01350840,1_1577:0.00622352);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a95d05de044567ddc9fe702d5c4fe2a10a3bd95e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000245_tree_id.txt
@@ -0,0 +1,2 @@
+((2_99:0.06194487,0_142:0.12491512):0.06317438,(3_2185:0.00069437,1_221:0.00185763):0.00465487,4_222:0.00458412);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a59f4acbaadf89a25eb8edf7cba02aa654f6c4c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000246_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_221:0.01445427,1_220:0.02510773):0.00049367,3_2184:0.00851065):0.00393796,0_143:0.16280417,2_100:0.04311483);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..19c7fed12e66fb165a125ae0e7bdfc54677f9ea1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000247_tree_id.txt
@@ -0,0 +1,2 @@
+(1_218:0.05066904,((0_144:0.22691267,2_102:0.37368433):0.15703396,4_219:0.05195589):0.01578361,3_2182:0.05637696);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75d06cd5a5ddc459d72fa788f1e2322d4187b2b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000248_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_217:0.00000000,4_218:0.00000000):0.00000000,3_2181:0.00000000):0.00587050,0_145:0.00185150,2_103:0.04003950);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42c05fa02e04cc8b5800cf6b0b4391b0a9cf6d8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000249_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2180:0.00832750,((2_104:0.50539600,0_146:0.15677500):0.18955400,1_216:0.01111700):0.01982250,4_217:0.03260050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b0115e3e214d87e02a07012981c50ea2c60fc54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000250_tree_id.txt
@@ -0,0 +1,2 @@
+((4_215:0.00027925,(2_106:0.10738850,0_148:0.00915050):0.01999325):0.00281325,1_214:0.00000050,3_2178:0.00000050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7160931b0c6dcbe064c8c1e88659d7aef8461a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000251_tree_id.txt
@@ -0,0 +1,2 @@
+(1_212:0.04758162,(3_2176:0.15195365,(0_150:0.24190567,2_108:0.12161833):0.12896122):0.01544385,4_213:0.01369338);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f9874b7df804ec9a132bc9fec184b7c65a236769
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000254_tree_id.txt
@@ -0,0 +1,2 @@
+(4_378:0.01315563,((0_2507:0.24400563,0_162:0.69008837):0.19894488,3_105:0.02130962):0.00826837,1_372:0.04072937);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c55fd15e8b2294f69fe4c0985dd385303e5985a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000256_tree_id.txt
@@ -0,0 +1,2 @@
+((4_204:0.00489422,(1_204:0.00294793,3_2148:-0.00013193):0.00370770):0.01958717,0_164:0.04598767,2_113:0.07332133);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f539db9213972144d51f9a1b69e7085cdb7c7be4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000257_tree_id.txt
@@ -0,0 +1,2 @@
+((4_203:0.00300900,(1_203:0.00000050,3_2147:0.00000050):0.00293250):0.01442100,0_165:0.01556750,2_114:0.08760250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5efd093203b56db0dcff9ba7ab3f4863c8ca39cc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000258_tree_id.txt
@@ -0,0 +1,2 @@
+((4_202:-0.00163625,(1_202:0.00000050,3_2146:0.00000050):0.00586375):0.11889875,0_171:0.10960325,2_117:0.60426975);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39f3b0f90bd58891c87a154f35a72b7cb5ed95e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000259_tree_id.txt
@@ -0,0 +1,2 @@
+((1_201:0.01807000,(3_2145:0.00308325,4_201:0.00757775):0.01163350):0.12390800,0_172:0.16888250,2_118:0.76893250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be57d2757d416407aaf891fde03dd7e58ebafd32
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000261_tree_id.txt
@@ -0,0 +1,2 @@
+((4_197:0.00201322,(3_2141:0.00249862,1_195:0.00000138):0.00425141):0.01094689,0_178:0.26616200,2_133:0.01144200);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..82e56d74050951f759a3e229154330005c58d190
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000263_tree_id.txt
@@ -0,0 +1,2 @@
+((0_188:0.19754975,(3_2142:0.00000000,4_198:0.00000000):0.00535925):0.06181075,1_196:0.00691375,2_130:0.00662625);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..58c7bfea681786960194b25aeb1bca0be025c639
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000271_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2126:0.00117051,(2_149:0.01688100,0_204:0.00741100):0.00084500):0.00082849,1_179:0.00000000,4_176:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84197ba0b8ffd52778417e8ed464959c535156e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000274_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_173:0.00984550,2_152:0.02676550):0.00751518,1_176:0.00363405):0.00150445,0_207:0.01971491,3_2123:0.00409009);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7beb9c1934106a01f6bd940b5cea4944bde210e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000276_tree_id.txt
@@ -0,0 +1,2 @@
+((4_171:0.00000000,3_2121:0.00000000):0.02990550,(0_209:0.01528850,2_154:0.67969150):0.03512050,1_174:0.01335050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edee9756f567a01085f13bd010376203cd9c65a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000277_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_173:0.00501125,2_155:0.35830775):0.00199625,0_210:0.01808064):0.00290786,3_2120:0.00000050,4_170:0.00000050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7932cc52317a4d964b9f7e09a5dfdee235f95f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000279_tree_id.txt
@@ -0,0 +1,2 @@
+((0_212:0.01407925,2_158:0.01649175):0.00583100,(1_171:-0.00002675,3_2118:0.00350675):0.00117350,4_168:0.00231150);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d8e7eab1416a49c3525e068378708b8f208335f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000282_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_222:0.03352167,2_161:0.07207533):0.01931617,4_151:0.00447651):0.00414749,1_143:0.00485136,3_2108:0.00883564);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea47afe4185fc976e0e08228b188be2602477455
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000283_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_142:0.00000000,4_150:0.00000000):0.00000000,3_2107:0.00000000):0.08896950,2_162:0.42449950,0_223:0.08312850);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d80c020c9ddfb1d8ca8090000c6ac9724e257b65
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000286_tree_id.txt
@@ -0,0 +1,2 @@
+((1_139:0.03265950,(3_2104:0.00000000,4_147:0.00000000):0.00024150):0.02437000,0_226:0.05571800,2_803:0.47649800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03caafae309fb394385b53b410fe562f3511396b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000289_tree_id.txt
@@ -0,0 +1,2 @@
+((1_135:0.07423383,3_2100:0.01497317):0.07325183,(0_231:0.09221810,2_165:0.08373190):0.03692447,4_143:0.02356970);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c0c26f6894537900d1110cc1bd9aee5ad53aeed0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000290_tree_id.txt
@@ -0,0 +1,2 @@
+((1_134:-0.00034687,3_2099:0.01988687):0.00034687,(0_232:0.04815462,2_166:0.23583038):0.04959538,4_142:-0.00034687);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..438c3ebfe47bc821b762a722f5bdb2be90bc4f02
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000291_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_167:0.32377133,0_233:0.40847667):0.06120969,1_133:0.00278206):0.00148794,4_141:0.00000000,3_2098:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..334b33e88807844e6e594cbe70b29e2f74cf6043
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000293_tree_id.txt
@@ -0,0 +1,2 @@
+((4_139:0.00000000,1_131:0.00000000):0.01371050,(3_2096:0.01965300,0_235:0.01782100):0.01078550,2_169:0.39521950);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2af52a5f8fe65a1654d0693841bf681964bd87b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000294_tree_id.txt
@@ -0,0 +1,2 @@
+((1_130:0.00377384,(4_138:0.00481782,3_2095:0.00464418):0.00485221):0.10445505,0_236:0.13179683,2_170:0.14281217);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9b4ee0f4477224bd1eab21786783d1862d40dd5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000296_tree_id.txt
@@ -0,0 +1,2 @@
+(4_136:-0.00112025,((2_172:0.33516725,0_238:0.11988075):0.08346650,1_128:0.00763750):0.01312650,3_2093:0.00949525);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8f2e5561a6d3b04b9d78f0fd9fb64368fb49420
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000299_tree_id.txt
@@ -0,0 +1,2 @@
+(1_123:-0.00013987,(4_131:0.02544615,(0_244:0.22657600,2_634:2.01153900):0.05240405):0.00346935,3_2088:0.00666087);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2ad3f903fc98ebe7485ae1fc030bd64341ee820
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000300_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2087:0.01114057,((0_245:0.04651433,2_179:0.10618367):0.06619971,4_130:0.00148713):0.00411137,1_122:-0.00000857);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8e37336ff41646087fc3e829bc367facbfdf5de9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000302_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2085:0.00534978,4_128:0.00306022):0.04006531,1_120:0.03502315):0.48311177,2_181:0.04740267,0_247:0.16059933);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71a9afc5c23122784c0f9c6b028506b7afd1b54f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000304_tree_id.txt
@@ -0,0 +1,2 @@
+(0_249:0.07218044,((3_2083:0.02373050,4_126:0.04389850):0.04831229,1_118:0.05352737):0.03728513,2_183:0.23509556);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3aa361e21e3b79e50318a45331fadebd282e2f09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000308_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2074:0.00000000,((2_191:0.14220833,0_258:0.08292467):0.07405109,4_115:0.00519526):0.00295974,1_110:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..040d80a169fb050d2825fa59243866f47599d446
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000311_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2071:0.00334266,1_107:-0.00015766):0.00080698,(2_206:0.60187017,0_264:0.07495483):0.10521451,4_102:0.00254069);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9172009ccf6964a3f02fb5d848690d616738bf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000312_tree_id.txt
@@ -0,0 +1,2 @@
+((1_106:0.00000000,3_2070:0.00000000):0.00121301,(0_265:0.00950767,2_207:0.01999333):0.03989866,4_101:0.00364799);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c931ac6bd1bd4c41dcbe919bab5b5e8cad758ea8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000313_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2069:0.00000000,4_100:0.00000000):0.00000000,(2_208:0.09142450,0_266:0.16624250):0.23617650,1_105:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62adab96cbf5fad4dc1501f196bd7098c1905cb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000316_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_97:0.00321775,1_102:0.00564125):0.00608925,3_2066:0.00419425):0.08213375,0_269:0.07285175,2_211:0.18883425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d339b7108295e29aff0b2e1933e16f2b266a0e67
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000317_tree_id.txt
@@ -0,0 +1,2 @@
+((1_100:0.03126850,(3_2064:0.01830575,4_95:0.02926825):0.00722050):0.09958650,2_218:0.67627875,0_271:0.25564225);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..713bd4f4224d7025930d2fcb4a94e91d07771042
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000319_tree_id.txt
@@ -0,0 +1,2 @@
+((4_93:0.00681512,(2_220:0.14599862,0_273:0.05065837):0.06593038):0.00046188,3_2062:-0.00007213,1_98:0.00588613);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ffa46c58f680bb7effe20a4c36af5608a199c5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000320_tree_id.txt
@@ -0,0 +1,2 @@
+((2_221:0.49769725,(1_97:0.00000000,3_2061:0.00000000):0.03374975):0.07018975,0_274:0.10549175,4_92:0.06095125);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5d1a436ce83e4bc3090ad605f98ebde49c5ba4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000321_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a874d9fff92a38271c253b607741574299033541
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000324_tree_id.txt
@@ -0,0 +1,2 @@
+((1_92:0.00605025,(4_87:0.00398725,3_2056:0.00083575):0.00690025):0.06690675,2_226:0.10235150,0_280:0.10072050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d82b78bf9976452734603eb2b0199c864a7a663
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000330_tree_id.txt
@@ -0,0 +1,2 @@
+((1_86:0.00000000,3_2050:0.00000000):0.00000000,(0_286:0.20444750,2_232:0.06429150):0.09737850,4_81:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dcdf0a2a8f2a99f54258a4e03c69e6da1a065cf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000331_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2049:0.00659638,((0_287:0.08692638,2_233:0.30054463):0.07564487,4_80:0.02709612):0.01805438,1_85:0.02446662);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e5eb520e7d6eaaff47b907e8146ff86d3977490
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000334_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2046:0.00124675,4_77:0.00074725):0.01531575,(2_236:0.51297675,0_290:0.02588925):0.00461675,1_82:0.01484925);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..650748f1631c37550309cd2386c1eda298a19697
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000336_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2042:0.00000000,4_72:0.00000000):0.00469318,1_78:0.00697782):0.09427661,0_296:0.10004733,2_238:0.11981867);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3f56b3177823714361e5eb1aec41fb84583dbcf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000337_tree_id.txt
@@ -0,0 +1,2 @@
+((1_77:0.00015175,4_71:0.00077325):0.00752275,(2_239:0.44382550,0_297:0.22157450):0.16860875,3_2041:0.00827975);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec730cb64ef769d44831e1c2c4f70e1a1b81307e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000339_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2039:0.00000000,4_69:0.00000000):0.03602742,(2_241:0.46041167,0_299:0.08744333):0.09421819,1_75:0.01657158);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..173c8739f067b133779494ea2b7364cc78ff3205
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000340_tree_id.txt
@@ -0,0 +1,2 @@
+((1_74:0.02081653,(3_2038:0.00000000,4_68:0.00000000):0.01642247):0.07027018,2_242:0.38749533,0_300:0.15698267);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f034dece963b88621115d6e646ad6227457c343b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000341_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2037:0.01058488,4_67:0.00990812):0.00463163,(2_243:0.21525763,0_301:0.02988737):0.01822413,1_73:0.00353188);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80a7e9b3febf8d11ad2a3e11776a2c2ce1059a7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000344_tree_id.txt
@@ -0,0 +1,2 @@
+((1_68:0.00000000,3_2032:0.00000000):0.00103644,(0_305:0.03159333,2_248:0.02025967):0.03325785,4_62:0.00461356);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e197c07824f3dbf97b8783a95f2b34bfc0b5ad18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000345_tree_id.txt
@@ -0,0 +1,2 @@
+((0_306:0.38568887,2_249:0.25292912):0.21657437,(4_61:0.02207212,1_67:0.01869188):0.02383387,3_2031:0.02788913);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4e5b614b7ff0dd46435c03ef9750fe37265e32f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000346_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2030:0.05044237,(4_60:0.01171688,1_66:0.00943012):0.00376913):0.12625863,0_307:0.17958812,2_250:0.15220787);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81b974d1a5a2d13b801b8850c065e45a12ca56bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000347_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_65:0.02031037,4_59:0.01654163):0.00656937,3_2029:0.01741313):0.19208538,0_308:0.37459713,2_251:0.29387887);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a652794f3016b2d4a336815f1e61403dcb90140b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000348_tree_id.txt
@@ -0,0 +1,2 @@
+((4_57:0.00241945,(3_2027:0.00000000,1_63:0.00000000):0.00401155):0.04508782,2_253:0.15225433,0_312:0.14802767);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad327e2099d8e4e97c864e9c6caacfd1606076c3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000349_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2026:0.00359182,(4_56:0.00792154,1_62:-0.00018454):0.00722372):0.06502239,0_314:0.11246417,2_254:0.07780483);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9a133272b7bf3fae0351910eabbfc3c47e093fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000350_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_315:0.06015900,2_258:0.11913700):0.02662956,1_61:0.00887067):0.00137533,3_2025:0.00755811,4_55:0.00354589);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8314ec9cc5fce543bf1df2bf02b3fc671f7b232d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000351_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_318:0.19578950,2_260:0.09457250):0.25124950,1_58:0.00399300):0.00474350,3_2022:0.00758600,4_53:0.00401300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3aa3c63cb50480d58913f5076f276299db8b2fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000352_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_52:0.00000000,1_57:0.00000000):0.00067765,3_2021:0.00841335):0.01551262,0_319:0.01827183,2_261:0.05684317);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a17ea8e39817c2b451d4150dd9223778ed7eb566
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000353_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_262:0.27109200,0_320:0.09774200):0.13905275,3_2020:0.01825475):0.00892275,4_51:0.00375275,1_56:0.00401725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf45d31c2a14c774a42aef156370c5eabae570dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000354_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_49:0.00286500,3_2018:0.00580600):0.00232300,1_54:0.00944300):0.08956600,2_263:0.40234025,0_322:0.07151175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb7ef893d5b9035437eae7abfb1dfa14e6a6435d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000355_tree_id.txt
@@ -0,0 +1,2 @@
+(1_53:0.00348725,(3_2017:0.00596050,(0_323:0.13407450,2_264:0.37743950):0.07292000):0.00086750,4_48:0.00294775);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fec07975c077facf953e6d69ba9904a5dc2717ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000357_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2015:0.00179475,4_46:0.00168425):0.00202975,1_51:0.00429225):0.03972425,2_267:0.09247775,0_327:0.02831825);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77398f87e3e23ad2408652c7d80f53589e112b6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000358_tree_id.txt
@@ -0,0 +1,2 @@
+((2_268:0.01200931,(1_50:0.00309908,3_2014:0.00627592):0.00230996):0.00119657,4_45:0.00516517,0_329:0.12956983);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7dd4134ea864731d64edfdb22b3e0feb01d74de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000359_tree_id.txt
@@ -0,0 +1,2 @@
+((1_43:0.00747350,(3_2007:0.00314150,4_38:0.03943350):0.01559750):0.20570750,0_333:0.17770825,2_281:0.53193275);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2a0ef6cfb76504205478e4f35373151192b247d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000360_tree_id.txt
@@ -0,0 +1,2 @@
+((4_37:0.00524525,(3_2006:0.00000000,1_42:0.00000000):0.00432275):0.07390475,0_334:0.16120675,2_280:0.37932725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2259cdad653661ed1e024dec46629cb8ff5fae28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000362_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_2005:0.00000000,4_36:0.00000000):0.00793884,1_41:0.01737416):0.15788589,2_283:0.24185283,0_340:0.13756717);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8ef62938a4a8bd37ca9c10f79a22e6a3488e03a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000363_tree_id.txt
@@ -0,0 +1,2 @@
+((1_40:0.03122400,(4_35:0.00504875,3_2004:0.00411425):0.02466900):0.03957100,0_341:0.09031975,2_284:0.15297025);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..668ea8601a6dd44e464cb87a2fb45c29cbf13a9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000364_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_342:0.07581700,2_285:0.14985500):0.08173700,3_2003:0.00000000):-0.00000000,1_39:0.00000000,4_34:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b65b5895f189a29e386e44a60573287a6e8b3695
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000367_tree_id.txt
@@ -0,0 +1,2 @@
+((4_30:0.00695600,(3_1999:0.00542250,1_35:-0.00033450):0.00122700):0.03733400,2_288:0.05969075,0_346:0.07705925);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ec57c125b73b3fe6e73a52534ab8a28e34ac6788
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000368_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_30:0.00537062,3_1998:0.00163337):0.00575613,4_29:0.00409888):0.04146462,0_347:0.06984588,2_289:0.06975713);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22aa606eb1fd0b932cf1b2479dc71e7115165c3b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000371_tree_id.txt
@@ -0,0 +1,2 @@
+(0_356:0.00247450,((1_21:0.00285875,3_1990:0.00010825):0.00481325,2_339:0.24990025):0.00041125,4_21:0.00346950);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fef6fcbcc8e4f5dbfe99a009fe0b34031a08d2cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000372_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_340:0.36106384,1_20:0.02596116):0.00245185,3_1989:0.04781418):0.01777735,0_357:0.02761267,4_20:0.03462033);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29734a73e466693f095c5329b9305daca96ad81f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000374_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_18:0.00017867,3_1987:-0.00017867):0.00783250,4_18:0.00946850):0.00253350,2_342:0.35010439,0_359:0.01900761);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e40e27b6d45ee6dea30a80f7a3cc8ce260618ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000376_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1985:0.05015538,(0_361:0.31858062,2_344:0.57534737):0.18180113):0.01567312,4_16:0.03828838,1_16:0.03629562);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..344e28ee3f0ae2b97d9476ca913a9484b9411631
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000378_tree_id.txt
@@ -0,0 +1,2 @@
+(1_14:0.00942187,((0_364:0.07851262,2_346:0.25258237):0.05883138,4_14:-0.00086838):0.00215538,3_1983:0.00361612);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9731a26208d23ebebb7480d1357acf7f800da85c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000379_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_365:0.27206613,2_347:0.30265487):0.08043312,3_1982:0.01731737):0.01075463,4_13:0.00604363,1_13:0.00656637);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52ada5f47a2f6f09dbc15fce72567817567715a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000383_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1977:0.01394133,1_8:0.00520267):0.00164457,4_8:0.00024798):0.07179493,2_2129:0.28412967,0_370:0.07437633);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7efee46b77b7b5c63d3c537536c75742406f0a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000385_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_390:0.00000000,2_2143:0.00000000):0.00000000,1_609:0.00000000):0.01111300,0_735:1.80487100,4_572:0.09302400);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb4383e04d9b0cd0f71f4814c147cc8c6646d872
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000387_tree_id.txt
@@ -0,0 +1,2 @@
+((1_7:0.02192175,(4_7:0.00000000,3_1963:0.00000000):0.00299325):0.07339575,2_351:0.73022625,0_398:0.05097375);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0d2549453b44045ceac9166f547db03c0a1fc7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000389_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1961:0.00117137,4_5:0.00028863):0.00216863,1_5:0.00543937):0.03064562,2_353:0.09787812,0_400:0.04376888);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1ec7720c87f5a62262fd315674ff6ca90aa8731
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000390_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1960:0.00000000,4_4:0.00000000):0.00158208,1_4:0.00412192):0.03846881,0_401:0.03235983,2_354:0.08937217);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d7f73182f8fbd139a2c5f736ca5b9f5e0224430c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000391_tree_id.txt
@@ -0,0 +1,2 @@
+((2_356:0.15793850,0_402:0.14478950):0.09826300,(3_1959:0.00000000,1_3:0.00000000):0.00457100,4_3:0.00368200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab4d22e865033bd0bd8e21641933572bc1176710
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000392_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1958:0.00563850,((2_357:0.09654850,0_403:0.05830350):0.06033825,4_2:0.00335525):0.00618325,1_2:0.00090650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..751f2c024d33fde46fa0e263303197da305e0839
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000395_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2251:0.00000050,3_1955:0.00000050):0.00000000,4_2193:0.00000050):0.02968900,0_406:0.01444750,2_360:0.02230850);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..908826b4910973c60d1409a03582115304f97a55
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000396_tree_id.txt
@@ -0,0 +1,2 @@
+((2_361:0.54122967,0_407:0.08010533):0.02494413,(4_2192:0.00000000,3_1954:0.00000000):0.01875061,1_2250:0.02690239);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..11c64868d68a5bfa6541c0693c1b1185909bf103
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000397_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1953:0.00000000,((2_362:0.15774475,0_408:0.02151325):0.00567525,4_2191:0.00255425):0.00507975,1_2249:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..801e8ad8899b69c78b5bce1befe8e27cfa57d484
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000398_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_409:0.02311500,1_2248:0.00423500):0.01900250,2_363:0.12728050):0.02793900,3_1952:0.00209800,4_2190:0.00432300);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a258f46ab495640a0e35b16772341928e8c66dea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000399_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2189:0.01042736,((0_410:0.15606767,2_364:0.28369033):0.10924591,3_1951:0.00642773):0.00551377,1_2247:0.00355864);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8a3f210546885a632c7ba73a934d9678852ea3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000402_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1947:0.00000000,1_2243:0.00000000):0.00000000,4_2185:0.00000000):0.04794000,2_368:0.08789800,0_415:0.01643900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0441f5a0831734504d77f836d9ef7123f135ec20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000406_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_422:0.02076583,2_376:0.07166917):0.01179948,1_2235:0.00469395):0.00095355,4_2177:0.00003118,3_1939:0.00631282);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000407_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000407_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfd17e071206c600e4d127b723def00db607438b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000407_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2234:0.00873650,(3_1938:0.00195025,4_2176:0.00534975):0.00362500):0.10764150,2_377:0.26446300,0_423:0.09129200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a499f655cd9cdf092347d6de4c6e4ff0a42bd008
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000410_tree_id.txt
@@ -0,0 +1,2 @@
+((4_258:-0.00016638,(1_260:-0.00016638,3_2224:0.01308138):0.00016638):0.68480038,2_380:0.59788763,0_426:0.69088538);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3563fb51a5a8073a1feaa1454d2b4fe6e2d6ad1c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000412_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2172:0.00000050,1_2231:0.00000050):0.00000000,3_1934:0.00000050):0.02225050,2_381:0.03820200,0_428:0.00091000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6113e7efd7b1a78baa581c332eec89c0b52b1465
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000419_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2221:0.00138017,3_1923:0.00089383):0.00166114,4_2161:0.00352144):0.00185304,2_389:0.01646167,0_436:0.01164433);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..539082e09ab3db0a83645b72eafe462774e88b31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000422_tree_id.txt
@@ -0,0 +1,2 @@
+((2_403:0.17688650,0_452:0.08949650):0.16105390,(3_2111:0.01072987,1_146:0.01583313):0.01304193,4_159:0.02331370);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..127d7145912251985029f3d8136b42b1d4e31c68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000424_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2195:0.00000000,3_1906:0.00000000):0.00000000,(0_457:0.02715700,2_413:0.02261700):0.03440600,4_2127:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cab7a562fd48f6c9c2776723eb8d2be0ba890951
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000429_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2117:0.00000000,3_1897:0.00000000):0.00000000,1_2184:0.00000000):0.06879750,0_482:0.07662550,2_494:0.65616750);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..486033a599f4f71a1d82f64980568d2e0b549129
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000431_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1892:0.00008375,(4_2112:0.00000000,1_2179:0.00000000):0.00320725):0.08549775,2_424:0.05826375,0_487:0.10256525);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c1275d3979b503ad514f859ca3acc2160b93e1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000432_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_488:0.05568552,3_1891:0.00246048):0.00128651,2_425:0.00566888):0.00210777,4_2111:0.00475300,1_2178:0.01218600);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..170da64662d72b98439c8efbe7cef91399acb8ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000435_tree_id.txt
@@ -0,0 +1,2 @@
+((0_500:1.17052670,(0_793:0.66891383,0_2335:1.11009217):0.26651190):0.65783393,2_867:0.13184750,0_926:0.04373650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a887999d8042ff7cce8d34d4305aa8cca86aae9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000437_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2098:0.00651737,1_2158:0.00080062):0.01615488,(2_448:0.43250362,0_509:0.37485938):0.42534287,3_1882:0.01410062);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ba506dc38c4a203a0439b49575037cf476b512f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000438_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2147:0.00849401,(4_2092:0.00000000,3_1871:0.00000000):0.02164699):0.03926734,2_451:0.61386600,0_519:0.07229300);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56b79407e3ddb1c71d21bcb41e2d4f2de72b75b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000439_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_2145:0.00000000,4_2090:0.00000000):0.00000000,3_1869:0.00000000):0.11674400,2_452:0.90502500,0_521:0.15886000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8641ad36453055a0a7c811f890ebb0fcb180d01c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000440_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_455:0.56280350,0_523:0.15097850):0.08226600,3_1865:0.00000050):-0.00000000,4_2086:0.00000050,1_2141:0.00000050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..122117e30ea1794734d69c71311a5f5a34ba8fc8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000443_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fe5c5e898b3afc1e66954ca426b825841b76ea6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000446_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c76ef77344d7a561a8e9a772bd186152ab1ac48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000452_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25a0f267948e3a6ed4467f911a1ae1ec51a041da
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000455_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2066:0.00745263,(3_1845:0.00421663,(2_479:0.22825487,0_551:0.10898913):0.07760738):0.00264038,1_2120:0.01221137);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64fc80d903ee4dc66c53d67f59b7ffb98427473a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000460_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3224c0c9eec238b347a5e59fd24d1b08b3d06544
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000461_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..006ea65a369d9617faed5f24c9cbc36c4e76c7a9
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000462_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bfb84699a11270980a6f777443365c587e3b8095
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000463_tree_id.txt
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+(1_2109:0.00464858,(4_2055:0.00451434,(2_491:0.26835767,0_564:0.07173633):0.07993545):0.00257916,3_1834:0.00532542);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1caf3f10e16955f645a493ebaf4ea4105395b18e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000464_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92624d63f40603f0d50e94ff107ea627bca2f593
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000465_tree_id.txt
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+(1_2106:0.00440563,(4_2052:0.03014213,(0_567:0.10695787,2_495:0.14318812):0.03944138):0.00966538,3_1831:0.00823937);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed75c81912313da261329ec7ef182809fe387d9a
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000466_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3ea32fc72adaab2ef93a77c51bce094c83d1359a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000471_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca60d06e2e581a97bf366a8fca6a4679d274125f
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000472_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2811a574248d99dcc9c312b18779e3618bd706f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000473_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000474_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5cdccc6c7c22b10829ee8c0b881fe49c95014d8
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b80394d79b0c28475ac2adca8a701f06a32538b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000475_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000476_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d2d1ae722ccffe37918b2c4ca99def847f672ce
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d52be6e7c523aa5ff22fb73c028112ebe67865eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000479_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000481_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2e4481a8cc40b8c9b61dc0a50c7c3b83fd19405
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000482_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e298ee2847887a8bb364de8cd8096ae2ddeac6e
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..217232a3c4967c6eb1648db62d432824b341a760
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000486_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dda1ce41137c0cb29d9255e196b54587ed8d1a3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000487_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_2017:0.00000000,3_1797:0.00000000):0.00000000,1_2078:0.00000000):0.08118550,0_615:0.09941650,2_540:0.29889050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5d70e4ac0e817473372f7fd29391a7eae5c1b19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000488_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2016:0.00000000,((2_541:0.20039600,0_616:0.05827400):0.09450872,1_2077:0.00361415):0.00417585,3_1796:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..123eb2808cc17c52ae83cf42cccb142ce71f2f23
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000489_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1795:0.00000000,1_2076:0.00000000):0.00000000,4_2015:0.00000000):0.03490350,0_617:0.06122550,2_542:0.13929450);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71869301016a9035270718413e20003ec324e72e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000492_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2011:0.00176025,(3_1791:0.00521025,(0_629:0.03493275,2_546:0.05481725):0.01726775):0.00754575,1_2072:0.00457175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40224ce2a2ed7d9ad620ba1fea7de33c148d975a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000497_tree_id.txt
@@ -0,0 +1,2 @@
+(4_2006:0.00000000,(1_2067:0.00231775,(0_634:0.00263175,2_551:0.01164425):0.00770475):0.00051925,3_1786:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f790789d86445b1e96fa9f828a52e45e60e3c191
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000500_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_555:0.24818113,0_637:0.10770888):0.03505163,3_1783:0.00591487):0.00925713,4_2003:0.01034263,1_2064:0.04014938);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a5d7e0ba52ccfe0fd09c28c503f2878dc2fa8bbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000501_tree_id.txt
@@ -0,0 +1,2 @@
+((4_2001:0.00000000,3_1781:0.00000000):0.01433244,(1_2062:0.01413100,0_638:0.07693800):0.00178350,2_557:0.00612956);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e44bdc4c5a97e4f1c3b1c95166462de987e7e7a6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000504_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1777:0.00553907,1_2058:0.00894793):0.05298274,(2_561:0.35096650,0_643:0.14772350):0.13646976,4_1997:0.02051442);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e2823bc346955e4d2baa7ff567097ed05c8bff5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000510_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1767:0.00768015,(1_2049:0.00160030,4_1990:0.05267470):0.00123337):0.07624068,0_650:0.05769933,2_568:0.12932967);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94342307a89fc0c3b83ac3d905e8527b26546043
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000511_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1766:0.01920649,1_2048:0.00895951):0.00548095,4_1989:0.01911182):0.00847908,0_651:0.03747983,2_569:0.34096417);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0c62b3f1f49190105aa3f159779212c0aa5f67b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000521_tree_id.txt
@@ -0,0 +1,2 @@
+((2_589:0.00715050,0_678:0.02412950):0.00152200,(1_2026:0.00000000,3_1742:0.00000000):0.00886208,4_1966:0.00480492);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aef5420fa10a91ef2f30ef11028738bd11e11aa6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000522_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1965:0.01125183,(3_1741:0.00000050,1_2025:0.00000050):0.00323267):0.00702011,0_679:0.00356817,2_590:0.00842883);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dc7cb40d3714a8a4404fc71d45a92d3ab7c25f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000523_tree_id.txt
@@ -0,0 +1,2 @@
+((2_591:0.00535725,(0_680:0.01007875,4_1964:-0.00005675):0.00326225):0.00753675,1_2024:0.00000000,3_1740:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..89f7a3b3c9d773a448a9551e6a014832981fd3ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000525_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1962:0.00415400,(3_1738:0.00000000,1_2022:0.00000000):0.00035200):0.01409350,2_593:0.01248050,0_682:0.00561550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f2e18d3afa3bb749e9eab611f8e876ee79161d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000526_tree_id.txt
@@ -0,0 +1,2 @@
+((0_683:0.01720175,4_1961:0.00143225):0.00246275,(3_1737:0.00000000,1_2021:0.00000000):0.00064325,2_594:0.01804975);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e47c40b59b9163999a35d1e4c928e5b89ffdbb89
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000527_tree_id.txt
@@ -0,0 +1,2 @@
+(0_685:0.01249000,((4_1959:0.00000000,1_2020:0.00000000):0.00065300,2_596:0.00460300):0.00001300,3_1735:-0.00067400);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..65d06152c6c4f260c8dcccd4929af916edbca7ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000535_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_710:0.13391900,0_746:0.11522100):0.14723600,1_1995:0.01358700):0.00653000,3_1712:0.00000000,4_1930:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..39fb1bfb3094ac1f7271a6f18c8c7e549b3603ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000539_tree_id.txt
@@ -0,0 +1,2 @@
+(0_762:0.21909373,((3_1693:0.00000000,4_1911:0.00000000):0.01255825,2_729:0.00557275):0.00619975,1_1975:0.01187627);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..841c483e7eb6065c79f4db9184a35dc58c7c73e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000541_tree_id.txt
@@ -0,0 +1,2 @@
+((4_925:0.00046134,(1_981:-0.20720139,3_705:0.52471339):0.22478705):0.08155576,0_764:1.27653983,3_704:0.41306017);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54f6490727026ed5476076ae9a04b4fba45dc268
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000542_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1909:0.00493973,0_765:0.04983427):0.00132862,(3_1691:0.00179267,1_1973:0.00087033):0.00481337,2_731:0.00613747);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b71db5cde0f1c59cb29ee5b1c856c89343bde249
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000545_tree_id.txt
@@ -0,0 +1,2 @@
+((2_735:0.01945083,0_774:0.02054017):0.00442938,(1_1966:0.00059990,3_1686:0.00216710):0.00137245,4_1904:0.00322852);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75442de8ea0b97e60b11147505ef73db85754569
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000547_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1902:0.07401000,(1_1964:0.01278415,(2_738:1.21360733,0_776:0.28134367):0.79222738):0.02774285,3_1684:0.03099700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..676cd8d0474dbeb777186abade926d83a39f0cad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000548_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1683:0.00244024,(0_777:0.00258306,4_1901:0.00219794):0.00259959):0.00482681,2_2039:0.55059383,1_1963:0.00472317);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e6949a73452fd1762a02ec2a2b0df2eac8c531c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000550_tree_id.txt
@@ -0,0 +1,2 @@
+((0_779:0.36923925,(2_740:0.03150350,4_1899:0.00614250):0.00120675):0.00223825,1_1961:0.00694850,3_1681:0.01370350);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4187b9d7481e07379bc6648fc08cff48a360a0ef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000553_tree_id.txt
@@ -0,0 +1,2 @@
+((0_786:0.02552638,3_1676:0.01205962):0.00182863,(4_1894:0.00008437,1_1956:0.01597663):0.00638312,2_745:0.01446087);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b30125f1ac358ca8f8d4679cc5e33f9c84aec097
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000554_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1893:0.00306450,0_787:0.04268450):0.00168400,(1_1955:0.00230600,3_1675:0.00161300):0.00198400,2_746:0.00423250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e3db67df76ad3a321ff6b218c1bf611a5bed2ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000555_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1891:0.00000000,3_1673:0.00000000):0.00319025,(2_748:0.10417525,0_810:0.07233275):0.05298875,1_1952:0.00389775);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38b5c0eb673924fade7d7014858206348e95e4b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000556_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1890:0.00402369,(2_749:0.10217500,0_811:0.03116300):0.02538756):0.00391831,1_1951:0.00788526,3_1672:0.00265474);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..618113d22ad718df6bf2418de6a879a2ef653e1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000557_tree_id.txt
@@ -0,0 +1,2 @@
+(0_812:0.03993247,((1_1950:0.01048800,2_750:0.11525600):0.01019038,4_1889:0.00757013):0.00944387,3_1671:0.00588653);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23b19d683e54ce6a5fca506ce21367e75bd0930b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000560_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1947:0.00409300,3_1668:-0.00042100):0.00140675,(2_753:0.01982125,0_815:0.02596475):0.01390875,4_1886:0.00635025);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adfed3a78bd52a9db553796651804248096212f3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000562_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1666:0.02160730,((2_755:1.44147933,0_817:0.25911567):0.25695372,1_1945:0.03866216):0.01232234,4_1884:0.02349670);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dae2b133340486fa5b3eb55e40cc9dff13df0e38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000564_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1881:0.01553263,1_1942:0.00355338):0.00660338,3_1663:0.01021763):0.04594287,0_820:0.03475238,2_758:0.21566462);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08c86a82075d2a163137f3351a0aa5d76dd24229
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000570_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_784:0.02642567,0_845:0.05049733):0.01057559,3_1637:0.00103878):0.00090872,4_1859:0.00193464,1_1932:0.00538436);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2159f63145a0db9a2cd84969444795f24679aaea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000571_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1931:0.00655537,((0_846:0.03374312,2_785:0.00900787):0.01511588,4_1858:0.00451412):0.00434088,3_1636:0.00897363);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5074b65356126f652751c85e46f877a1710eac05
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000573_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1634:0.01376156,(1_1929:0.00741055,(0_848:0.03806617,2_1720:0.21332183):0.03307435):0.00203245,4_1856:0.00002744);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..678dbc7965fca378aa36ea605f25ff2737244540
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000574_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40b6fbb166037ecca0ee54a84cc43b5a7afd5d03
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000576_tree_id.txt
@@ -0,0 +1,2 @@
+((2_789:0.02653250,(0_852:0.00000000,1_1925:0.00000000):0.00017350):0.00282050,4_1852:0.00234300,3_1630:0.00277200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..67416463eb89dabd7db1876d66e8286a97d36494
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000579_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1847:-0.00000295,((2_794:0.00462750,0_858:0.31868150):0.00222161,1_1920:0.00098033):0.00243667,3_1625:0.00097895);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c30dd020f04dc038e9a8af36895f5e8c092c697
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000583_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1618:0.06053350,(1_1913:0.03155975,4_1840:0.00830325):0.00699600):0.19710750,0_865:0.37915275,2_808:0.55663725);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bea849d7b1134c4f2c895b4b6688782fdce9ba10
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000585_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1911:0.01177363,(4_1838:0.00668012,3_1616:0.00260188):0.00903587):0.12754237,0_868:0.16536862,2_810:0.41977638);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1b9fc6362aec89f9f0e948b09a4555cd265d2b16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000587_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e860a6a161c6304b8e877115aad02e7fdf0975e9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000595_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1591:0.00155517,2_831:0.01207683):0.00301239,(4_1804:0.00506707,0_892:0.02097593):0.00102802,1_1884:0.00289974);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b50ee969d99e9d48286dadca4f53ceb9796c9e7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000596_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f91cdf1534f501b8ca9424ed33d34c3e22e39db
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000597_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f396102330c1a511449b82d713a456c4193cbc3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000599_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22cd8a5f325d8ed4d3d728c2d0238e35a4c9ae54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000600_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1877:0.00000000,(3_1584:0.01229035,(0_902:0.08476800,2_837:0.17363600):0.07833478):0.00540665,4_1797:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a05c25fa532c5e9d2192fa5102018b1afb82ea4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000604_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..349a5b8a6c10bd00e4642f76654759fc89e2d8fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000605_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a1e3a61dbbcc97fb92b6cac2c873c378dbebd27
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000607_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85b84dadb4b852091529214c9824f1bfb5fe4bc5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000611_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ca7917613a44f2bf03ee1daca4508fd47378703
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000612_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a8e6a7071c9c4d4c4554d08538c608f042770c1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000614_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1302122909de59ff4830f19eb4a691aa52205b06
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000615_tree_id.txt
@@ -0,0 +1,2 @@
+((0_921:0.02681337,2_857:0.24881063):0.01989113,(1_1859:0.00822213,3_1566:0.00503588):0.00581763,4_1780:0.00035138);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24979c1fe4e85af0ac6f82b2eb343a84109992b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000616_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1779:0.00497062,((1_1858:0.00582112,3_1565:0.00175488):0.00376587,2_858:0.03810062):0.00151638,0_922:0.02440537);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c15e04312529e38d2488a9f92d606a26b961dfd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000618_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15468383c44f9d44754dd8c7302ed3bfd5b3b68d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000622_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..197b5d545fde1ab7807fbedb8b318e70cc3d8065
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000623_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fb837b767adb529541b539ddc18180db04c7af8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000624_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb72cc822f11851c1cd05e527094b3e0f06bc5dd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000625_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000626_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..751d951a78e16c31761d3a348b9b1d135e808cca
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eb496cbf632869bd0649e9d49fd72b15c51aa5df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000628_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000629_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9f6e1bf5e15e1e60c5c7e2ca495baf49f17d902
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6eddb86e4c45f452d88c54dbbc8ded31725ec618
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000630_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81dd922b860708d5d532897ac19f74fc34c590c3
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000635_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22b5d7cd01cb7ac780b18b118a6c59f89c10f214
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000636_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0fac28977c75e44588ad50508cd8e5f45d17f193
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000645_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57bc31bc7390a7ddf4425159a6ef7098d338829e
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000648_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e25324b959f781f21d065ba21b43e1580cb4ca16
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000650_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23d17df47e995ac5ecb50933b30b873aa8b2c565
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000652_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..31aefb016a67983a9d5d2ceff5f10adf73392ea4
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000653_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3071fc14f54aabe626e125601fbda984ee666d6a
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000654_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..011062a34132049363ee6148f8210238fef85f35
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000655_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9f041df942dfeddc87b5a22a1fe386977c43c71
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000656_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000656_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c07c1d0ce1799b540c0aad55de11fa24bdc4e4d
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000658_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90b5967a613480db270109c06e022fb6960c5267
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000659_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e71c9b2b7e39a3fa2bd257f1397ba844624fa012
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000660_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92516f0c1d03699e98165546c492e065b099cc4f
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1116a4557a9d261a88737c0d56cc903916b3d04f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000664_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1719:0.00483425,((0_986:0.05097750,2_931:0.17605450):0.03307400,3_1505:0.00395800):0.00183450,1_1798:0.00336275);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8a84c72d7244729fb5f2e2524c25f1e80d2e0b8f
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000665_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000666_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000666_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32f9fd4aea3bd981cce7a58474e2841de8634cf4
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000667_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..af0c162875efcc6aa2a6bf4eb7be2ff67b401ebe
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000668_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000668_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8de195118417277c9b239af9648f3eab6812a4a
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000669_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f31a4885e9c6323b5704ef7ef891bf44852adfd3
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000671_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..74c11e36923523d5aec7204a739ec7749b41876c
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000672_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4920a445d1b33e55629b794d988b0ec38d3baf42
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000674_tree_id.txt
new file mode 100644
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000675_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2e538ce7809a68e8c2c2eb3faa4651a4b32d524
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000676_tree_id.txt
new file mode 100644
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000679_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..407eed5bbb7414fdb1dab869658374da82f8c3fe
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000681_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..35e37397088ca6285f26dfa31fc38d8d0f415a9b
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000682_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..225ac779f6605e75acf86e4bf7f8e4fbe77e26c9
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000683_tree_id.txt
new file mode 100644
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000687_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..716f99ea1b3929433ab74ad239044adcac60e5e9
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000688_tree_id.txt
new file mode 100644
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000689_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a57b7c0ad1f424ff37d7881dbd37205b24520b0
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000691_tree_id.txt
new file mode 100644
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000692_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000692_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c8283d6ddc6e9ddefa12d25d6486909b0c0781d6
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000696_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eacf792530f382ae0b8f497b0c355ee964a30cb6
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000697_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79acff14fc5b60fca8dc2c4a1987f1790f17fe0e
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000698_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000698_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90a709303e3e9f9e8c2b3819d609ed841808306c
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000699_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e962c23072746b752d7158ac892ce54475b9706
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000701_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e69b30768c787d7567e5f1013fcd5dfa8f6f91d
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..698b06aeb02db1578ed58a8ff63acf86993952de
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000705_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1459:0.00361123,((2_979:0.76260500,0_1043:0.21625100):0.30053812,4_1673:0.00736137):0.04062063,1_1751:0.02277677);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c36fbe373d6e49b75e7899e0208bf7bc86e9e6e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000708_tree_id.txt
@@ -0,0 +1,2 @@
+((2_986:0.23064650,(4_1666:0.03241675,1_1744:0.06169625):0.09494600):0.22317400,3_1452:0.00693275,0_1049:-0.00085375);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4a2c2607650a292348ccb9bbb1d65b3cbcb7cf07
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000710_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1664:0.01796579,2_988:0.00599421):0.00393217,(3_1450:0.01051633,0_1051:0.01815867):0.04091671,1_1742:0.01247540);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42c517a1e28b3ec0f4ccc43b361fe460a76727f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000712_tree_id.txt
@@ -0,0 +1,2 @@
+((2_990:0.07261117,0_1053:0.01740983):0.02461429,(3_1448:0.00024933,4_1662:0.00658067):0.00099514,1_1740:0.00029003);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a54fb63158332ac4aacadac9ed5a48c3f8659098
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000713_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1659:0.00797110,1_1739:0.00365490):0.00108137,(0_1057:0.05233950,2_993:0.20869650):0.03426492,3_1447:0.00385276);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a459f7560c1b06ea63c3798b378a33c1a1797464
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000718_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1653:0.01212662,(1_1724:0.00396188,3_1441:0.00280013):0.00427238):0.07776387,0_1075:0.07296088,2_999:0.11915713);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f97f116f1390ff99ce7e57c0f1e0b58d92c2b39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000719_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1652:0.00170687,1_1723:0.00110112):0.00908138,(0_1076:0.15046312,2_1000:0.71248787):0.07797688,3_1440:0.00599013);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bcaff6b4ffbd80ff56c323820298a0ba2acb900
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000722_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1717:-0.00060829,((2_1006:0.17113383,0_1081:0.11628917):0.03811493,4_1646:0.00571928):0.00700272,3_1434:0.00506929);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..edfa707303114c21a1492e4ef764748d64c5f521
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000723_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1433:0.00014778,1_1716:0.01436622):0.00908217,(2_1008:0.06157750,0_1082:0.05616950):0.03678525,4_1645:0.00965968);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7468ba4d4eabdab4c0cd11adb503335afcfd141f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000725_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1011:0.14985300,0_1084:0.07290100):0.07972050,4_1643:0.01763200):0.00311600,1_1714:0.00000000,3_1431:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24b3e28db6c5370e852f576925953490cd7fb21d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000727_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1087:0.09650150,2_1014:0.41381950):0.06430354,(3_1428:0.00000000,4_1640:0.00000000):0.00718787,1_1711:0.01789213);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1a1e396b752c3500982d5ab021f7c916018579ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000728_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1710:0.00458600,(4_1639:-0.00048800,(2_1015:0.09113575,0_1088:0.00016025):0.00999900):0.00048800,3_1427:0.00043800);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5dcf14f96ebc4b8e4904d221daccf80cc82f10ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000729_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1708:0.00054063,(3_1425:0.02347462,4_1637:0.00856038):0.00570637):0.12733037,2_1016:0.85479512,0_1090:0.10587387);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99a41d86cb7600f4fb6aa16adafc4083e3502d7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000730_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1424:0.01973552,((2_1017:0.30426033,0_1091:0.06212167):0.05904184,1_1707:0.02715151):0.00319749,4_1636:0.00997448);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ba0beff1ac5ccd46edf31fb5f9b4f08c4d842fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000733_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1633:0.00151425,(1_1704:0.00000000,3_1421:0.00000000):0.00533675):0.03643225,0_1094:0.04036975,2_1020:0.06457525);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e48fbf918a626394b1ba969553faf6906c32cb0a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000734_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1632:0.00462294,(1_1703:0.00000000,3_1420:0.00000000):0.00725806):0.03128298,0_1095:0.08940767,2_1021:0.64747733);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..62df2ad73fdd6653fb56564028be5538e83c127c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000735_tree_id.txt
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+(1_1702:0.00000000,((0_1096:0.07416150,2_1022:0.21609750):0.05434816,4_1631:0.01602899):0.01999801,3_1419:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ea1c44823b7bd1611bb595efee480719db3f3ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000736_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1701:0.00000000,4_1630:0.00000000):0.00000000,(2_1023:0.33891250,0_1097:0.22293250):0.20638350,3_1418:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2b9dc1efe147656e48daed461c4da97ac2b333ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000737_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1629:-0.00085175,(1_1700:0.00000000,3_1417:0.00000000):0.00980075):0.02323175,2_1024:0.18248475,0_1098:0.05101625);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d1f8c6c110169c8b19c26dbe5165cde4c346dd9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000738_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1699:-0.00032475,((2_1025:0.25856400,0_1099:0.05133800):0.06881225,3_1416:-0.00032475):0.00032475,4_1628:0.01463775);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..44ccf86d07260b23c797ab0bf4e7e4c08d283e0c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000739_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fb1d1e0eaca9897c03ac7382284ba850a53a1ef1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000741_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1696:0.00000000,((0_1102:0.07145217,2_1028:0.30189083):0.06344313,4_1625:0.02964489):0.00698911,3_1413:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5be94ad84af5f1d6f404b6f07e27ea6f47ebc4c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000743_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1030:0.07754600,0_1104:0.02587200):0.00916600,4_1623:0.00000000):-0.00000000,1_1694:0.00000000,3_1411:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..342a5fd4e09b097fe943a40e20f01c6426fb9aab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000745_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..607021caab6e22f3cb80ebb3d9c2c4312e60b6ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000746_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ade7920f7aff8fee4cabdc8addf7a6914394d2f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000747_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1407:0.00000000,1_1690:0.00000000):0.05204504,(0_1108:0.08301125,2_1038:0.38252475):0.05029625,4_1619:0.00382196);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02e93f22b842b628cfa355a9434f0d9cef6d0028
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000749_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1405:0.00000000,1_1688:0.00000000):0.00000000,4_1617:0.00000000):0.05425900,2_1040:0.16812700,0_1110:0.05485700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3b0fddb317ce04c660b698660c4605f08e190f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000750_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1404:0.00000000,1_1687:0.00000000):0.00534956,4_1616:0.00099144):0.05044948,0_1111:0.08563433,2_1041:0.26948567);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..21d59cc570ad088a3fdc36b0696dbabffcb7fca4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000751_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1112:0.18631087,2_1042:1.03789413):0.15991363,(3_1403:0.00402087,4_1615:0.00140513):0.00591263,1_1686:-0.00047163);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d060b1f838bf0a416c9b565243f6d75260e6307d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000753_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1045:0.43199250,0_1115:0.21729850):0.25946685,3_1401:0.01268605):0.00276295,4_1613:0.00034700,1_1684:0.00639000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..38e87751d1085f749d11bacb070e8b4a0cf7159e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000754_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1683:0.01194811,((0_1116:0.13877533,2_1046:0.21387267):0.10350466,3_1400:0.01504097):0.01391353,4_1612:0.01251589);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e0717fe428f5ac64105c27750198eadb6a4b76b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000755_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1611:0.01026625,(1_1682:0.00951275,3_1399:0.00798225):0.00804675):0.05525025,2_1047:0.15470850,0_1117:0.03153750);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b49b3d66b3f3f070215514b7e0fb183264d6a8ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000756_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1610:0.00522611,(3_1398:0.00056087,1_1681:0.00530313):0.00661888):0.03529855,2_1048:0.09797117,0_1118:0.07803783);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c79d7151ce77d5473e28af84c1f7db40963a6c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000758_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1120:0.10176867,2_1050:0.19848333):0.05614001,(3_1396:0.01031177,4_1608:0.01818023):0.02203291,1_1679:0.01857445);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9931d062bc0044f28717c27ec13ff0ccdabe9541
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000761_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b3e80782d3fae29dae877d33ca3e8be4d9420b6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000763_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1055:0.02741550,0_1125:0.01355250):0.00850850,4_1603:0.00000000):0.00000000,3_1391:0.00000000,1_1674:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e335379b841e2f0f8457472fafebeac0e821a6f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000765_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1601:0.00000000,(1_1672:0.00207050,(0_1127:0.00416650,2_1058:0.00416650):0.00626150):0.00207050,3_1389:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7dc584a553a2dbb414eafcd513e245a45a097a7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000766_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d253d3cb75fec3cb662d779e5e78ebcaaea7dbd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000768_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1669:-0.00009450,3_1386:0.00330650):0.00009500,4_1598:-0.00009450):0.00884450,2_1061:0.01599450,0_1130:0.00538550);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0a5a5eb226c2b6103de958bb3feaf5122f99f54
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000769_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1385:-0.00176456,(4_1597:0.00000000,1_1668:0.00000000):0.05055456):0.18253315,2_1062:0.46761633,0_1131:0.10622167);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7351601bfb734dd7b0c82aebdf714f36654a3901
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000776_tree_id.txt
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+((3_1378:0.00000000,(4_1590:0.00000000,0_1138:0.00000000):0.00000000):0.00000000,2_1069:0.00522200,1_1661:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df8dea1513fd2a260cf778fb7e1218852b62c489
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000778_tree_id.txt
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+(3_1376:0.00000000,((0_1140:0.01140533,2_1071:0.04442167):0.02278321,1_1659:0.01574164):0.00237936,4_1588:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..758a5af9d4b58cf32fb2b808fad5d54db36fc8bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000779_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e066687a7c375eb7418d1ffeb3937a416d005dfd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000780_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cbde1b1de95b27e8d0fefb15295a60d7d7679b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000782_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8884b2caae7194be382ce2aa0fe1bf2e0b251f5b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000783_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab48169ab23902d0270fb79e49d04a4f6f76136a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000786_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eac4cf6eec4ba3231a96e3e17bb3bded199b874d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000787_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc7c3ec303012fddef9609baa650fdd4feefe2d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000788_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae204c3d89cc718872bc89982a4eef0d29ed3f53
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000791_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5904b44beed11887f169ed4712c252743b187ffc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000794_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1156:0.00000000,(2_1087:0.03919100,3_1360:0.00000000):0.00000000):0.00000000,1_1643:0.00000000,4_1572:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a4121e5e374f50e33d0202374c22a93a34ed4fc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000795_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1157:0.00000000,(2_1088:0.02263300,1_1642:0.00000000):0.00000000):0.00000000,3_1359:0.00000000,4_1571:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40ba1715b7088e50127d10fed96f9e82dfe46627
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000798_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1356:0.00308145,((0_1160:0.00258617,2_1091:0.04709983):0.01179279,1_1639:0.00214887):0.00098113,4_1568:0.00161355);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47785d7eb0a8c562b1f711d2b8f86523954309f8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000800_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1354:0.01290975,((2_1093:0.32235000,0_1162:0.07041600):0.09186550,1_1637:0.00975850):0.00283100,4_1566:0.00386325);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..523e4439eb2f5e3d111322fe7cae5dd3d29c4f1d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000805_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1168:0.15010100,2_1099:0.82590900):0.24099700,3_1345:-0.00000000):0.00000000,4_1560:0.00000000,1_1631:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8201d74b4eed5dfed1178f04d1d98491c13a3ef7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000806_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1630:0.00094228,((0_1169:0.19418650,2_1100:0.11949150):0.20499146,3_1344:0.00394489):0.00489911,4_1559:0.00100472);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6f14a3128d63f4002f894eb4e22c8c6f0752396c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000807_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1628:-0.00043075,((0_1171:0.04670200,2_1101:0.20323900):0.07533725,4_1557:-0.00043075):0.00043075,3_1342:0.00343575);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be3c4385bb1be5f423ea6c351a5f999e3c7f2b7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000809_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1624:0.00000000,(4_1554:0.00308700,(2_1104:0.10491400,0_1175:0.04257300):0.02162000):0.00470500,3_1339:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34b75dd09367df8164ecec2d1d4bc2a3d8801985
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000810_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1623:0.00422587,3_1338:0.00193413):0.02507563,4_1553:0.01317837):0.11699063,2_1105:0.55185038,0_1176:0.15657263);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ef2efb7c100965cdd0cf5e0a5222b3c28c2dc3b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000811_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1622:0.00000000,((2_1106:0.19473075,0_1177:0.03326425):0.02481425,4_1552:0.00251475):0.00146125,3_1337:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..991459a8f472770260f48b68ab3216a324d404de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000812_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1551:0.00963918,(1_1621:0.01396540,(2_1107:0.43837500,0_1178:0.10413600):0.09123513):0.00429710,3_1336:0.01405282);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95662673cb9a26586a190e2c28d567a3df7e1b5a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000813_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1550:0.00643394,(3_1335:0.00943163,1_1620:0.00896437):0.00982898):0.10669625,0_1179:0.14141117,2_1108:0.37031483);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..92abd29ba6590db2622d60db6e1014bce90754f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000815_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1181:0.02780533,2_1110:0.22180367):0.03652620,4_1548:0.00611861):0.00388739,3_1333:0.00996940,1_1618:0.00293360);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9146fab079ac28d79db4b10cab24eafe42aa4a16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000817_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1112:0.10587400,3_1331:0.00619000):0.00760125,(1_1616:0.00325700,4_1546:0.00657800):0.00270075,0_1183:0.01285975);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8db9b3dd99c8c4f2c86819705580b1827c6f546b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000818_tree_id.txt
@@ -0,0 +1,2 @@
+((1_638:0.03241250,(3_384:0.00211575,4_608:0.00059625):0.03477050):0.06571800,0_2249:0.09560025,0_1195:2.82543175);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eed30e6e67b3846ca94bb4d407f6adef6c9cb9f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000819_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1544:0.00705604,1_1614:0.00702296):0.00369900,(0_1201:0.10530583,2_1113:0.09830017):0.05547250,3_1329:0.00783400);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2e1b35337c1ea92b31c5072f93f3d735a1e45c4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000822_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1611:0.01162322,(3_1326:0.00336831,4_1541:0.00359169):0.00044810):0.03714149,0_1204:0.03759183,2_1116:0.12505317);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3af39b79ab507a8fee6543dd1497f41ef99f85a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000823_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1610:0.00337400,3_1325:0.00823200):0.00247387,4_1540:0.00428944):0.20502440,0_1205:0.06540700,2_1117:0.11450800);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0480545e6b56d0f860653e023c1dfd07887f5f4d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000825_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1323:0.02491659,0_1207:0.16844541):0.00827628,(1_1608:0.02197983,2_1119:0.06661217):0.00881046,4_1538:0.00579900);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aad059eb6f84501ad0c8c8497de7a727f7738f93
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000826_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d3a4af669bc68c63f049510734b9f46b4613e23a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000827_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1121:0.00439500,(4_1536:0.00469750,0_1209:0.13985550):0.00204800):0.00366250,1_1606:0.00872075,3_1321:0.00434125);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0aaeaf2e2fd70208e63054b3960bb0c4f8c40e15
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000828_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba2f7fcd9b72e988b182171d954ff0230efb0f6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000829_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd34cb1261b5ebdfcc435397f4792476210a5d88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000830_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1600:0.00644987,(3_1315:0.00195137,4_1530:0.00090563):0.00216763):0.05268113,2_1126:0.11959963,0_1214:0.05932238);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3febf79370e22287fc98ef271a36d2b9d7628676
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000833_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1527:0.00186375,((2_1129:0.26214175,0_1217:0.10736725):0.12305050,3_1312:0.00741700):0.00559150,1_1597:0.01110225);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b53861adaea6432538f0bf7179f4a5fffb59c8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000834_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb0f9f70c5984d284781a5c6a9969ed88958b7ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000835_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1310:0.00393487,4_1525:0.00786013):0.00348462,(2_1131:0.07840717,0_1219:0.01310283):0.01033944,1_1595:0.00212791);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee32327f9f0ceacc33e1fe12eaa4ed55d9a98c36
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000839_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1306:0.00738400,(1_1591:0.00269400,(2_1135:0.49385375,0_1223:0.08973525):0.07311350):0.01073050,4_1521:0.00353000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7580d0b6c5bf191a11689bf41bfa5d51254ea6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000840_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1224:0.04895650,2_1136:0.24530650):0.02136260,(1_1590:0.00841522,4_1520:0.00550578):0.00495123,3_1305:0.01562860);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d3f23aae461f2b91111a22396726651ed58059e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000845_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1585:0.04435589,(3_1300:0.01583248,(0_1231:0.41546900,2_1141:0.57258700):0.29656183):0.06392902,4_1514:0.11144611);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f8270deb8aa5ea42a99b42f38ba12cd1d31086be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000846_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1513:0.00416725,(1_1584:0.00000050,3_1299:0.00000050):0.00002225):0.02786175,2_1142:0.04214075,0_1232:0.02745725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1446d0785a78a9bcd319ce6cd892cfa18e7620ee
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000847_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1143:0.35317938,0_1233:0.08611963):0.06381237,(1_1583:0.00010963,3_1298:0.00820837):0.02802288,4_1512:0.02378512);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91bce0ccef8bb0b8be2df41483bae5e9907d2826
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000851_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1578:0.00764363,(4_1507:0.00676988,3_1293:0.00751613):0.00306238):0.01544588,2_1148:0.07540812,0_1238:0.03902188);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5afd51ad3de19587e6800ec62bf2e6c1ed3cdcb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000852_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1576:0.01712995,(3_1291:0.00705658,(2_1150:0.28855417,0_1241:0.06658983):0.05488603):0.00462642,4_1505:0.00618305);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8176009a25ed7ff309c5bcb5abbfd3e83b3453d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000855_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1288:0.14946166,((4_1501:0.00519700,1_1572:-0.00009300):0.10643875,0_1246:0.12006325):0.00691075,2_1157:0.17611434);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ab66669ae57b564e5235d2a9e38678cc2f10305
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000859_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1476:-0.00003356,3_1271:0.00766156):0.00003356,(0_1266:0.06448467,2_1175:0.01592633):0.00276459,1_1549:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed1dc5c5fbcb4ec6a8988da03f6ad4a4ea363f48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000864_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1470:0.00739041,(3_1265:0.00000050,1_1543:0.00000050):0.00470609):0.04849980,2_1183:0.07167067,0_1273:0.05014033);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8ffb2e3d35e1483454ad7f4ba64609951aea130d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000865_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1464:0.02976462,(1_1537:0.00000000,3_1259:0.00000000):0.00619038):0.10691971,2_1195:0.13807550,0_1275:0.10150450);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c7f02dd887e1b8158076546257b70bc09585fc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000868_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1256:0.01555686,(4_1462:0.00133500,1_1535:0.00133500):0.01236614):0.02420395,0_1308:0.03087000,2_1207:0.42643300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a6077a9d96121f0ecb31a33408c71653fa6d6f43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000869_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1254:0.00263968,4_1460:-0.00006868):0.00121794,(2_1209:0.40737483,0_1310:0.30091317):0.00267284,1_1533:0.00206074);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b08626f58cade96dc118b36997745762d226f61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000870_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1526:0.01297105,(2_1212:0.00405967,0_1318:0.19491933):0.00843002):0.01137795,3_1246:-0.00071142,4_1453:0.00516042);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..059fa355b5979b06ac1717482a5480f4785aee4b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000872_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1451:0.00076050,3_1244:0.00237150):0.00268100,(2_1214:0.01833800,1_1524:0.00373300):0.00316000,0_1320:0.19763600);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ecd67934a3a4033afd7e2a3149b27aed1dbbc81e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000875_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1241:-0.00132450,(4_1448:0.00433250,1_1521:-0.00132450):0.00132450):0.12095100,2_1218:0.11643675,0_1324:0.65569025);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b610d0a58f720c2ccf8e9c481f68d1960abe2da9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000877_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1519:0.00077194,4_1446:0.00681306):0.00356095,3_1239:0.00416975):0.05107532,0_1326:0.03684867,2_1220:0.11603633);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da00660295ec5c3fbbc207106c91f6ff0682b865
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000882_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1233:0.00000000,1_1513:0.00000000):0.00461875,2_1226:0.25187825):0.00017575,0_1334:0.00521125,4_1440:0.00329875);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..397c12e4916a6b60476a322bfe2cc706f24a7853
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000883_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1227:0.23485567,0_1335:0.07012233):0.06283573,4_1439:0.00298020):0.00223480,3_1232:0.00312964,1_1512:0.01076736);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb713abcfbb10bd3a5482b74cfba681e2297add2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000886_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1228:0.00000000,1_1508:0.00000000):0.00193237,4_1435:0.00657863):0.02923388,2_1231:0.05122467,0_1339:0.00543533);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a000d50cff456c3abeabdf9e1e5b59cf6e7b35b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000887_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1434:0.00951679,3_1227:0.00332121):0.00742121,1_1507:0.00388513):0.04772559,0_1340:0.04147633,2_1232:0.15034867);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..63de55cc4dc50075d7bc2d48b88a5793c98d8f2d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000888_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..443af9b8800dd7ce5f3db41faef5d3d4950b2e71
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000889_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1224:0.00696588,(4_1431:-0.00009051,1_1504:0.00417551):0.00213564):0.08315777,2_1234:0.09019050,0_1342:0.03034650);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fba3710877b84a655cd96a7527f7912aa904857
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000891_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1502:0.00000000,((2_1236:0.20320300,0_1344:0.09003200):0.07641300,3_1222:0.00465000):0.00007100,4_1429:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad3f2771e8c9d57119c4317399f17831caa85a2d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000893_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1500:0.00052025,4_1427:0.00228775):0.01928600,3_1220:0.00739200):0.06525750,0_1346:0.06381725,2_1238:0.11223775);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0cf3787fc912054a33db2b68a39b09d65f4c3be9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000894_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1499:0.00044650,((2_1239:0.15738300,0_1347:0.02972300):0.05153050,3_1219:0.00367450):0.00054800,4_1426:0.00142450);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41c140b3efb0ffb168081b308b7246f100814e51
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000895_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1498:0.02417806,4_1425:0.00554494):0.01578688,3_1218:0.02370776):0.07167424,2_1240:0.27458783,0_1348:0.10834817);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40320ac0f555f4bb88daee0597e5433b99912278
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000897_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1216:-0.00065613,(0_1350:0.01394113,1_1496:-0.00065613):0.00065613):0.00065613,2_1242:0.05521513,4_1423:-0.00065613);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6597cf32b6e482a08ace203b74100d8f8551f59a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000898_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1494:-0.00001178,((0_1352:0.16046433,2_1244:0.95279667):0.13774057,4_1421:0.00061772):0.01043328,3_1214:0.00184178);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e517c074af3aad3fd105c20bfa7cd9627b27ff61
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000899_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1420:0.02771759,((1_1493:-0.00845750,0_1353:0.63040850):0.02409050,3_1213:0.03341600):0.01457850,2_1245:0.54478141);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..905c8bc553041cf1ca1add1b2694fee413ef206a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000901_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1418:0.04100375,(1_1491:0.00000000,3_1211:0.00000000):0.04831125):0.13366225,0_1355:0.10364425,2_1247:0.27928275);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23d9a4044b7a7503e010f95072a899d3e8ac03c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000902_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1210:0.00000000,((2_1248:0.15994350,0_1356:0.02815750):0.04089591,4_1417:0.00686224):0.00284976,1_1490:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71cdbfc3ddbc87481fda2670956ec09d2294ee31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000903_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1209:0.06463812,(4_1416:0.00313812,1_1489:-0.00071413):0.06290737):0.07264787,2_1249:0.39885362,0_1357:0.14495037);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca9ec5727951d33bf9f0e404e826f58f1d121d3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000905_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1251:0.12893967,0_1359:0.04878633):0.04579437,(3_1207:0.00177743,1_1487:0.00161657):0.00468346,4_1414:0.01259336);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d40fbe11864ae030a5ad6095727f85b8dbb07c24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000906_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1486:0.00767400,(3_1206:0.00000000,4_1413:0.00000000):0.00843500):0.10149750,0_1360:0.12071950,2_1252:0.10775050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb26090b14d8f857d57f9c58830cbeb55b32f821
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000907_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1204:0.01179308,(4_1411:0.00564568,1_1484:0.02263932):0.01062233):0.12149697,2_1254:0.28752483,0_1362:0.09936917);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95ca4c04b9ef4bf74078a51f483f3f73f95439d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000909_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1256:0.98690450,0_1364:0.22611750):0.04386250,1_1482:0.00825600):0.00524500,4_1409:0.02951175,3_1202:0.00218425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3d88b073e039abe6761960f3b5292876d9081d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000913_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1405:0.00000000,3_1198:0.00000000):0.00000000,1_1478:0.00000000):0.04170900,2_1260:0.14061300,0_1368:0.05441700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..438f8c1e6b16659bb8599cabda7966d535d53779
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000915_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1476:0.00371675,3_1196:0.00265825):0.00406375,(0_1370:0.04149050,2_1262:0.18983650):0.02992825,4_1403:0.00412725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..788f1994214a8342cf41defe8b4d54e50ad372b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000917_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1194:0.00000000,((2_1264:0.50379017,0_1372:0.04094783):0.04169797,4_1401:0.02161941):0.01463959,1_1474:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a81c2f26e236204297c7900ff8103c04b1f90767
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000918_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1400:0.00000000,(3_1193:0.00579425,(0_1373:0.02095025,2_1265:0.39250075):0.03695925):0.00813775,1_1473:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7a36a7086f24b92f639641e6f25f6c663de9b9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000919_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1399:0.00701425,3_1191:0.01364075):0.00341400,0_1374:0.03090550):0.00591900,2_38:0.31090775,1_1472:0.01229525);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da153a37924a65fc5ba4e0b853dd18a621d1d0de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000923_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1378:0.09603338,2_1278:0.48404562):0.20633212,(1_1468:0.00916263,3_1187:0.00930838):0.02045213,4_1395:0.00960337);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa0340c4112b68dc3d0c6408e1403afdd6306ffc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000925_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1466:0.00937391,(3_1185:0.00222334,4_1393:0.00347466):0.00529875):0.05495659,0_1380:0.08047183,2_1280:0.29398817);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf94dd9f50dde098e804a1b0bce59c020107a9bb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000927_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1282:0.49129900,0_1382:0.07556300):0.07442850,(1_1464:0.00144550,3_1183:0.00008750):0.00837400,4_1391:0.00822350);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79257a1aa9d0dcee7f8bcfd01bf5344a26c00ac7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000929_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c9c62fa081dd785e874499da96ef8764897fcf5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000932_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1385:0.00407001,(3_1177:0.00053426,1_1458:0.00511274):0.00140290):0.04387945,0_1388:0.05562233,2_1287:0.19604567);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df65661d9d3f6490745e9445695549b4951c19a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000934_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1434:0.00423563,3_1175:-0.00083663):0.00083662,4_1383:-0.00083663):0.06857512,2_1290:0.24726712,0_1390:0.08384588);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30a11e2c23fae733526b96b9aa2d1e8e554e3672
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000936_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1432:0.01334438,(4_1381:0.00435113,3_1173:0.00242887):0.00921962):0.15574612,2_1292:0.47258963,0_1392:0.20457837);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..245e914d13b4773d45096f36d81e6d47247d6e8e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000937_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1380:0.01183613,(1_1431:0.04491937,(2_1293:0.20444562,0_1393:0.02814737):0.04952362):0.01391912,3_1172:0.00008088);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3cf8d0821ae37e7aefc91b96e61f75db43d688a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000939_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1378:0.00000000,((0_1395:0.17817625,2_1295:0.17696675):0.06950825,3_1170:0.00711025):0.00798975,1_1429:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3fc0927ce18a65ae185a6b0cae6866cf1d0becd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000942_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1298:0.17844350,0_1398:0.17586650):0.11632050,3_1167:0.00000000):0.00000000,4_1375:0.00000000,1_1426:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86872d71d33541759e116a372965b08eff1abd50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000943_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1301:0.03079175,(1_1423:0.01478525,(3_1164:0.00250925,4_1372:0.00099575):0.00945825):0.00277825,0_1399:0.18292725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c91c1cea45b4a8328a9e029436b8e59e7cfcbb3d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000944_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1163:0.00025493,1_1422:0.00235807):0.00580513,4_1371:0.00244376):0.02819757,0_1400:0.03891450,2_1302:0.11742250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcd5081d6c5cd040954ce8f2e1084cf98a8601fa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000945_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1162:0.00000000,((0_1401:0.16090625,2_1303:0.20688875):0.09722075,4_1370:0.01207875):0.01420825,1_1421:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c91494755be06fa3b63dd241e714566a5816261
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000946_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1161:0.00810053,((0_1402:0.12831333,2_1304:0.14847967):0.16009895,4_1369:0.01657586):0.01220014,1_1420:0.02236047);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eca549fdb2b26fae0c6144cdc58b8bc582d2dbf2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000947_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1368:0.00000000,1_1419:0.00000000):0.01337450,(2_1305:0.08761000,0_1403:0.02679100):0.02050500,3_1160:0.00682350);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..935ad731f07c6cc55b08835cc4425d1b19e3727e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000948_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1366:0.01997888,(1_1417:0.02214563,3_1158:0.01603837):0.00791712):0.10371762,2_1307:0.51346238,0_1405:0.08992662);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6efc68b43b4fc6f553bc4869e738f8f6f30ee5a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000950_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1156:0.00014024,((0_1407:0.05730950,2_1309:0.30480050):0.04693593,1_1415:0.00272728):0.01006772,4_1364:0.01286876);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d546024fb0baca17cc8783c930b6fc88676bafe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000951_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1408:0.02966538,2_1311:0.11235362):0.02011188,(4_1363:0.00339512,1_1414:0.00294888):0.00214138,3_1155:0.00638763);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a5179e37bc128907d61bd91b13debe1f3d7a57e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000954_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a0bf1f71a4d00192f152aee1340c923ff7298a2
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000957_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4bb0f283e8b2e26d3d108d25c58658a7ba5c3fb4
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000958_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a92ba545ca9370bdf768373a9270a6b4d842a20f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000962_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd79543c1e59098b1fa596a1a22bcdb1597a58b0
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000965_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..386362c1928be10dc3d6a8aa4fcc4a089b727303
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000969_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..acef062777bd7a42d82cd6280963ddb64e286bb6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000970_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000971_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d175ef9321acd1c0f2f821012ed3777445e0eb96
--- /dev/null
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@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2dd4ba0bd70f630fec39ea2f6487aa3a40e2829
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000972_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000973_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5fd79934fb42b52670ddf70a3a859d0b9a21bdcb
--- /dev/null
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@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa54165215365725a51332493a36f008a4200e44
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000980_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8b56f5f43d96bb1e4c86e0766f3b1f94a6257680
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000981_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70acd2cef7110cdfdae77a7fc9a0c12f5a09ffe5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000982_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84b7ff31a4f9bdd86471c0f5d19c8a6b8519fa86
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000983_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f360bb4aa3ef7783b42d4e9b1e86ea766ccf0f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000985_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2483dd4f6b2ebffe39148047a7b7591bf490225d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000986_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f51732c6280a520c39da074fe34beef1e7368f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000987_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1374:0.02394690,(4_1323:0.00000000,3_1114:0.00000000):0.00673410):0.12270263,2_1355:0.30275833,0_1447:0.09854567);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d7102467eba427c0172d251e4c74a5e57c864cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000988_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1113:0.00245662,((2_1356:0.19240688,0_1448:0.12924712):0.16738912,1_1373:0.02880137):0.03215113,4_1322:0.00916037);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9a7b8d3d44d705fbfdef21bd9c46e513dfc2a542
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000991_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1319:0.00914470,1_1370:0.00560830):0.02054223,(0_1451:0.04933650,2_1359:0.18057650):0.02197723,3_1110:0.01050997);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b6f464eefbce1e4370222697c433b83b4f034cb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000992_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1109:0.00787925,((2_1360:0.28057400,4_1318:0.03787700):0.02579275,1_1369:0.02727525):0.01339625,0_1452:0.01399675);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..368f1595d5c189ef0af19342d1b9eb6d53be2096
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0000996_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1313:0.00193400,(1_1364:0.00000000,3_1104:0.00000000):0.00159100):0.04093450,0_1457:0.02730350,2_1364:0.33557550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4dd377644bb034de8546da68147f3f5f74889483
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001000_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1094:0.00196925,((2_1374:0.10139175,0_1462:0.19745625):0.01138550,1_1355:0.00351150):0.00128750,4_1304:0.00054875);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a30097df4dce2f8b74fe4f7b35c0c1f8d03f3ee1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001003_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1332:-0.00057236,3_1061:0.00645636):0.00057236,4_1286:0.00000000):0.01925685,0_1482:0.01647067,2_1377:0.20035833);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1eccaf8d1683594d851e6f29413da903f1fb68a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001004_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1060:0.00000000,4_1285:0.00000000):0.00860950,1_1331:0.00412650):0.02672000,0_1483:0.10575900,2_1378:0.34208400);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..725b16aa7330de16a90e72f65611da16ec0e9442
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001005_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1484:0.11933600,2_1379:0.46271000):0.07707010,1_1330:0.01274830):0.01589320,3_1059:0.00053175,4_1284:0.00479925);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..80829665b9d6a90b6fb7a5b19b9aa887a3d605a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001007_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1282:0.00783675,(3_1057:0.00571900,1_1328:-0.00024000):0.01152825):0.02264975,0_1486:0.02018300,2_1381:0.21994200);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91913fe3240ab2c0427bd50548cd7338997a95f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001011_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1278:0.00000000,((2_1386:0.33114750,0_1490:0.11038550):0.15527350,3_1053:0.00279050):0.00391350,1_1324:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0d83ef799b02a23993a1e1689a724282d3a603d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001012_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1277:0.00633425,(3_1052:0.03480725,(2_1387:0.11721825,0_1491:0.06399775):0.01595775):0.01431275,1_1323:0.00334575);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..818bd547be18da9c28b5635eb3bce5eb2932a7bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001013_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1276:0.00000000,1_1322:0.00000000):0.00094500,(2_1388:0.11354633,0_1492:0.01268567):0.00621667,3_1051:0.00118700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e86fe1925e3fcbb2b9220840d9d3857e80be751
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001014_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1049:0.01120551,(0_1495:0.14452567,2_1390:0.51877533):0.08117650):0.01407149,4_1274:0.00498047,1_1320:0.00726353);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..816ffc764cc20fa4dd8eff412949ce66e3b33935
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001016_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1272:0.00661777,(3_1047:0.02744393,1_1318:0.00671107):0.00370733):0.12760878,2_1392:0.27066133,0_1497:0.10789467);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..466299b2bb2c789aa6f53a9bc338e2622250b5bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001020_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1043:0.00320321,(0_1501:0.04323067,2_1396:0.14790533):0.01937340):0.00807779,4_1268:0.00000000,1_1314:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02a95bfc0d30dd0819b011a466caf0e3a94290c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001024_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1264:0.00016239,1_1310:0.00302861):0.00296114,3_1039:0.00379509):0.05982055,0_1505:0.32603383,2_1400:0.10807917);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4be93d100396ad4cdbf782d5bbbf8d10a46d3d60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001025_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1308:0.00846400,(3_1037:0.00379825,4_1262:0.00353475):0.00186700):0.05271050,0_1506:0.05862525,2_1402:0.12339575);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e183b35529ad3ff4412096971edeb5a564a260d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001026_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1403:0.43202200,0_1507:0.08630700):0.06937218,(4_1261:0.00602530,1_1307:0.00715870):0.00307660,3_1036:0.00433868);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bacbf47ad2db29ea7edbf87a72fa1c87aea88bf5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001028_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1305:0.00401200,3_1034:0.00088800):0.00384850,4_1259:0.00352100):0.06127500,2_1405:0.16394875,0_1509:0.05281725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..890cce48001a8c12412ebc4083c36eac570a31ea
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001031_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1256:0.02809725,(1_1302:0.01663250,3_1031:0.01883450):0.00338525):0.10460425,2_1408:0.43995425,0_1512:0.16539175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adf7b043848474b2c39d708defacb8fb7b840265
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001035_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1412:0.47199200,0_1516:0.30311000):0.14409075,3_1027:0.05078126):0.06962574,1_1298:0.01822338,4_1252:0.00432062);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9fd92a6893f04a96679a73fe5d845d82e97d24c6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001037_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1250:0.00509850,(3_1025:0.00809225,1_1296:0.00137175):0.00639700):0.02021800,2_1414:0.11385225,0_1518:0.09439675);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b334161b28f22583a1240a9e18b4052ca6087b3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001039_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1294:0.00000000,3_1023:0.00000000):0.00000000,(0_1520:0.03359800,2_1416:0.07212000):0.02451300,4_1248:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6f08304cb6259a82ddcef8d92d41aee7c6f86f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001040_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1021:0.00020030,(1_1292:0.00766536,4_1246:0.00119464):0.00214572):0.02377290,0_1522:0.03259050,2_1418:0.10369250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0e15a82938642e7c2e4c8eaca232abe2a38337a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001041_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1291:0.04475749,(3_1020:0.00000000,4_1245:0.00000000):0.01594251):0.12394600,2_1419:0.35880317,0_1523:0.12608883);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1bf0276b7811da6942fbaf8b8efbd133a3295626
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001045_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_1015:0.00000000,1_1285:0.00000000):0.00133525,0_1528:0.00547975):0.00144975,2_1424:0.09592925,4_1240:0.01302975);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f4ea778823e7a6a95a56f9bf24e57b711e2b561
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001048_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1012:0.00260425,(4_1237:0.00000000,1_1282:0.00000000):0.00110875):0.00150325,2_1427:0.07266475,0_1531:0.01420725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..77cbae6813bbf519da7538bba68a0661e5f97a9e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001051_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1534:0.00000000,((2_1430:0.11006125,4_1234:0.00552175):0.00110825,3_1009:0.00784825):0.00096275,1_1279:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eef80b5a468ac9a6c12bc0d2d3842b358dc13190
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001052_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1535:0.13642312,2_1431:0.15294188):0.03849912,4_1233:0.01372138):0.02052163,1_1278:0.00229463,3_1008:0.00034137);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee0d0f5248b6e346fbc2d191b2564231db85cf4f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001053_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1536:0.02486000,2_1432:0.01161100):0.00150875,(4_1232:-0.00050525,1_1277:0.00162425):0.00105775,3_1007:0.00118325);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..416cc1bff7b3603b08f5f25620795906f555bfcc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001054_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1006:0.00354919,(1_1276:0.00872350,4_1231:0.00726050):0.00536596):0.03963970,2_1433:0.19826850,0_1537:0.09221250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3daccbfaaee44ddaaace05c5c97912bb28489eed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001055_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1275:0.00000000,((2_1434:0.27088250,0_1538:0.06536850):0.05334656,3_1005:-0.00038781):0.00694481,4_1230:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..abc7c60f6b82d9689fe330301cef565a4db3be82
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001056_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1274:0.00111462,4_1229:0.02092938):0.01774462,3_1004:0.03913787):0.34435512,2_1435:0.84406063,0_1539:0.54167238);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0fdd7122b051a713e3cd756c5dc5d8b5353c033
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001058_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1272:-0.00118425,4_1227:0.01208725):0.00118425,(0_1541:0.02182950,2_1437:0.20219450):0.04574025,3_1002:-0.00118425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..22b6c4d53ae70004a48310a9b783b483b6c22afe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001059_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1226:0.00190040,(1_1271:0.01669751,3_1001:0.00193249):0.00097742):0.00452603,2_1438:0.07535900,0_1542:0.02172900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ffbfe86689a33afdcff69c42fbeaa5d0af6e258f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001060_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1270:0.00070729,(4_1225:0.00797131,3_1000:0.00227769):0.01417823):0.02597974,0_1544:0.02482433,2_1440:0.16050067);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17d78528341783a8e2f9e6032806ad9bf7878e0d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001061_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1269:0.00944228,(0_1545:0.05988683,2_1441:0.22083317):0.03837493):0.02306122,3_999:0.00940292,4_1224:0.00301008);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fdbda9adf96f4f9b62486a63ca699bab792d839f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001063_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1265:-0.00010075,0_1549:0.00391175):0.05029925,(3_997:0.00000000,4_1222:0.00000000):0.11480650,2_1445:0.05331850);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..132adffaca19fdd6292a4f644a91833fa5ec7c0c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001064_tree_id.txt
@@ -0,0 +1,2 @@
+((3_996:0.00334300,4_1221:0.00347600):0.15413250,(1_1264:0.00000000,0_1550:0.00000000):0.06305200,2_1446:0.10683000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7ba1ecea459b09f38cd7f1fa5f0547be6d97298
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001065_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1263:0.01175601,((3_995:0.01119083,4_1220:0.01655017):0.33026759,2_1447:0.23314828):0.19842522,0_1551:0.01152399);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5c5ebb47e110a62819cc26f0361d6aab80048b81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001069_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1555:0.03887750,2_1451:0.19348650):0.06193035,1_1259:0.00775955):0.00469445,3_991:0.00000000,4_1216:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f85de53e708b3fd7b5786bcdb723b0677fa4501
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001071_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1256:0.00000000,3_988:0.00000000):0.00000000,(0_1558:0.11981700,2_1454:0.31884000):0.14037500,4_1213:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8f95b37e610a5c46cdaefa179e6e501f0743650a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001075_tree_id.txt
@@ -0,0 +1,2 @@
+((3_984:0.00000000,1_1252:0.00000000):0.00000000,(0_1562:0.06112100,2_1458:0.44301600):0.12996400,4_1209:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..01d1def50403d381c1906a14c216b899dc514268
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001077_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1250:0.00044875,(3_982:0.00000000,4_1207:0.00000000):0.00176625):0.05868875,0_1564:0.07547175,2_1460:0.31742125);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f447dcebf064610de01e39eb01c9f0104ee8e2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001078_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1565:0.07154950,2_1461:0.31714650):0.09274450,4_1206:0.00000000):0.00000000,1_1249:0.00000000,3_981:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b403dc7dec7a3eda9c1d0f3248be421a2621eb7e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001081_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1568:0.03122838,2_1464:0.12551663):0.02610387,(1_1239:0.00196963,3_967:-0.00006063):0.00074238,4_1196:0.00269962);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaa3ea16ae18bc9437b95c5c8ab034b7bccca996
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001082_tree_id.txt
@@ -0,0 +1,2 @@
+(3_966:0.00000000,(1_1238:0.01392625,(0_1569:0.06184475,2_1465:0.39397425):0.09063825):0.01555575,4_1195:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e7e2749f7222b3cebf228110dba18f50784929ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001086_tree_id.txt
@@ -0,0 +1,2 @@
+((1_210:0.01286315,(3_2155:0.00000000,4_211:0.00000000):0.01793185):0.32721472,0_1574:0.26374133,2_599:1.07248067);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d28d8613f29b5ab4890c59c55d7773aaa2a0b39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001088_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1232:-0.00058683,(4_1189:-0.00002581,3_960:0.00374981):0.00185364):0.05975847,0_1576:0.37817250,2_1471:0.25079550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bc272dcfdcffe5d6d15183d5899fa44ad3357f13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001089_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1231:0.00671925,4_1188:-0.00059725):0.00059725,3_959:-0.00059725):0.12550625,0_1577:0.14638325,2_1472:0.36475075);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac2df0316e8b006600d58d049de32fbe82299e88
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001091_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1186:0.00000000,3_957:0.00000000):0.00579775,1_1229:0.01233925):0.09233675,0_1580:0.09469675,2_1475:0.23339325);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9aa0c9c3cd59bc739977c94ecc848346f9ed7e4a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001095_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1479:0.19282475,0_1584:0.06495425):0.07117075,(4_1182:0.00000000,3_953:0.00000000):0.00152725,1_1225:0.00097275);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a0ffb0d4445d662e15713d2c27c395998d358bf4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001096_tree_id.txt
@@ -0,0 +1,2 @@
+(3_951:-0.00160188,((0_1586:0.14038138,2_1481:0.57742862):0.16015537,4_1180:-0.00160188):0.00160188,1_1223:0.00771788);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..985e155069e312123750a351db3609ecf678858a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001098_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1483:0.22276450,0_1588:0.05042150):0.03774950,3_949:0.00000000):0.00000000,4_1178:0.00000000,1_1221:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45960ff82cd3d45540dd0d4f6d384175305b72b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001101_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1591:0.06706417,2_1486:0.15710983):0.09934036,1_1218:0.01771859):0.01044641,4_1175:0.00000000,3_946:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a55610eadb22781901203cac594eb10462af5058
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001103_tree_id.txt
@@ -0,0 +1,2 @@
+(3_944:0.01507775,((0_1593:0.12453575,2_1490:0.31889925):0.09127950,1_1216:0.02044600):0.00364800,4_1173:0.00072525);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b048c755fcc920ee5e02df94eff6d3bc0741f397
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001105_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1492:0.09953400,0_1596:0.15955600):0.09178900,4_1171:0.00000000):0.00000000,3_942:0.00000000,1_1214:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ff8fa26d01dbcd0f72e1622e36ee1f707d891db4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001106_tree_id.txt
@@ -0,0 +1,2 @@
+(3_941:0.00000000,((2_1494:0.09946167,0_1597:0.17131933):0.13109947,1_1213:-0.00009958):0.00189558,4_1170:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa8be210d4c04b1092b7d3e017bf9946b4da6141
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001107_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1168:0.00000000,3_939:0.00000000):0.00398100,(0_1598:0.06742850,2_1496:0.12663450):0.05579200,1_1211:0.00337000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c90851e981d838c2eaeb31a04722c274d8419b9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001109_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1209:-0.00032325,(3_937:0.00000000,4_1166:0.00000000):0.00282625):0.00534025,0_1600:-0.00032925,2_1498:0.00282925);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40bf785654ff2e6133d41cac83cc96c627e0e39b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001110_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1208:0.00000000,(2_1499:0.95352800,0_1602:0.19198400):0.33738000):-0.00000000,3_936:0.00000000,4_1165:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..659038ab4cee9c8bd1e006bb0a8a9cb865daf802
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001111_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1164:0.00088188,3_935:-0.00000888):0.00461313,(2_1500:0.05364037,0_1603:0.04093563):0.02471763,1_1207:0.00929437);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f155bdebfff94a83ef381f7b2652f2b17eb83df1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001112_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6674fba5de23031dc7ebbf531e5c79942936864e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001113_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1204:0.01660650,(4_1162:0.00000000,3_932:0.00000000):0.01006450):0.10469000,0_1606:0.11092700,2_1503:0.36782300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f3a9e5e57b0e0dc2911de4e6eeb3875789fe3b94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001118_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1508:0.08990250,0_1611:0.02564350):0.02205950,1_1199:0.00000000):-0.00000000,3_927:0.00000000,4_1157:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3609a3ead46fdf997e6bc9725a722fec584c036f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001119_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1198:0.00000000,(2_1509:0.13029900,0_1612:0.06254300):0.03472700):0.00000000,3_926:0.00000000,4_1156:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5aa3ec2db1b06fabc45f52f9076d2c15de068d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001120_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45b1b6b6dd4df3609bb05361f29ff40079272690
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001121_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14b8d1137cc1bbce894a2f5549e026bc9d4f6e1a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001122_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1195:0.00000050,((0_1616:0.03197700,2_1513:0.14894900):0.02947100,3_923:0.00207400):0.00367350,4_1153:0.00000050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46f90f4a943604b565bafb19109d74523668489e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001123_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a53d0f94f17d7d97c6ea03aad7f8b5691b78f6b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001124_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c709265324804e3e1f78b638e6336285a00c2e3f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001125_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0ffa507bdb457d7774cd3b8345fc185b6995ff5d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001126_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bac5f35b8c1bca0ca5c2e555df0f644e71daf9de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001127_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d17f69bb7ece7f26dfaf50273f49533b7be302d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001130_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e02371c8ea4efb2eae56570b0a193c931a6563ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001131_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1522:0.23271067,0_1625:0.19215733):0.14357615,(1_1186:0.04022904,3_914:0.02988696):0.00795638,4_1144:0.02012834);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..42993b1fe77a029a4bdb6925bb8b3e83b77fba12
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001132_tree_id.txt
@@ -0,0 +1,2 @@
+((3_913:0.01284022,(1_1185:0.00577085,4_1143:0.00583915):0.00805180):0.12078238,2_1523:0.17035267,0_1626:0.14188733);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2371086c115e3ab8785c982d5e731cf7240847c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001134_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1183:0.00527456,(3_911:0.00000000,4_1141:0.00000000):0.00566444):0.01816769,2_1525:0.39946783,0_1628:0.06281817);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..808033f38f90b0ac3af8772a67e68a8b23414674
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001135_tree_id.txt
@@ -0,0 +1,2 @@
+(3_910:0.02530674,(1_1182:0.17824039,(2_1526:0.56233883,0_1629:0.38074717):0.22154096):0.08131761,4_1140:0.00191226);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20dc52fd10cc02db8853e4b6126d3afe258632a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001137_tree_id.txt
@@ -0,0 +1,2 @@
+(3_908:0.00000000,(1_1180:0.00367166,(0_1631:0.04487267,2_1528:0.17784333):0.04699389):0.00679234,4_1138:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..02c5b73e9198c36d85e179db8b430ba7522adcdf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001142_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1174:0.00188315,(4_1132:0.00656725,3_902:0.00741575):0.00162943):0.02871778,0_1637:0.07324083,2_1533:0.11109217);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2517f72c51666b1bfd873b918325f2ac48089e99
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001143_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1173:0.00500644,4_1131:0.00142456):0.00601526,3_901:0.00043161):0.04786705,0_1638:0.04644000,2_1534:0.15185800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54c245ba2d65ffbb92a4aacefb2973ca1d3912c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001145_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1129:-0.00005400,3_899:0.00330800):0.00643225,(2_1536:0.25010650,0_1640:0.08078450):0.07458125,1_1171:0.00286475);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..475e2d6c99c45f804701c4b256f64b6c670e700b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001146_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1127:0.00000000,1_1170:0.00000000):0.00000000,(2_1537:0.16976250,0_1641:0.05575550):0.08050550,3_898:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e5b8e795154c5e1f3fba5568368d407a47e83c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001147_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1126:0.00000000,3_897:0.00000000):0.00000000,1_1169:0.00000000):0.03105050,2_1538:0.09421550,0_1642:0.04738550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf9d4f4f2d5a1d93a02c7eb54d14c263882fc28e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001149_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1124:0.00525997,((0_1644:0.02192450,2_1540:0.15638350):0.03284128,1_1167:0.00161634):0.00040616,3_895:-0.00041197);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09eef7c6e0e76d0d6276ddd843b5c380cb5cc50a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001150_tree_id.txt
@@ -0,0 +1,2 @@
+((3_894:0.00267863,(2_1541:0.07302288,0_1645:0.01842112):0.02728838):0.00347487,1_1166:0.00083387,4_1123:0.00004313);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0289286146b1d86fd5ba502efee2518b8c2e410e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001151_tree_id.txt
@@ -0,0 +1,2 @@
+((3_892:0.00925810,(4_1121:0.00000000,1_1164:0.00000000):0.01273290):0.01397653,2_1543:0.14831417,0_1646:0.28594683);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a1401832d73c1631397343ceb1bc7a2a1692d94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001153_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1119:0.01020262,(3_890:0.00912662,(0_1648:0.03183663,2_1545:0.20835138):0.03436887):0.00476488,1_1162:0.00561038);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a9c6cd96fdc8191e99d7cb5daed1c4205dc480b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001157_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1158:0.01874376,4_1115:0.00500224):0.00263839,3_886:0.00753985):0.01649347,0_1652:0.01793750,2_1549:0.17019450);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe4dc66462437b5c93f764af517e724ee919ac76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001158_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1653:0.00334963,2_1550:0.02965738):0.01333213,3_885:0.00666587):0.00079113,1_1157:0.02085188,4_1114:0.00316912);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dacf5491a7daa7a8016b99ef996c12a04e38e8bf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001160_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1552:0.12299975,(3_883:0.01217150,1_1154:0.01709850):0.00971375):0.01196475,4_1108:0.01134200,0_1656:0.03082100);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b34b14cbc0b15a27db61284e097b2213e988e4d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001161_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1657:0.01108750,2_1553:0.09856050):0.00421825,4_1107:0.00539175):0.00259625,1_1153:0.01138475,3_882:0.00107025);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..47d54f099adcd344cc645977f35be0c6217a44d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001164_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1150:0.00439681,(3_879:0.00000000,4_1104:0.00000000):0.00011119):0.06313827,0_1660:0.05179567,2_1556:0.09935433);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..00f67bf427674dcfde2cdbd1bc5a08065c867e3f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001168_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1096:0.00106925,((0_1665:0.09624225,2_1563:0.56858375):0.11766500,3_874:0.01142850):0.00811950,1_1146:0.01133275);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4acd42f54985a09f9122ad18767a03a2fa921b8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001170_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1144:0.00000000,((2_1565:0.44134883,0_1667:0.06658017):0.13844234,3_872:0.00504153):0.00463547,4_1094:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..45b88dbf38dfb69448bdfbc53b1e156eac03c263
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001171_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1143:0.00000050,4_1093:0.00000050):0.00271225,3_871:0.00743125):0.06079975,2_1566:0.21117275,0_1668:0.06057625);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..88f3c8d30adf07b8a893b2ee302e5b4752d39d43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001172_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1669:0.02778558,((1_1142:0.00000000,4_1092:0.00000000):0.00415175,2_1567:0.18642325):0.00281825,3_870:-0.00000558);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1bde248fc22344faa5a0400e38be285c1619868
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001175_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1672:0.04208963,2_1570:0.20084837):0.05293637,3_867:0.01359612):0.01067188,4_1089:0.00161487,1_1139:-0.00030987);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4daf45519d9541676dc60064b4dc4d3744079ff3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001177_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1674:0.11727250,2_1572:0.56200650):0.06973650,1_1137:0.00000000):-0.00000000,3_865:0.00000000,4_1087:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e877be586746ca943a06cefe02f5472c662bf32b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001179_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1676:0.02693662,1_1135:-0.00051962):0.00051962,3_863:-0.00051963):0.00051962,4_1085:-0.00051962,2_1574:0.01548763);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..34797274f5fa03f336b3376a2120d117798e8393
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001180_tree_id.txt
@@ -0,0 +1,2 @@
+((3_861:0.00114738,(4_1083:0.00189287,1_1133:0.01120613):0.00184662):0.02883512,0_1679:0.05340888,2_1576:0.16146412);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64fa0f1ab269172ab7654d54120010360e6d40f6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001183_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1579:0.49847313,0_1682:0.01986388):0.02173737,(1_1130:0.01604737,3_858:0.00448163):0.03984787,4_1080:-0.00380037);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..158c0955d13eeff3fd383f076e2ea0da4884397a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001184_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_857:0.00207600,1_1129:0.00098600):0.00170225,4_1079:0.00887425):0.00299025,0_1683:0.01024950,2_1580:0.26897150);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd011a8565f19a6712f88ee58dd39125cc80c13b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001186_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_855:0.00271487,4_1077:0.00019213):0.00026688,1_1127:0.00155312):0.01333837,0_1685:0.02264212,2_1582:0.17831288);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aae7d862e00001f401dab68cb87c8e897fbf2e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001188_tree_id.txt
@@ -0,0 +1,2 @@
+((3_853:0.01373188,1_1125:0.02173512):0.00419337,(0_1687:0.15738263,2_1584:0.20324637):0.13368588,4_1075:0.02619812);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76149038af7dbe9118d4464e171f09c2446531ab
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001190_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_1123:0.00000000,4_1073:0.00000000):0.00106275,3_851:0.00605025):0.05862275,2_1586:0.15619825,0_1689:0.06342175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e9c3be84bb6379cc30202ad39f3c32cb5381db7b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001191_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1072:0.00000000,3_850:0.00000000):0.00000000,(2_1587:0.06920450,0_1690:0.03480350):0.07396650,1_1122:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66cdab9a971855690634b0362a6125e330d021c5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001192_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1121:0.00000000,4_1071:0.00000000):0.00000000,(0_1691:0.03360450,2_1588:0.09451450):0.01707450,3_849:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8d2bfec9c9efef0e218467c3a4818c5dcd5235e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001197_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1066:0.00060825,(3_844:0.00459575,(0_1697:0.06594525,2_1593:0.30177875):0.04481575):0.00607925,1_1116:0.00243075);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57d5d0673c3029e976b2d0b20f8a95fd6c2176a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001201_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1061:0.00000000,1_1111:0.00000000):0.00000000,3_839:0.00000000):0.01177700,0_1701:0.01353400,2_1598:0.09482500);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..137690307d120b6377b39f0884eb772de11d5bc4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001204_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1057:0.00000000,3_835:0.00000000):0.00000000,1_1107:0.00000000):0.00864550,2_1601:0.01170950,0_1707:0.00864550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..03fd4e788fa2c86ff3879397277d1c826df20fb6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001206_tree_id.txt
@@ -0,0 +1,2 @@
+(3_832:0.00000000,((2_1604:0.19009817,0_1711:0.06504183):0.07151003,1_1104:-0.00070742):0.01005342,4_1054:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc831a16a133574e46464322537000bfef7a9c20
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001208_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1102:0.01106700,(4_1052:0.00000000,3_830:0.00000000):0.00946200):0.02540150,0_1713:0.04326650,2_1606:0.05363350);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81b6e1092772a3985791d8ec571db98b4fe0cfa3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001209_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1050:0.00985425,(1_1100:0.00859550,(0_1715:0.15511125,2_1608:0.50047375):0.15791900):0.01923850,3_828:-0.00130325);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..446976122e206c1b2be53a30ff36008f3ebae572
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001210_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1098:0.01560618,(3_826:0.00000000,4_1048:0.00000000):0.00813582):0.07689989,0_1716:0.12086983,2_1610:0.20624717);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3dcb1dfa1de62d16bfec97ac5ea5ab06ff943ec9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001213_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1720:0.00160254,((4_1045:0.00000000,3_823:0.00000000):0.01286450,1_1095:0.00263450):0.00291400,2_1613:0.03885246);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ab3e8046ebf89a18a68b11ab882dadb090a87765
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001216_tree_id.txt
@@ -0,0 +1,2 @@
+((3_820:0.00111275,4_1042:0.00043725):0.00059575,(0_1723:0.01404500,2_1616:0.04225700):0.01103925,1_1092:0.00095425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46f8ee9a0411f3e2be8193d511310929aa4c7cdd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001219_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1039:0.00584337,3_817:-0.00048437):0.00048437,1_1089:-0.00048437):0.05715187,0_1726:0.09495788,2_1619:0.19270912);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ca597be4ddef5ddcada1a9655708c97246e13342
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001223_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1035:0.00037200,(3_813:0.00000050,1_1085:0.00000050):0.00252650):0.04272100,0_1730:0.05258050,2_1623:0.19615050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cd9acc7b7644f185215411d9bef0b096085620a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001224_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1034:0.00053340,(1_1084:0.00000000,3_812:0.00000000):0.00291160):0.05283563,0_1731:0.07645617,2_1624:0.25991183);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb51c4c2bf1a57575f570262c13d48e79b65c042
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001229_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1736:0.03997037,2_1629:0.13964662):0.03171388,3_807:0.00223513):0.02142637,4_1029:0.00060137,1_1079:0.00140763);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..56486aeb6fbdbf0073b4935b73b4e4fb88d029e1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001230_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1630:0.09982850,0_1738:0.03190950):0.02807575,3_806:0.00386625):0.00206625,4_1028:-0.00005975,1_1078:0.00153875);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a4bd34f33fcd83ec1b0cb95a5856f06c2ad39ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001232_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1026:0.00000000,(3_804:0.00269195,(0_1740:0.02260967,2_1632:0.08350233):0.03685832):0.00334405,1_1076:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..355a47909ba05a3e26ae4e55d2577ae9eab68296
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001233_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1025:-0.00051168,1_1075:0.01098968):0.00579405,(0_1741:0.04588567,2_1633:0.21543433):0.03666498,3_803:0.00445163);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..79c4cb0f118c9d2b9b5ebefaacbaf83c1255a77c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001234_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_802:0.00000000,4_1024:0.00000000):0.00000000,1_1074:0.00000000):0.05787900,0_1742:0.05642500,2_1634:0.18182600);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0332f684dbce5b21388ca66f8059adf3832d8de0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001236_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1746:0.02943010,((3_798:0.00000000,4_1020:0.00000000):0.01251300,1_1070:0.01223500):0.00191150,2_1638:0.18470390);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..889911a3cdc4113f9db22a6566e7ea965fc68aa9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001239_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1067:0.00000000,4_1017:0.00000000):0.00081075,(0_1749:0.12069375,2_1641:0.27141725):0.09309025,3_795:0.00637025);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..253a8404d9e3c17bb8baa4078a971eb203c8c859
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001240_tree_id.txt
@@ -0,0 +1,2 @@
+(3_792:0.00000000,((0_1751:0.34818900,2_1643:0.90143300):0.29099098,1_1064:0.02579295):0.00628005,4_1013:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..de52fdb7110b6318df7b180435a30dbb61a772fe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001241_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1063:0.01300590,(3_791:0.00000000,4_1012:0.00000000):0.02384110):0.09043347,2_1644:0.49749817,0_1752:0.16946783);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2f2c5d7d6ec537afb197195502bc577d838c7f97
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001243_tree_id.txt
@@ -0,0 +1,2 @@
+((3_789:0.00000000,1_1061:0.00000000):0.00000000,(2_1646:0.27173600,0_1755:0.06552900):0.04347000,4_1010:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..413ce3079352b6928ac08fafb841a8add3631ea9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001244_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1008:0.00000000,3_787:0.00000000):0.00388722,(0_1758:0.11571517,2_1648:0.48208783):0.13306176,1_1059:0.00390378);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28c7f7fc22a37b07b0cbbfa43cdf2b0e6aa542c9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001245_tree_id.txt
@@ -0,0 +1,2 @@
+(3_786:0.00191182,((2_1649:0.45357133,0_1759:0.26857367):0.26893284,1_1058:0.00761953):0.02169947,4_1007:-0.00065482);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e852778277345cb3015f31b8d22e4724445e2174
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001248_tree_id.txt
@@ -0,0 +1,2 @@
+(3_782:0.02114764,((2_1653:0.28380283,0_1764:0.08894717):0.10846026,4_1003:0.02347729):0.00687721,1_1054:0.00551636);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59e3179316453e3f223e03722c4610393f073e43
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001250_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1052:0.00000000,(0_1766:0.06326650,2_1655:0.11338950):0.07633650):0.00000000,4_1001:0.00000000,3_780:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5e94665ba685e4be72a9342c75304f824c761d13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001251_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_1000:0.00000000,1_1051:0.00000000):0.00000000,3_779:0.00000000):0.05612400,0_1767:0.11860600,2_1656:0.12819900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17bb2cc3dbe71e0762f7fd0ded2324e446292840
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001260_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1778:0.02690800,2_1665:0.25370600):0.02298200,(3_770:0.00000000,4_991:0.00000000):0.01627750,1_1042:0.01106350);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b2393530b611757c29d3d10a7c12e0eac392603
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001265_tree_id.txt
@@ -0,0 +1,2 @@
+((4_986:0.00000000,3_765:0.00000000):0.00382516,(2_1670:0.15600350,0_1783:0.03811750):0.02331278,1_1037:0.01282184);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9688282c9ff47db316d9bb4ab91c295e9392ab91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001267_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1035:0.00277950,(0_1786:0.05781850,2_1672:0.09406750):0.02015300):0.00432250,4_984:0.00000000,3_763:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b5780ec1a1f8d6d557e3859dd9b2be3310cfa8d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001272_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_745:0.00296045,1_1017:0.00116355):0.00204005,4_964:0.00099688):0.04502554,0_1792:0.04195883,2_1681:0.08640117);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa069364169bb398f68b0eb01a65a61173ff0a08
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001274_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1683:0.20963837,0_1794:0.08185163):0.06918837,(1_1015:0.00996387,4_962:0.00617812):0.00841137,3_743:0.00901813);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8c69920fc1cc468ac6809cc1d36076ce3b330917
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001277_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1012:0.00374706,((2_1686:0.18146767,0_1797:0.06463633):0.05442977,4_959:0.01093931):0.00591369,3_740:-0.00031406);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4af82bc9b84792323f787df82b7fd0ae58572c6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001279_tree_id.txt
@@ -0,0 +1,2 @@
+((3_732:0.01115100,(4_951:0.00120150,1_1010:0.00041550):0.00679350):0.03275450,2_1688:0.12261300,0_1799:0.04407600);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa7f7ce17a48d61b6bc5b8f9be88fbf956ff2236
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001282_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1007:0.02015053,(2_1691:0.21388517,0_1804:0.06203583):0.07390934):0.00722247,3_729:0.00428324,4_948:0.00785476);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eaae782db1587bdb385c22566fa2d62342d6e01d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001288_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1811:0.01354371,2_1700:0.02472429):0.00328309,4_938:0.00120414):0.00824808,3_718:0.00445767,1_996:0.00043133);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ff359ee1e94712bca0724b849817fa8bef1f524
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001290_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_994:0.02641562,4_936:0.00235038):0.00111312,2_1702:0.00260388):0.02566562,0_1813:0.00479312,3_716:0.00702288);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a64eacc5df686bf2c5005cc235afc2be0bddd847
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001291_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1814:0.01955366,((1_991:0.00264883,4_935:-0.00059383):0.02720358,3_715:0.02922125):0.00612125,2_1703:0.01888834);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c6cf75e7c8193fc12e27871e4131d11a9707074
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001293_tree_id.txt
@@ -0,0 +1,2 @@
+((4_930:0.00231625,(3_710:0.00399925,1_986:0.00365775):0.00227775):0.02872625,0_1822:0.02616250,2_1708:0.06369850);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..09a166a47ca9a63cf59b37ec07de3b8cc6f1ee19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001296_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1714:0.06833562,1_983:-0.00057263):0.00057263,3_707:-0.00057263):0.00057263,0_1825:0.02289262,4_927:-0.00057263);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f1a1784959df6c09b469e4a328351d02582371a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001297_tree_id.txt
@@ -0,0 +1,2 @@
+((4_926:0.05242450,1_982:0.00001350):0.01328050,(0_1829:0.09799025,2_1721:0.24688175):0.11994750,3_706:-0.00357250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d12b58f877b076f248f0bece6429b9e6511ea972
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001298_tree_id.txt
@@ -0,0 +1,2 @@
+(1_980:0.00255983,((0_1830:0.51742617,2_1725:0.97699183):0.20239010,4_924:0.01546579):0.00809471,3_703:0.00730017);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..adb90d88a92e4344fc9ea33f35ebda363cf205de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001299_tree_id.txt
@@ -0,0 +1,2 @@
+((4_923:0.03642562,(1_979:0.00939587,3_702:0.00358713):0.07433488):0.09803987,0_1831:0.11350612,2_1726:0.49800587);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2cb13bf83ca2bcf23e69c48e1c0e1e2fb07af660
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001300_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_978:0.02154671,3_701:0.01284529):0.01106231,4_922:0.00810904):0.10093137,2_1723:0.47130650,0_1832:0.15029250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e39f3c2a6b9cd817416a21ca0ab13b61456ba3c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001301_tree_id.txt
@@ -0,0 +1,2 @@
+(1_977:0.00220175,((2_1724:0.13302600,0_1833:0.06776800):0.01415725,3_700:0.00446675):0.00279625,4_921:0.00864725);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b33410b04d04212011673da59cb4b40e5205a394
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001304_tree_id.txt
@@ -0,0 +1,2 @@
+((4_912:0.01466491,(1_969:0.00000000,3_692:0.00000000):0.03559709):0.15648714,0_1844:0.21317583,2_1770:0.32748817);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..757192697bf62b1e5973b56c4d7bedf7ac6a09ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001305_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1845:0.05741900,2_1771:0.10204900):0.04540400,(1_968:0.00000000,3_691:0.00000000):0.00979650,4_911:0.00501850);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8336fcfd2d3724034d4f6187addeca0d485e2b7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001308_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_965:0.00039048,3_688:0.00020652):0.00813547,4_908:0.00216675):0.04705013,2_1775:0.22290550,0_1848:0.05612550);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..30187f810733d2df3c4a2c2d31b350e73b68e44e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001309_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_687:0.00298941,4_907:0.00833959):0.00334952,1_964:0.00251078):0.06766103,2_1776:0.19475483,0_1849:0.05048917);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1fbbacd662a88602215dd37c47778bdb4385f8ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001311_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1851:0.00000000,(2_1778:0.06414400,3_685:0.00000000):0.00000000):0.00000000,4_905:0.00000000,1_962:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..49908b25902910f67fb76e6fe7f8d36a5575cc24
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001312_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1779:0.03479050,0_1852:0.01061850):0.01049050,3_684:0.00000000):0.00000000,4_904:0.00000000,1_961:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1f4148ef36cace723521349df16baa1589b0083b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001314_tree_id.txt
@@ -0,0 +1,2 @@
+((4_902:0.01541255,(1_959:0.00000000,3_682:0.00000000):0.01053645):0.11207035,2_1799:0.20466850,0_1854:0.12010650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2ad673ffba86ed9fdf233e2e294411d341d86a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001316_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_956:0.00293675,3_679:0.00017025):0.00135311,4_899:0.00368329):0.05664340,0_1856:0.22713217,2_1802:0.12639183);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27d1e871a35f369856f8174b19bad7b667f328e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001317_tree_id.txt
@@ -0,0 +1,2 @@
+((1_955:0.00310912,(3_678:0.00253988,4_898:0.00361712):0.00074388):0.01060337,2_1803:0.09738163,0_1857:0.01585737);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9aaae1630dc10fffb7e115f72f1f980c4cfbf426
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001320_tree_id.txt
@@ -0,0 +1,2 @@
+((3_673:0.00184286,(2_1808:0.01165717,0_1862:0.01656983):0.02277679):0.00138114,4_893:0.00000000,1_950:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb3f4dee051581832a82536484f30aed7a424d8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001322_tree_id.txt
@@ -0,0 +1,2 @@
+((1_948:-0.00000550,(4_891:-0.00000550,3_671:0.00399350):0.00000550):0.00000550,2_1810:-0.00000550,0_1864:0.00798650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5b1f0def386f16b080618c76001bd55e3f905f6a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001324_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1812:0.00120124,((4_889:0.00000000,1_946:0.00000000):0.00370750,3_669:0.00107550):0.00022850,0_1866:0.43962376);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..830f8db1e6f9769cb14f5ef070a2d0919ef0b0de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001325_tree_id.txt
@@ -0,0 +1,2 @@
+(1_945:0.00000000,(3_668:0.00634600,(2_1813:0.00755800,0_1867:0.01917000):0.02609300):0.01669400,4_888:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e0672857759a8a9af665cef711fbbc7ea1b0f09
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001326_tree_id.txt
@@ -0,0 +1,2 @@
+(1_944:0.00000050,((0_1868:0.17405925,2_1814:0.00469575):0.00328625,3_667:0.00390025):0.00208125,4_887:0.00000050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3c15eb660f7716056d8c8094f8988f223c431e5b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001327_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1869:0.14504138,(2_1815:0.00469712,(3_666:0.00171487,1_943:0.00164213):0.00176688):0.00110337,4_886:0.00127862);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c53c56ad5f66c901b93ecd9f44c6eadc381b7ad1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001329_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_884:0.00000000,1_941:0.00000000):0.00000000,3_664:0.00000000):0.33496750,0_1872:0.09108050,2_1818:0.07228450);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0226cb3d3104a3d4f5188dc216c8ba8bef25785
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001330_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1873:0.01467850,2_1819:0.03928950):0.02795950,3_663:-0.00000000):0.00000000,1_940:0.00000000,4_883:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bbce2af53b0e294b616c0bb170ac4a3a053ce6d5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001332_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1875:0.00572550,((3_661:0.00000000,4_881:0.00000000):0.00674525,1_938:-0.00048525):0.00225975,2_1821:0.07868350);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3cb8ecfc5ba876f30140bd42e207545c538c3ca
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001333_tree_id.txt
@@ -0,0 +1,2 @@
+(4_880:0.00549190,(3_660:0.00412507,(0_1876:0.03698733,2_1822:0.14199267):0.00884169):0.00184293,1_937:0.00706210);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08b0449295d41cad5f4ead24d95e77b8b687aab2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001335_tree_id.txt
@@ -0,0 +1,2 @@
+(4_878:0.00176582,(1_935:0.01375934,(0_1878:0.10399333,2_1825:0.25920567):0.08889678):0.00353366,3_657:0.01860818);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..130f668603c767991282995067d62da4d9533a73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001336_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_653:0.01059842,1_931:0.01517258):0.00376700,4_877:0.00818549):0.04090900,0_1880:0.04229183,2_1827:0.15840917);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c9c3ec71a35a13b499c83347ac9108cfb6c9d2c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001338_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1883:0.08968355,3_650:0.01153845):0.01212142,2_1831:0.12592211):0.01893083,1_928:0.00468250,4_874:0.01655650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3992565594dce6a701fff77f2a8d3d8f2b448b3e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001339_tree_id.txt
@@ -0,0 +1,2 @@
+((1_927:0.00265275,(3_649:-0.00000575,4_873:0.00091275):0.00007275):0.00435675,2_1835:0.07749100,0_1885:0.01540700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf1bbc43a71bd12aec9bba392119138e9eb4a1d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001342_tree_id.txt
@@ -0,0 +1,2 @@
+((3_646:0.00558338,(1_924:0.00430687,4_870:0.01431513):0.00399962):0.07924762,2_1838:0.20213337,0_1888:0.36999862);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7a9224e2893b1934068711274df99c6c3ecbeb73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001343_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1889:0.04282187,2_1840:0.19982813):0.04217087,(1_922:0.00500863,4_868:0.00801438):0.00307438,3_644:0.00086162);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..90cdaacf9351d5751e15030eb8966a36bdf259c8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001344_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1890:0.08917788,2_1841:0.05748113):0.01118837,4_867:0.00605012):0.00255888,3_643:0.00642838,1_921:0.00215663);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16ce573db7d312182b27df3e56f16439676e6785
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001345_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1848:0.03137900,0_1948:0.09840300):0.00579944,1_913:0.00665333):0.00054117,3_641:-0.00221082,4_861:0.00699582);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8701f716a940b06e9e4c33da60945833bbcf57bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001346_tree_id.txt
@@ -0,0 +1,2 @@
+(4_569:0.00000000,((4_860:0.13382275,0_1952:0.01439625):0.33931925,2_2139:0.12376625):0.03111575,1_612:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b23b34ce6d6577f2fdbb1ea3f93479a61dd4e699
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001347_tree_id.txt
@@ -0,0 +1,2 @@
+((0_1953:0.10742500,2_1849:0.17703100):0.05040550,(1_909:0.00499250,3_637:0.00290150):0.03062350,4_859:0.02102200);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b5d9ea1685865e00f83ae4deda861d46c4eba11
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001348_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1954:0.12589025,2_1851:0.03999475):0.01051000,4_857:0.00662250):0.00205600,1_908:0.00325000,3_636:0.00812300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..854670d25ffe8d73db1562774b1f27d87a41c4a0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001352_tree_id.txt
@@ -0,0 +1,2 @@
+(4_853:0.00386950,((0_1959:0.04611200,2_1855:0.85160600):0.12544025,3_632:0.02184475):0.01471025,1_904:0.03238250);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe47309a7de0fe4f12bd891bfacc291f705d883a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001354_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_1961:0.00603413,3_630:0.01310987):0.00406205,4_851:-0.00102408):0.00496651,1_902:0.00763350,2_1857:0.26760650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2a7034c37b806ec1aec538574c39df9c1201e9d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001355_tree_id.txt
@@ -0,0 +1,2 @@
+((1_901:0.00160425,(4_850:0.00000000,3_629:0.00000000):0.00421175):0.01956775,2_1858:0.07291725,0_1962:0.02031675);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a92b3020d7b6ff78afc9ace01fea53b24a280d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001356_tree_id.txt
@@ -0,0 +1,2 @@
+(4_849:0.00000000,((2_1859:0.10053600,0_1963:0.04491300):0.03223750,1_900:0.00442050):0.00080150,3_628:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b6a3bc4f630eff104438f71328698ab1af9bf401
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001358_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_626:0.00000000,1_898:0.00000000):0.00000000,4_847:0.00000000):0.00522350,2_1861:0.05505550,0_1966:0.00270650);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..96d087f22ebbd5810a7d2c8a9b9da46a84b9a6a9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001363_tree_id.txt
@@ -0,0 +1,2 @@
+((3_621:0.01498077,(1_893:0.00000000,4_841:0.00000000):0.00426523):0.15955392,2_1870:0.51781867,0_1972:0.10147233);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a70583fadd0a5e83605e544329bf911e3887f4fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001364_tree_id.txt
@@ -0,0 +1,2 @@
+(1_892:0.00000000,(3_620:0.01028037,(0_1973:0.06579567,2_1871:0.25044433):0.03696679):0.00053063,4_840:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6e6689f7028bfa336286136862b0133aba32748c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001365_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1872:0.01675525,0_1974:0.05505475):0.00606350,1_891:0.00179800):0.00105750,3_619:0.00077925,4_839:0.00003575);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e893e15f0093de11b1af6f866af8347c334b348f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001367_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_889:0.00911918,4_837:0.00081282):0.00734999,3_617:0.00376151):0.05485501,2_1874:0.16711217,0_1976:0.09841083);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3af0ed4aa19b0a33c4c2626ed69ff2014a5e633
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001368_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_888:0.00065887,4_836:0.00155913):0.00027129,3_616:0.00050023):0.03013705,2_1875:0.11230167,0_1977:0.08358633);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b4a1414670241670effc8a29d10a36958d25747
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001369_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_887:-0.00009612,3_615:0.01334112):0.00009613,4_835:-0.00009613):0.01684362,2_1876:0.01684263,0_1978:0.00643137);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c2c5ee1addaef339492b1c44859f19b2d466eed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001371_tree_id.txt
@@ -0,0 +1,2 @@
+(3_613:0.00000000,(4_833:0.00288100,(2_1878:0.22871600,0_1980:0.04571300):0.03204600):0.00431600,1_885:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55643d29639f58e8e8a85c222bc47ea10beac653
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001372_tree_id.txt
@@ -0,0 +1,2 @@
+(4_832:0.02193582,(3_612:0.01086968,(2_1879:0.36094983,0_1981:0.11070617):0.11236573):0.00513332,1_884:0.02303418);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0af26afbe4f2e6e5afb09579d1dd1fe0e7fd19e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001374_tree_id.txt
@@ -0,0 +1,2 @@
+((3_610:0.00512858,(4_830:0.00000000,1_882:0.00000000):0.00516242):0.08972453,0_1984:0.07634800,2_1881:0.25693900);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..43cadc22cfb03a952af3cbe4748c3586d0f3594c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001376_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_880:0.00000000,4_828:0.00000000):0.00000000,3_608:0.00000000):0.05202400,2_1883:0.15097500,0_1986:0.00511300);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d6acc20aa153dd60f02926a57f542216b41273f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001377_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_879:0.00000000,4_827:0.00000000):0.00000000,3_607:0.00000000):0.08231650,0_1987:0.10550750,2_1884:0.37170050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cd0576dec986e11bc92fb20679e3a54342b75d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001378_tree_id.txt
@@ -0,0 +1,2 @@
+((1_878:0.00000000,4_826:0.00000000):0.00000000,(0_1988:0.21598850,2_1885:0.63590150):0.10016350,3_606:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed2e5639c1b4b0f97ddc55e173982c6beec234e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001380_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d401463797b302eddd30a1c15290000cdec14b4b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001381_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba3ed59945fae88f61c50005e80ebf4f254f915d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001382_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3b19f3c9cae945542c3128ecdd182e65a2be772c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001385_tree_id.txt
@@ -0,0 +1,2 @@
+(3_599:0.00097325,(1_871:0.00935200,(2_1892:0.09462075,0_1995:0.02000325):0.02368900):0.00136850,4_819:0.00107775);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c14c00acbb8ed8c3ab0873ef87ef024910964111
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001386_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1893:0.16390950,(0_1996:0.00000000,1_870:0.00000000):0.12372750):0.06900550,3_598:0.01391200,4_818:0.01318500);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa6bc6d090db26d2fd2a4dcb3f5a15a90b8cb538
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001389_tree_id.txt
@@ -0,0 +1,2 @@
+((1_862:0.00495950,3_593:0.00510950):0.16015125,(4_813:0.79621050,2_1896:0.50977250):0.25204575,0_1999:0.19314475);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e3bd1dad747458a261c093d9572770ad1aedc8e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001392_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_852:0.00005075,3_583:0.00117825):0.11408275,2_1901:0.11576875):0.08540625,0_2008:0.00519950,4_810:0.00646050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..236c28770fa06d7dce3d5ce706d82b01e43825a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001393_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1903:0.30522250,(1_849:0.00710275,3_580:0.00688325):0.05590550):0.08374500,4_808:0.02303725,0_2010:0.04458175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b80bd456aff1473d81b4db42882ac0712a66f8d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001394_tree_id.txt
@@ -0,0 +1,2 @@
+(4_807:0.01328023,((2_1904:0.56094067,0_2011:0.10521133):0.12770509,1_848:0.01622327):0.00037273,3_579:0.00785977);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..767bba7220e79b50bbc0ce88055a38c29e7fee18
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001395_tree_id.txt
@@ -0,0 +1,2 @@
+(4_806:0.00983425,((0_2012:0.05762850,2_1905:0.18196950):0.05574350,3_578:0.00599850):0.00151450,1_847:0.00271075);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..76743d97130b7d53fd8632e6d8b0c1e4c1ebe902
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001396_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2013:0.03961675,2_1906:0.17330825):0.00308425,(4_805:0.00000050,3_577:0.00000050):0.00717578,1_846:-0.00009228);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..32b168003c8598d5d2a77b9f22da6d73c81cad91
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001397_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1907:0.03864650,0_2014:0.00751550):0.00769450,1_845:0.00000000):0.00000000,3_576:0.00000000,4_804:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e1a0c7524c728f7d870ffc3ff637e24765c70d9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001398_tree_id.txt
@@ -0,0 +1,2 @@
+((3_575:-0.00050187,(4_803:0.00684488,1_844:-0.00050187):0.00050187):0.03505838,0_2015:0.02817963,2_1908:0.25308038);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d3c510a758822f854d900bba7fc64f1fcbaff25
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001402_tree_id.txt
@@ -0,0 +1,2 @@
+(4_799:0.01130221,((0_2019:0.03900500,2_1912:0.21295800):0.05881986,1_840:0.00763059):0.00195791,3_571:0.01686879);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12affb5a4f13f586829e0517b168bc83309f4ac9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001403_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_798:0.00773245,1_839:0.00537655):0.00321381,3_570:0.00702973):0.02193519,2_1913:0.16761500,0_2020:0.07413400);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be56dfd53939f6f3406ced9448c23718463968fb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001404_tree_id.txt
@@ -0,0 +1,2 @@
+(3_569:0.01488738,((0_2021:0.13995537,2_1914:0.67809063):0.09421687,1_838:0.03891413):0.00914588,4_797:0.01527263);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..06320daed7f765a6f07a1153ce237a665cd77dde
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001407_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_835:0.00096338,3_566:0.00235262):0.00459163,4_794:0.01008837):0.04725963,0_2024:0.05254187,2_1917:0.14924013);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..818006f8d572091178ebaa30801262bd9612be34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001409_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1919:0.22734700,0_2026:0.07216100):0.13272977,(4_792:0.00695601,1_833:0.01863799):0.00073428,3_564:0.00542020);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0a89b1c67a62b29b196a95fb1e7c8e35186025ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001410_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_832:-0.00050944,4_791:0.00388244):0.00025598,3_563:0.00250545):0.01524390,2_1920:0.04071667,0_2027:0.01604133);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..db1ecc92666f65ef6b9f0654b4003138537752ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001414_tree_id.txt
@@ -0,0 +1,2 @@
+((1_828:0.00284375,3_559:-0.00019475):0.00538250,(2_1924:0.13044600,0_2031:0.07858000):0.04507750,4_787:0.00260050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c4b9ef03128285b3577edba6f89f3f9f6b0a426a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001416_tree_id.txt
@@ -0,0 +1,2 @@
+(3_557:0.00769550,(1_826:0.00583683,(2_1926:0.17266750,0_2033:0.20745350):0.07367711):0.00184667,4_785:0.00578950);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66839316a0280c486a6a424a3cc5975a96562058
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001421_tree_id.txt
@@ -0,0 +1,2 @@
+((4_778:0.00000000,3_550:0.00000000):0.00248633,(2_1939:0.02800517,0_2040:0.05129983):0.01131506,1_819:0.00572167);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cf9e5a8d841db0a60592a4869db1b4d09adbdbf
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001422_tree_id.txt
@@ -0,0 +1,2 @@
+((4_777:0.00000050,3_549:0.00000050):0.00139540,(0_2041:0.02480533,2_1940:0.15320767):0.05617837,1_818:0.00293610);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46fce74b953657c0b1363611968b76d36dc0fc48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001426_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_543:0.00000000,1_802:0.00000000):0.00000000,0_2046:0.00000000):0.00061100,4_772:0.00571800,2_1944:0.07942600);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d4c8320f4498da100a66a33c9e9367569e2be5f4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001428_tree_id.txt
@@ -0,0 +1,2 @@
+((1_798:0.00000000,3_539:0.00000000):0.00200938,(2_1946:0.03408650,0_2048:0.06986950):0.02734537,4_767:0.00382962);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7e6066cd03f131b06a064f9356a3c6635107bb13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001430_tree_id.txt
@@ -0,0 +1,2 @@
+((3_537:-0.00040869,(0_2050:0.01725500,2_1948:0.10739900):0.04399477):0.00040869,1_796:0.00000000,4_765:0.00300800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eae1b5a6d8d2556a9041927acf775897e2ea324d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001431_tree_id.txt
@@ -0,0 +1,2 @@
+((3_536:0.00000000,1_795:0.00000000):0.01392292,(2_1949:0.35563667,0_2059:0.11105233):0.10763569,4_764:0.00705508);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e912c91d98fa928c26049bbc57e3f534eefc0eec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001432_tree_id.txt
@@ -0,0 +1,2 @@
+((4_763:0.00518500,(2_1950:0.12645350,0_2060:0.04497650):0.05715000):0.00289900,3_535:0.00000000,1_794:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..957fcabcf50db51959265afab0eaa9b3089a9325
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001436_tree_id.txt
@@ -0,0 +1,2 @@
+((1_790:0.00091075,4_759:0.01703725):0.00195950,(0_2064:0.18861450,2_1954:0.27763050):0.21270850,3_531:0.00150650);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e4bc05c32954dd618ac53ed2bc930ffc128e7c59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001440_tree_id.txt
@@ -0,0 +1,2 @@
+(4_755:0.00174900,((2_1958:0.16242775,0_2068:0.05410125):0.06863600,1_786:0.00180300):0.00672100,3_527:0.00272000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9d855fff7073e851bdbc4713af52286ea8c6506b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001442_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2070:0.13998667,2_1960:0.41647733):0.14512571,(4_753:0.00119066,3_525:0.00302034):0.00537620,1_784:0.00255536);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..077a4226921b05504c366173df7d1831925f77a5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001443_tree_id.txt
@@ -0,0 +1,2 @@
+((3_524:0.00000000,(2_1961:0.28171550,0_2071:0.06140850):0.05663850):-0.00000000,1_783:0.00000000,4_752:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1bd586af2103f8492c9b05a5bacdc097f0366d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001444_tree_id.txt
@@ -0,0 +1,2 @@
+((3_523:0.00000000,1_782:0.00000000):0.00000000,(2_1962:0.18830100,0_2072:0.01509100):0.00612400,4_751:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bd8a7377582730c0d9b63dd84effce2d5c2d0f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001445_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2073:0.03389509,(1_781:0.00187550,(4_750:0.00000000,3_522:0.00000000):0.00381950):0.00263450,2_1963:0.42876291);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a07160577d9ca78eafd63048ec985efc025bd56f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001449_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1970:0.07224717,0_2078:0.07509083):0.07101240,(4_743:0.01200221,3_516:0.00591279):0.00370432,1_776:0.01488101);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60e2b87cf12ec435cc1553ac3120faa919620572
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001450_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_515:0.00763600,4_742:0.00263800):0.00475502,1_775:0.01336644):0.10965636,0_2079:0.09838483,2_1971:0.23695017);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b8acc9508ab9b4ff52df653d3b41be44135b8437
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001451_tree_id.txt
@@ -0,0 +1,2 @@
+(3_514:0.01358975,((2_1972:0.32608425,0_2080:0.13310175):0.13617250,1_774:0.02805850):0.04899750,4_741:0.01190725);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0e9b59997e21d9a04a02744b36538feac6563df3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001455_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2084:0.21298213,2_1976:0.95127388):0.17286737,(3_511:0.02229363,4_738:0.00906537):0.02140738,1_771:0.00817612);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6d7165cc3768de48b29157a883b10830a1ef3d57
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001456_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1977:0.11424208,((4_737:0.00000000,3_510:0.00000000):0.01046400,1_770:0.00421200):0.00422300,0_2085:0.01384892);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57603b000eecb2156dc5920a4fb083704dfb5de0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001458_tree_id.txt
@@ -0,0 +1,2 @@
+((4_735:0.00329739,(1_768:0.00000000,3_508:0.00000000):0.00030661):0.02829330,0_2087:0.01167483,2_1979:0.06084817);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ce9c4f3a010f82880b3102a486b3a5a2fd8e04f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001463_tree_id.txt
@@ -0,0 +1,2 @@
+((4_730:0.00251706,(3_503:0.00000000,1_763:0.00000000):0.00041294):0.01110202,0_2092:0.01619400,2_1984:0.16057800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2770747471747e0d7e597a4e0e9c2c31ec5059a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001465_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_1986:0.25533050,0_2094:0.08482050):0.10270392,4_728:0.00580827):0.00891773,1_761:0.00000000,3_501:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..620f69432df55b4593d0924940238ef0060899df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001466_tree_id.txt
@@ -0,0 +1,2 @@
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+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..921c7a3554b7b4082f1f5fceebbbf5e1a2da5862
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001467_tree_id.txt
@@ -0,0 +1,2 @@
+(1_758:0.00000000,((0_2096:0.04028250,2_1989:0.14595450):0.02038350,4_725:0.00153400):0.00210300,3_498:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..72e4d69a2cc144027595ac203819f8032239e755
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001475_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_717:0.00000000,3_490:0.00000000):0.00000000,1_750:0.00000000):0.00210650,2_1998:0.15801050,0_2104:0.00786350);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4ffaf4c129b2327da514d66558442814be575b8d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001476_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2105:0.03866900,((4_716:0.00204650,2_1999:0.22187450):0.01527440,3_489:-0.00004430):0.01408930,1_749:0.01029200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7623a8e7ed9dba3f0a39f089dbbaed3ebf225f85
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001478_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e2b3151d9365592f42b931060feac46c9b808663
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001480_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_745:0.00794187,4_712:-0.00057487):0.00567063,3_485:0.00616987):0.06973912,0_2109:0.04167138,2_2003:0.18943762);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70b96807185f3dddf202085404e88262f61e4ee7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001482_tree_id.txt
@@ -0,0 +1,2 @@
+(4_707:0.02143587,((0_2111:0.15029312,2_2006:0.13690888):0.11154712,3_483:0.01243637):0.00744363,1_743:0.00469212);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2a68033babe4f09cbbf7e581a6d0c2bdc2e746f3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001484_tree_id.txt
@@ -0,0 +1,2 @@
+(3_478:0.00440477,(4_703:0.00545513,(2_2009:0.14584517,0_2114:0.06179783):0.05132121):0.00475187,1_739:0.00708923);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cc1023f30d8441a4e4f10eac9ceb42217d3417ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001487_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f91ee0d6f14506e805c3efd433245148ff06df7d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001488_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c5f04cc9305ed2111cd69581e1a2aed844b569d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001489_tree_id.txt
@@ -0,0 +1,2 @@
+(3_472:0.01301710,((2_2015:0.25588650,0_2121:0.30476750):0.18692920,4_697:0.01675911):0.00689989,1_733:0.01703190);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a88bd084926025a5e5698a2f00f8281965c73649
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001490_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05d2b4b9e7f42e739f4cc2f700f2b20643981ce7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001491_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_470:0.00000000,1_731:0.00000000):0.00839825,4_695:0.00352775):0.06095025,2_2017:0.12599775,0_2123:0.06467925);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5ee7b6ccf42655ac537a31aa88b9d83cfc88c003
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001492_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_730:0.00290813,3_469:0.00240287):0.00167613,4_694:0.00739588):0.05237762,2_2018:0.21637788,0_2124:0.04857413);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..365aa903287b9cc52aedf45a6b9b472dbf58f30d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001496_tree_id.txt
@@ -0,0 +1,2 @@
+(4_690:-0.00030838,((0_2128:0.04818838,2_2022:0.19671063):0.05563287,1_726:-0.00030837):0.00030838,3_465:0.00543838);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c7d8e99dac7668a265dbc317fb2ed57d3efde248
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001497_tree_id.txt
@@ -0,0 +1,2 @@
+((4_689:0.01851387,(3_464:0.01647263,1_725:0.00723938):0.00120563):0.13421563,0_2129:0.15025512,2_2023:0.38540788);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1ed6e46d0ed21b78409f97576347e53229267807
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001498_tree_id.txt
@@ -0,0 +1,2 @@
+(1_724:0.00559325,(4_688:0.00229275,(0_2130:0.03550350,2_2024:0.15939450):0.01406925):0.00199475,3_463:0.00297175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4e3edae7fbfc317ea9f91e8da24508d614eb7cc5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001499_tree_id.txt
@@ -0,0 +1,2 @@
+((1_723:0.00516865,(4_687:0.00203849,3_462:0.00626751):0.00375656):0.02134578,2_2025:0.09248050,0_2131:0.02780750);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14b2191bdd89a24f809e8087ec3e76c6761d6f4f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001500_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_719:0.00000000,4_684:0.00000000):0.00000000,2_2031:0.00000000):0.00148400,0_2134:0.01072500,3_459:0.00764800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d70956eef1df28335dea3003a2e3c179b7f600b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001501_tree_id.txt
@@ -0,0 +1,2 @@
+((4_683:0.00513438,(0_2135:0.04156929,3_458:0.00251171):0.00388827):0.00417543,2_2032:0.00120117,1_718:0.01278483);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f046b5b8aad7838e0648543d2dd25418fd3198b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001503_tree_id.txt
@@ -0,0 +1,2 @@
+((1_716:0.00032141,(3_456:0.00029888,0_2137:0.01157412):0.00134862):0.00363109,4_681:0.00395633,2_2034:0.00396467);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5f1ece473d57e0cd2a422b85180e0cbef90c018
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001504_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2138:0.01168813,4_680:-0.00038013):0.00249138,(3_455:0.00140363,2_2035:0.00352038):0.00000237,1_715:0.00210562);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9f8ea647af542dc5cc696534aaf8e985e821566
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001505_tree_id.txt
@@ -0,0 +1,2 @@
+(4_679:0.00000000,((2_2036:0.04578150,0_2139:0.01799850):0.02109350,3_454:-0.00041500):0.00258300,1_714:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d856cc5c71949ba5c95103e0221df05ba970113
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001506_tree_id.txt
@@ -0,0 +1,2 @@
+(3_452:0.00553025,((2_2040:0.63655425,0_2142:0.13671575):0.14720950,4_676:0.00877500):0.03023100,1_712:0.00174275);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..daac7f919f1e73ca75a1298badbce619964758c2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001507_tree_id.txt
@@ -0,0 +1,2 @@
+((4_675:0.00952475,(3_451:0.00000000,1_711:0.00000000):0.00391725):0.14725125,2_2041:0.62585325,0_2143:0.18253075);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8acb312aeae3cc341a2c9bc057b8c994357c29b4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001512_tree_id.txt
@@ -0,0 +1,2 @@
+(3_447:0.00689288,((2_2045:0.17897562,0_2170:0.02880637):0.04769012,4_671:0.01183688):0.00447612,1_707:0.00238912);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..943b735f949f5cb3c129fc9698e42dda2ae7f954
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001513_tree_id.txt
@@ -0,0 +1,2 @@
+((4_670:0.00117493,(3_446:0.00000000,1_706:0.00000000):0.00073207):0.02301098,2_2046:0.11831367,0_2171:0.03998033);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a258821791acbb2795ca985c3b352fa3ab4dd8be
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001514_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2173:0.21248950,2_2048:0.24113150):0.12155375,(4_668:0.00196300,1_704:0.00842700):0.00346675,3_444:0.00763025);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..399a1d5aa3ed395ba5fe512f372799645d7a8799
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001519_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2183:0.10444350,2_2054:0.25816150):0.22922800,4_663:0.01661400):0.00344400,3_439:0.00000000,1_699:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..399179c0beef88a4a2dbf89dbf0fac0559f63ac2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001523_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2058:0.11484550,0_2187:0.01822950):0.01855850,3_435:0.00000000):0.00000000,4_659:0.00000000,1_695:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9f7459977202785284221108b20db28cb85bb261
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001524_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2188:0.01981175,2_2059:0.12972325):0.03020525,4_658:0.00155025):0.00286975,1_694:0.00000000,3_434:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b53f6e58b495268794b160a802acbc6b63201fbe
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001525_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_657:0.00370663,1_693:-0.00003863):0.00003863,3_433:-0.00003863):0.00162312,0_2189:0.01191637,2_2060:0.04588563);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0714f00ffa8f390a7165874878402f88e4474e50
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001527_tree_id.txt
@@ -0,0 +1,2 @@
+((3_431:0.00000000,(2_2062:0.53960850,0_2191:0.06099750):0.07053650):0.00000000,4_655:0.00000000,1_691:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..60a7462a6b783ade79e583781d5db79e31250611
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001529_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_653:0.00329744,3_429:0.00007356):0.00440174,1_689:0.00565349):0.02733402,0_2193:0.03312217,2_2064:0.09657083);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2894e75d3fa377b0a76c0b0007128e686022384
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001532_tree_id.txt
@@ -0,0 +1,2 @@
+((3_426:-0.00009312,4_650:0.00606913):0.01367812,(2_2068:0.01902037,0_2196:0.01119063):0.24269962,1_683:0.00747538);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fb36d265b6342061f17d073e7ada78290cbf68c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001533_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2199:0.16768712,(3_425:0.00380038,(4_649:0.00509312,1_682:0.00516987):0.00290613):0.00136812,2_2070:0.01409788);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2bf7ecfa90b645e339fdc39e471fbe63418e5e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001535_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2201:0.07185525,2_2072:0.04177375):0.02345325,(4_647:0.00000000,1_680:0.00000000):0.00012875,3_423:0.00283425);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..884d40f9682edced33edfaced4e09a35a117d404
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001536_tree_id.txt
@@ -0,0 +1,2 @@
+((1_679:0.07142462,(4_646:0.01949912,3_422:0.02152788):0.04029887):0.18822388,2_2073:0.29543838,0_2202:0.22781962);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2e64a58171ebdd4230255af423b5a698d9783ba3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001538_tree_id.txt
@@ -0,0 +1,2 @@
+((1_674:0.00000000,3_420:0.00000000):0.00000000,(0_2204:0.04509250,2_2075:0.19689550):0.02536250,4_644:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ae3bf56107ef94b4fd752f0788ae752675d8d758
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001539_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_643:0.00000000,1_673:0.00000000):0.00000000,3_419:0.00000000):0.17725850,0_2205:0.04679250,2_2076:0.17537050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a267678bf602baf7496e65e799f894d9b8c1eb5f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001540_tree_id.txt
@@ -0,0 +1,2 @@
+((1_671:0.03966188,(3_417:0.01089870,4_641:0.02474130):0.00785772):0.16679749,0_2207:0.12844400,2_2077:0.51318300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c12ba4348cc3b49a44687f6a456169e93860a747
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001541_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_416:0.00025775,4_640:0.01452125):0.00384825,1_670:0.00296225):0.04452475,0_2208:0.02302600,2_2078:0.16477800);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c5d13a20f3f600d89f480d66fd2a2299c8a58420
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001542_tree_id.txt
@@ -0,0 +1,2 @@
+(4_639:0.01210949,(3_415:0.01930547,(2_2079:0.21164217,0_2209:0.18631783):0.09750632):0.03563903,1_669:0.02072151);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dea79bac205b058b594a052e73f6105d411221d4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001543_tree_id.txt
@@ -0,0 +1,2 @@
+(3_414:0.00043513,(4_638:0.00445938,(2_447:0.52350312,0_2210:0.00609087):0.00783862):0.00103462,1_668:0.00047887);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ed361b637e464bf06ddf32f32f1856ebdd0a0dc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001545_tree_id.txt
@@ -0,0 +1,2 @@
+((1_665:0.06955700,(4_635:0.00108800,3_411:0.00364500):0.00471700):0.11669850,2_2081:0.55980125,0_2214:0.10386475);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c45ea7b273dc8b79832c9edae3613df7b10805fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001546_tree_id.txt
@@ -0,0 +1,2 @@
+((3_410:0.00000050,1_664:0.00000050):0.00000000,(2_2082:0.15212350,0_2215:0.06528050):0.08673300,4_634:0.00000050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fe87358a3affe07b6cbc04d6eb5d55f152b1e0d6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001548_tree_id.txt
@@ -0,0 +1,2 @@
+((1_662:-0.00015062,(3_408:0.00120662,4_632:-0.00015062):0.00015062):0.01499263,2_2085:0.05495687,0_2219:0.02244012);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a7d8a184364d7e433a2e5d04e87dd6d56a3e498a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001551_tree_id.txt
@@ -0,0 +1,2 @@
+((4_629:0.01032289,(0_2228:0.15937067,2_2088:0.23186033):0.13553230):0.00640961,1_659:0.01951663,3_405:0.00152737);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..213f5916d2ce83b78ba0d9a27e72958c2bc3be8a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001554_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2231:0.03499500,2_2091:0.10620600):0.06008500,4_626:0.00000000):-0.00000000,1_656:0.00000000,3_402:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..40dc7f3880393704a9a4c6ff39083fa46c6e3fb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001555_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2634a36909a05ef7b8c1102b1ce5ebfdaedc1c1f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001556_tree_id.txt
@@ -0,0 +1,2 @@
+((4_624:0.00531950,(1_654:0.00000000,3_400:0.00000000):0.00011650):0.02602100,2_2093:0.09050500,0_2233:0.03608100);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..187e2493da99a30fbcf9647d439ca7e57b686326
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001558_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2235:0.02405200,2_2096:0.17280400):0.02917500,4_621:0.00000000):-0.00000000,3_397:0.00000000,1_651:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad49ba6221db9d68c726e510c07283ddfb2d0210
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001559_tree_id.txt
@@ -0,0 +1,2 @@
+(3_396:0.00000000,(4_620:0.00038275,(0_2236:0.10987325,2_2097:0.41384575):0.12732275):0.00650525,1_650:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5bf086e32fb35753748b737facf4a9ac9064246c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001561_tree_id.txt
@@ -0,0 +1,2 @@
+(3_394:0.00337120,((2_2099:0.05348767,0_2238:0.15070933):0.06032770,4_618:0.00079011):0.00089789,1_648:0.00169680);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9581851def30acdfa1ea5407c1f862c48675ea16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001564_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_391:0.00000000,4_615:0.00000000):0.00000000,1_645:0.00000000):0.07363650,0_2241:0.05833450,2_2102:0.22160950);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2ac6b090b47c154fcd8ea17a673bfc3dbcedcc7f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001565_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e8c1aee454f017bbd9366c6e679c9b1a3978b230
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001566_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e74b6e69d1dd5569925f80cfe6dfba455d1a8726
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001567_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a78d9f6ef0c3b29efd4bb0834ab712fc65d51cf2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001571_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1f7bcc29d112a13c083e6565062486023067768
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001572_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4cd204e642dff48305533c36b702081ecbd0b0b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001574_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4655b65b9702cf0d585168575a7dd627f41b96b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001575_tree_id.txt
@@ -0,0 +1,2 @@
+((3_374:0.00000000,4_598:0.00000000):0.00000000,(0_2259:0.02046050,2_2115:0.13539750):0.01119250,1_628:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..59c1bf84995ce544bb3194daaa65fa7dec934afb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001577_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7671b1d3f5cc6a8db8d7fcd0fa49aa71db26de2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001579_tree_id.txt
@@ -0,0 +1,2 @@
+(1_623:0.02261200,(3_369:0.01305075,(2_2120:0.49772775,0_2264:0.06987025):0.04240925):0.01467675,4_593:0.01485100);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41e1678ce73c8d7edbac344d5685a34cf59002d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001581_tree_id.txt
@@ -0,0 +1,2 @@
+((1_620:-0.00080200,3_366:0.00273400):0.02445300,(0_2267:0.05214425,2_2125:0.25146275):0.00669800,4_590:0.01341500);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6fddd026505653324bf38e8fa823eaef11c13f73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001586_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2298:0.89455333,3_302:0.05820067):0.01579212,2_2192:0.08459538):0.05375429,4_561:0.07714417,1_560:0.05117983);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..28c3be31cedc5ce67bf4fafe53bc2a870b36a7aa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001588_tree_id.txt
@@ -0,0 +1,2 @@
+(4_557:0.02396275,((2_2194:0.12987075,0_2301:0.11919725):0.08123575,3_298:0.02430375):0.00319075,1_556:0.01928925);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..449ef189487b565a837baf4807842aebc18f1438
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001589_tree_id.txt
@@ -0,0 +1,2 @@
+((1_555:0.06252100,(3_296:0.00804075,4_556:0.00502525):0.02820650):0.05630650,0_2302:0.16537450,2_2195:0.31298150);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..41cf23b3c399388945faf3103600bfd2eee7e5f7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001590_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..875b480fed31f2014de45550b07275a8bfb80131
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001592_tree_id.txt
@@ -0,0 +1,2 @@
+(1_549:0.01692562,((0_2308:0.22608213,2_2198:0.16885288):0.75582938,4_550:0.02109763):0.01251337,3_290:0.01134438);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99e545b049f44d5d048424ea21e648a36d367750
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001595_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ebdca42fbb3623bf967ef5f31caa98b2c3289a3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001598_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..010a908d18b890d57133d70b9593b6a57a498fef
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001599_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..08370e679ed242aac42781a5627b06e639aa597c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001606_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fa17c7d19b1c1704d33544bd3d6e03b6e270c740
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001608_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e21f990473726b49e059416c6ae8414e51477569
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001613_tree_id.txt
@@ -0,0 +1,2 @@
+((3_256:0.01273525,(1_522:0.00000000,4_525:0.00000000):0.02786575):0.28814475,0_2349:0.15009625,2_2232:0.69071375);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4d4da01630d2decb36bfe4519bda17649f9a4d3b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001614_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a28e56fa04b7402a5d0a6cfd66f42e678a51839e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001615_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..98579f770275e5465813f028173d4c266b3546e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001617_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..401fe1275c3d2a878322f4a122f2587c2d57b7f1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001619_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..46d8a6ce179229f2613652f4429ccb631555db34
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001620_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..eacdd15c698af68bf416347a2162141d91916fb0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001621_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e67b77214803148e1968dd993d61107050dfea29
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001625_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2c1cb3050bd9194fe0e5dec35f69831c10dd56f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001626_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6279bf82cb87f341a20b74c46bdb4e8cdaa717a4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001627_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3442f44c0733dae6311e9a102ccd33e4652ea465
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001631_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001633_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84497f22493c2f85bad31e8c9d0fa2d279b6ff64
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d7bf6dcd325acf863991851dc6bee96656ff0ed
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001637_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001638_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29c1d5b9a885734e3691139b1c1a318de25ebe22
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001640_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..70fa3804a3bf6d0ff342c6e569bf309475e5da85
--- /dev/null
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95e15c6b293bd5108bf13a0e5f6d3901e04c97ac
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001642_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d1cac3f5de449ad39490b7e2d5fdcfbecbf3f614
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001644_tree_id.txt
@@ -0,0 +1,2 @@
+((1_474:0.00276577,4_473:0.00094923):0.00246713,(2_2280:0.08892967,0_2397:0.04123033):0.05069805,3_204:0.01027378);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4b21a5010b609aa14de677680c7156b808aaeb30
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001648_tree_id.txt
@@ -0,0 +1,2 @@
+(4_468:0.00359975,(3_199:0.00489050,(0_2402:0.02871575,2_2285:0.13366625):0.03322850):0.00255850,1_469:0.00179825);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..97c05fcc53a422548c2d8e338f1c973acd7f35ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001649_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_468:0.00375393,3_198:0.01461207):0.00330734,2_2286:0.18040373):0.00581348,0_2403:0.00684233,4_467:0.00038867);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95e24b577ef4595a454edb4b6ee53b499729926b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001650_tree_id.txt
@@ -0,0 +1,2 @@
+((3_194:0.01556851,(1_465:0.00270658,4_465:0.00027442):0.01451016):0.03281360,2_2288:0.24599067,0_2405:0.04919933);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0bd061b08d722e6ebfcff280fea28f17e3ab8bc
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001652_tree_id.txt
@@ -0,0 +1,2 @@
+((1_463:0.00566379,(4_463:0.00290529,3_191:0.00552671):0.00311112):0.09302306,0_2408:0.35435967,2_2290:0.25429733);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f1b47d26b28ed4e5b33654035ae124c384c057fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001653_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_462:0.01086225,1_462:0.01525975):0.02325000,3_189:0.03862400):0.06456500,2_2292:0.53066050,0_2409:0.10742850);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9955dcb6ff191c041790b5ae2f3ba54b431b0028
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001654_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_461:0.00235087,4_461:0.00008513):0.00026088,3_188:0.00120163):0.01979287,0_2410:0.01253737,2_2293:0.05617663);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bb0b4624c51579fc0d9f43a24f4ab397019821ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001655_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_460:0.00000000,4_460:0.00000000):0.00000000,3_187:0.00000000):0.10857300,2_2294:0.42185600,0_2411:0.22192000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..256d48b572f6a63bf29fed6a22fa4cfd27c8cc73
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001656_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfed3b68ccf82eceb18005173c69042d610a2650
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001659_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..91a6ec7aa91f5c617bc47cce2d5a935a4776f851
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001661_tree_id.txt
@@ -0,0 +1,2 @@
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+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..84e650e72227d4e8c5c656c0dd4d0db674035e16
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001663_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d95fb57fcf797dba972a42e358ca14a281af92a2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001664_tree_id.txt
@@ -0,0 +1,2 @@
+(1_450:0.00000000,(4_450:0.00697889,(0_2421:0.16775667,2_2304:0.45429433):0.07749930):0.00949911,3_177:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..605bb0502341e2c90054e1857a6130fae505bc08
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001666_tree_id.txt
@@ -0,0 +1,2 @@
+(((4_448:0.00000000,1_448:0.00000000):0.00000000,3_175:0.00000000):0.01837900,0_2423:0.01944600,2_2306:0.05402400);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86199bb3d5ca1a6ad66e79570d10df25696fb86f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001667_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e46b2d10f00eea677b9da943736ccc6b1a4839ad
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001673_tree_id.txt
@@ -0,0 +1,2 @@
+((4_440:0.00775494,3_167:-0.00102094):0.00102094,(0_2430:0.10305217,2_2314:0.75464783):0.09123725,1_440:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..16022b1b2dec63485d0edf89f8f0ab644417fa04
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001676_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5a9fb3e64ee4c9428abfd173a07a28aafc244aa8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001677_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ea5c183b41323dd75e4ae7d4e730f1657feda2d0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001680_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e32f2caf8eeb8d41522d13140baa9bcade3ee01f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001683_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7dc9d8463e401e4ce5a6edd65c92a0c8d8a876de
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001686_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..27445dde381454ccc5a4a7389b67d61f8e5946d3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001687_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a4da288ed0e84d96fa168323305d9af4625a76c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001689_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ceac569b94c89c92e3f66db77bedc5a2f3f2220
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001694_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e66e0c396c86bd7cef1e4539692a495d6e817e28
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001696_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be49e2bc8dbf7f830c7d449613c2a05ee2b38113
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001697_tree_id.txt
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d0bfb1976745aea1070cb326ff15066735385d31
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001698_tree_id.txt
@@ -0,0 +1,2 @@
+(3_141:0.04788295,((0_2469:0.18371417,2_2340:0.60971283):0.31785837,1_411:0.02998861):0.02561839,4_414:0.04168705);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d93185598045bdf9ca6b631724b5c33a99638002
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001700_tree_id.txt
@@ -0,0 +1,2 @@
+((3_138:0.00469725,(4_411:0.00113125,1_408:0.00275275):0.00309825):0.21668825,2_2342:0.23172175,0_2472:0.13961825);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fddf72732908484b413f077083ad634e5ba5452e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001701_tree_id.txt
@@ -0,0 +1,2 @@
+(((0_2473:0.12005475,2_2343:0.14604425):0.09348475,1_407:0.00283525):0.00241575,3_137:0.00201950,4_410:0.00948050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1dbdbe29d5e55289ddf5a55173d2759fa372ef4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001706_tree_id.txt
@@ -0,0 +1,2 @@
+(3_131:0.00009567,(4_404:0.01918165,(2_2350:0.15418550,0_2480:0.04700750):0.03764905):0.00433535,1_401:0.00613033);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4159408cecce8de186d9a9146a0a4b860de0e9b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001708_tree_id.txt
@@ -0,0 +1,2 @@
+(1_400:0.00325601,((4_403:0.02141667,2_2351:0.01897233):0.00382878,3_130:0.01176633):0.00096517,0_2482:0.05577099);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..24d9a6702e47404acf1d9fb184febe9e665f0e67
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001709_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2352:0.00356400,3_129:-0.00001600):0.00001600,4_402:-0.00001600):0.00001600,0_2483:0.03605600,1_399:-0.00001600);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..05394041512ba0d51df72c4c6c74b683fc845003
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001715_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2492:0.01403375,(1_390:0.00000000,3_119:0.00000000):0.00702025):0.01281575,4_393:0.01155325,2_2360:0.01322275);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1637237c6f65d3280c10197b115688d4edc9ac58
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001718_tree_id.txt
@@ -0,0 +1,2 @@
+(((3_116:0.00700138,4_390:0.00894462):0.00282513,1_384:0.00611388):0.01213013,2_2363:0.36640137,0_2495:0.00945762);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..94b030081910de0ebe056c1d75894e3d2d052af3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001719_tree_id.txt
@@ -0,0 +1,2 @@
+((3_115:0.01399923,(1_383:0.04686705,4_389:0.00665795):0.00373267):0.02388154,2_2364:0.29957167,0_2496:0.03448133);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0be78b5f4dcf9224909334781e9ae7ffea1c7720
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001720_tree_id.txt
@@ -0,0 +1,2 @@
+((3_114:0.00794200,(1_382:0.00206725,4_388:0.00992975):0.00733250):0.00971500,2_2366:0.10317475,0_2497:0.02433725);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..df545eeeeadc3ac8f95ce1d35747145ec4ee7e8b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001721_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2369:0.09197073,0_2500:0.02322027):0.00742050,1_380:0.02294566):0.01296501,3_113:0.00080500,4_386:0.00392900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6da1c01bbf3c2ad2439abe2d4a4bf3fc7b9677e3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001722_tree_id.txt
@@ -0,0 +1,2 @@
+((3_112:0.00282125,(4_385:0.00922350,1_379:0.00533250):0.00192925):0.06271075,2_2371:0.13750800,0_2501:0.05339400);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7fb6424ad0e53d2a1db11602651e578e19317b38
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001726_tree_id.txt
@@ -0,0 +1,2 @@
+((4_381:0.00021501,(1_375:0.00022221,3_108:0.00102279):0.00264527):0.02971414,0_2505:0.06544517,2_2376:0.09931083);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..75581a6946cc7887bcdfb7fee6949014ff6ea7e8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001729_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2380:0.14667750,0_2509:0.09169350):0.07897017,(4_376:0.00138532,3_103:0.00712968):0.00246533,1_370:0.00515622);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5cb4006781ba005c2b0e18e840e52e6dffad90d8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001730_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_368:0.00332038,3_101:0.00364562):0.00496213,4_374:0.00999337):0.08510512,2_2382:0.51136613,0_2511:0.08124287);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2dfc5b73e7f11436c890d834ee9a575126af9882
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001732_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1718:0.02978115,((3_97:0.00000000,1_364:0.00000000):0.00619475,4_370:0.00664925):0.00550825,0_2514:0.01627485);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a2c797690fc6240a6381e5c47e50bde4a9b3a90d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001733_tree_id.txt
@@ -0,0 +1,2 @@
+((3_96:-0.00103925,(1_363:0.00000000,4_369:0.00000000):0.00512025):0.00898625,2_1717:0.40181225,0_2515:0.01512575);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..091a5115a54aa687e4213176860b959846b69f05
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001735_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_361:0.00904121,3_94:0.00863579):0.00114938,4_367:0.00453833):0.02024233,0_2517:0.02590717,2_2389:0.00317683);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d1eed0241da68173758ac990e7e69fc13741437
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001737_tree_id.txt
@@ -0,0 +1,2 @@
+(1_359:0.00000000,((2_2391:-0.00125125,0_2519:0.01709325):0.02731575,3_92:-0.00025525):0.01211325,4_365:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..467b7cce3f947bc9093b2ae75bed7d55cef5f770
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001738_tree_id.txt
@@ -0,0 +1,2 @@
+(((2_2392:0.11160900,0_2520:0.00306600):0.00153300,3_91:0.02039828):0.00466472,4_364:0.00000000,1_358:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c96bfecbda29c360b06c84815d637758fc60d82
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001742_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bd415eadfd5560c7d3b80649e40c8950f29f56b5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001743_tree_id.txt
@@ -0,0 +1,2 @@
+((1_345:0.00000000,3_70:0.00000000):0.00000000,(0_2539:0.01995350,2_2398:0.14658550):0.00241450,4_352:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1078c7953663c4c4990e55b2207f60ad82830ab6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001745_tree_id.txt
@@ -0,0 +1,2 @@
+(3_68:0.00613463,(1_343:0.00744838,(2_2400:0.10518213,0_2541:0.03544087):0.03558812):0.00153062,4_350:0.00768237);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ad846ecdd0aad4949cf17ed739e1437a83f810a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001748_tree_id.txt
@@ -0,0 +1,2 @@
+((1_340:0.00724550,(3_65:0.00000000,4_347:0.00000000):0.12926550):0.29644350,2_2403:0.61855500,0_2544:0.14718200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b9d3637554818682f218df2139d824425ae89d48
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001749_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6a8cd875948aa8b141dc27c3f51fad60db55e70c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001751_tree_id.txt
@@ -0,0 +1,2 @@
+(3_61:0.00253078,(1_336:0.00741382,(0_2548:0.09355450,2_2407:0.33966450):0.10188644):0.00358168,4_343:-0.00000078);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..123b19b13354dac38f0409b6bd58d68307bc0c81
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001753_tree_id.txt
@@ -0,0 +1,2 @@
+((1_333:-0.00107995,(4_340:0.00000000,3_58:0.00000000):0.01229395):0.18074452,2_2410:0.36916383,0_2551:0.16225617);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3160e1d936388b9db7fa2f16d322cb834fd470c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001755_tree_id.txt
@@ -0,0 +1,2 @@
+((4_338:0.01700200,(1_331:-0.00008875,3_56:0.00310375):0.01153250):0.12463600,0_2553:0.06035875,2_2412:0.50420125);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..26a9e13a761d358ce1160d0047d4cc1faf94e4df
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001758_tree_id.txt
@@ -0,0 +1,2 @@
+((1_328:0.00278826,(3_53:0.00110802,4_335:0.00127598):0.00278119):0.02887982,0_2564:0.06572867,2_2416:0.13112833);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..488b2bf7b32ac6bde772b5d1031f78c704d092d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001761_tree_id.txt
@@ -0,0 +1,2 @@
+(1_324:0.01787888,((0_2568:0.10013012,2_2419:0.35353488):0.14011788,4_331:0.00815963):0.00921337,3_49:0.00466412);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cfa6e1301cdac607ae131694e1f56addad30b4eb
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001763_tree_id.txt
@@ -0,0 +1,2 @@
+(1_322:0.01096938,(4_329:0.02719888,(2_2424:0.67611138,0_2570:0.17380563):0.11817312):0.01953862,3_47:0.01798562);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8aa0ca14baba3b5d14dd0404cbc300e545276914
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001764_tree_id.txt
@@ -0,0 +1,2 @@
+((0_2614:0.18978312,2_2425:0.57144488):0.15653662,(4_328:0.00894312,3_46:0.01837888):0.04606963,1_321:0.01341788);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1218da019ffcdd46c1ce6b9df15e485869f935fd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001765_tree_id.txt
@@ -0,0 +1,2 @@
+(((1_320:0.00683914,4_327:0.00583886):0.01794908,3_45:0.00803715):0.07496108,2_2426:0.24042100,0_2615:0.09558900);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9b09696a0c9411c61c3b19ea167bbaf11396a802
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001770_tree_id.txt
@@ -0,0 +1,2 @@
+((4_322:0.00000050,3_40:0.00000050):0.00454000,1_315:0.00041650,0_2:0.05145150);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d61115a3bd8405827855b06a2fa788cd541632f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001771_tree_id.txt
@@ -0,0 +1,2 @@
+((3_39:0.00000000,1_314:0.00000000):0.01124900,0_3:0.12614800,4_321:0.00566900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..559ddcae3b01d86a4087eafe7351406cabfca36a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001772_tree_id.txt
@@ -0,0 +1,2 @@
+(1_313:0.00000000,(0_4:0.11948500,4_320:0.00804300):0.00335800,3_38:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..020c4980f16dbfa4237b868aeea3ce732b295a6d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001773_tree_id.txt
@@ -0,0 +1,2 @@
+((4_298:0.02938025,3_8:0.01312075):0.03430375,0_45:0.26479182,1_291:0.06581218);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36ba26a537737f88a5f7ea8460c45b005712f46e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001774_tree_id.txt
@@ -0,0 +1,2 @@
+(3_2250:0.00133450,(1_277:0.02208650,0_59:0.15235150):0.01994450,4_283:0.01752050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7bf1d7af9d5272e3db420ba9e79be084873f363f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001775_tree_id.txt
@@ -0,0 +1,2 @@
+((4_266:0.01204825,3_2233:-0.00235925):0.03820725,0_70:0.43037800,1_267:0.00635200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b82c3fc8c1d779555c60bcc481b2d680b0fcee8f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001779_tree_id.txt
@@ -0,0 +1,2 @@
+((1_243:0.01959975,3_2206:0.00294725):0.00132975,0_109:0.02497175,4_243:0.00080825);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..57cb73ba0479df50643df5bd10898b1f78cef9ce
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001781_tree_id.txt
@@ -0,0 +1,2 @@
+((0_133:0.33981625,2_95:0.58183175):0.02769125,0_789:0.88267713,1_1976:1.65499887);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..36977af589fad922a605c8ea0c3013b77fe7eb17
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001783_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2153:0.00000000,4_209:0.00000000):0.23009100,1_209:0.69109600,0_158:0.37739100);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7ab6b6f4879b1bcc33bf58d49fe6a1d2c72b4c5f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001785_tree_id.txt
@@ -0,0 +1,2 @@
+(1_191:0.00000000,(0_184:0.28936100,3_2138:0.01452500):0.02925000,4_194:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f0e817b7ab374d308e36e693ec333a48e66c148b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001787_tree_id.txt
@@ -0,0 +1,2 @@
+(1_193:0.00930050,(3_2139:0.01334100,0_195:0.25589000):0.00106050,4_195:0.02090250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..15ddb1019f9dab9374863106c23df5dd975d889b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001794_tree_id.txt
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+(3_2043:0.01109613,(0_294:0.22637975,4_73:0.24223825):0.01657675,1_79:0.01141287);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a50bff2444ae8e0051881a0b9a33831ae52dc3e4
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001798_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1978:-0.00239550,0_368:0.22281350):0.00239550,4_9:0.03187400,1_9:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dd75b67467eab672bdb4d1ff62e30a312e38187a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001799_tree_id.txt
@@ -0,0 +1,2 @@
+(0_384:0.01313650,(4_578:0.00618175,2_2149:-0.00002575):0.00023725,1_603:0.00357650);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2481e6792c80bee941fc30947feb4d7a64e77659
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001800_tree_id.txt
@@ -0,0 +1,2 @@
+(4_577:-0.00108377,(0_385:0.01446425,1_604:0.00323375):0.00029725,2_2148:0.00694777);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..523185b5ba6f97a3d92935358830f2507c7117c7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001801_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d7ab4f7c564750fd517b7c6c28032f7a20f804b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001803_tree_id.txt
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+(0_435:0.03195650,(1_2223:0.00247075,3_1925:-0.00002275):0.00343625,4_2163:-0.00035150);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c678e48954fd87c654c1bfa6f257212af104b5d7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001805_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..981be0c994a97d770663df928cdee65adba63a5b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001808_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1877:0.01089200,(1_2153:0.01081950,4_2093:0.01081950):0.00313450,0_512:0.16496300);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e879417a7bddc903348c98fff73584828c0a9d46
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001815_tree_id.txt
@@ -0,0 +1,2 @@
+((0_543:0.22397525,1_2127:0.23466675):0.03358475,4_2073:0.00694225,3_1852:0.02506075);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7b5ddf9fcd642eba49f82be5bcc4503e47b8eeb8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001818_tree_id.txt
@@ -0,0 +1,2 @@
+((0_584:1.58006550,4_2038:-0.00191450):0.01164350,3_1818:0.01468600,1_2094:0.04111900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aca8a071a78deb5076af31294f4e039066ccec76
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001821_tree_id.txt
@@ -0,0 +1,2 @@
+((2_524:0.00933025,0_599:0.03335975):0.12906125,4_2027:0.07391268,3_1807:0.00582032);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c1474a219792bfd463f8b720eaa02e90ce68cccd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001822_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2074:0.01087600,0_619:0.02236600):0.02127400,3_1793:0.00000000,4_2013:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0bafde199148d4d5045c48e5b2374ce2314f9caa
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001825_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2040:0.00000000,(0_660:0.43192600,4_1981:0.01347300):0.01048300,3_1758:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4567db7cda9c557b138f7f481b2563031dfa89c0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001826_tree_id.txt
@@ -0,0 +1,2 @@
+((0_661:0.51821200,4_1980:0.00015500):0.00764800,3_1757:0.00000000,1_2039:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1e49baafdd6f1d889b6385a4af0c78fff315b568
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001828_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2030:0.04264425,(0_669:0.00494925,3_1749:0.02244975):0.00307025,2_586:0.02688175);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..69bac83ae7e838b9a3bb3b0b4d51555c54ea3e5c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001829_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2029:0.00525750,(3_1748:0.00521550,0_670:0.01609950):0.01540600,2_587:0.01433050);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1d857aa0a517adc08078a64c667402c8a3447e90
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001830_tree_id.txt
@@ -0,0 +1,2 @@
+((0_672:0.00784650,3_1746:0.01659750):0.76391400,3_82:0.61195450,0_757:0.82868150);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..33a9a46de824431c6019f6b5c132869bd3d98c39
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001831_tree_id.txt
@@ -0,0 +1,2 @@
+((2_595:0.02988100,0_684:0.01250000):0.00446200,3_1736:0.00000000,4_1960:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c9db739b568723fbb05a92b3bc7f1fc94175c91c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001832_tree_id.txt
@@ -0,0 +1,2 @@
+(2_680:0.00431447,(2_404:0.32284625,0_694:0.31567275):0.19492775,2_703:0.02373453);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4eca105ca743505095badb14cce17dfd71b8d252
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001833_tree_id.txt
@@ -0,0 +1,2 @@
+(0_715:0.00000000,(0_2277:0.06747700,2_398:0.13660700):0.19025700,0_732:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..37658e20aa6f3488c4690ac36358cb04d7d2ed55
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001836_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1928:0.03719252,1_1993:0.11807448):0.43149725,3_1710:0.18253425,0_748:0.60451375);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e56bb5910e11fc9ff660ed2ce0cb1f03f25e8fec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001840_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1571:0.01464500,3_1287:0.03518800):0.30823600,0_799:1.24933400,4_1500:0.16030800);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c0504bf68afca7caf31f0b6a08210cbf6dcd5e0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001844_tree_id.txt
@@ -0,0 +1,2 @@
+(2_767:0.21064200,(3_1653:-0.00168600,4_1871:0.00449500):0.20206500,0_829:0.32545600);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d387d2c0fb478e89cdd4b1766e0b87f032278233
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001847_tree_id.txt
@@ -0,0 +1,2 @@
+((2_770:0.12952800,0_832:0.01972500):0.01444400,3_1650:0.00000000,4_1868:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7d723caa8e5bc292f0e19cc79ee92dd61299716a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001851_tree_id.txt
@@ -0,0 +1,2 @@
+((0_851:0.00650900,3_1631:0.00000000):-0.00000000,4_1853:0.00000000,1_1926:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..010debeea6b917fadea77c61d7bd1c2d75d40890
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001852_tree_id.txt
@@ -0,0 +1,2 @@
+((1_1916:-0.00604600,0_862:0.18599100):0.05243950,4_1842:-0.00065350,3_1620:0.01500450);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..645248a9d2cbfa05691ce2040011466beeab21d2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001859_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..333cf90f1ea8ed50d773716cb1389debfc964a59
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001861_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4034cabffbb04ee492eadf310c727aae1cb46b2d
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001862_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..13459d0034bb417ded134734f1f6070e8507c89b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001863_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1759:0.00425692,(1_1838:0.01220400,3_1545:0.00451000):0.00448850,0_941:0.45627508);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7c323fbb335b594815a461a88486a20ce386f462
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001864_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1756:0.00000000,(0_943:0.09357450,3_1542:0.01217750):0.01470150,1_1835:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..aa0e9d64d56a12b853b22ed4f292d11484e0713c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001865_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1833:0.00940438,(3_1540:0.01356000,0_945:0.56561300):0.00537550,4_1754:0.00677862);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1506b5d1791a34ba20dc8c4c40c4d5eee6351600
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001866_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1820:0.00000000,(4_1741:0.01184100,0_959:0.34637500):0.05761700,3_1527:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0593caebc6190407988fdf2a133c8190e65fe8e2
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001869_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1708:0.00772274,(1_1787:0.00184900,3_1494:0.00207700):0.01183250,0_1001:0.15413326);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7acb6346ca9c7440a1b87d14d14b7cd84fdc4632
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001875_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..beb4c8a6da4a10e9b751b469cfc9bb52f2b61cb1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001876_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1280:0.00411813,(2_1165:0.01254000,0_1260:0.00971400):0.00415900,1_1560:0.00414687);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d82df02876a26380a7bc81044bcf9d0589a8f370
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001878_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1309:0.02213950,(1_1534:0.00000000,4_1461:0.00000000):0.00110950,3_1255:0.00053950);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..71b50ff7100de7ed5421f18d1e0324758a9e9912
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001881_tree_id.txt
@@ -0,0 +1,2 @@
+((4_1387:0.00277000,0_1386:0.05935100):0.00339700,3_1179:0.00000000,1_1460:0.00000000);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..5f2e4b65be2a3bd3ae0716ef3b0f4aac88f5c503
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001884_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1605:0.14826985,(3_933:0.02264050,1_1205:0.02355350):0.14217450,2_1502:0.47486115);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dfac5e15d00aeeeddf49f41359fb78b1f05123b8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001887_tree_id.txt
@@ -0,0 +1,2 @@
+((3_794:0.00114050,0_1750:0.07013650):0.00809000,4_1016:0.00225300,1_1066:-0.00035900);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c2ba947cfbda40b32e524074dd5d8d40caee8d05
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001888_tree_id.txt
@@ -0,0 +1,2 @@
+(4_919:0.00223706,(1_975:0.00394925,3_698:0.00224575):0.00000775,0_1836:0.00848094);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6b53e1093fc7db8445c10bb500b7506f4c2251ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001889_tree_id.txt
@@ -0,0 +1,2 @@
+(0_1839:0.03439750,(4_915:0.00000000,1_972:0.00000000):0.00238550,3_695:0.09468250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ee726f758889c4379acfd4a6d3a45731eb37df9a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001891_tree_id.txt
@@ -0,0 +1,2 @@
+(3_640:0.00678166,(0_1949:0.08394325,3_1070:0.96883875):0.09919725,1_912:0.00847134);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..85534233f2faef22fd059cfa08f3cb2e350c8d6c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001892_tree_id.txt
@@ -0,0 +1,2 @@
+(3_547:0.15253625,(4_775:-0.00549525,0_2043:0.47995425):0.11479525,1_816:0.01821275);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..93007726ff3501cb2491ec1d7d04f6e9c68c9ba7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001893_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2140:0.18329045,(0_2610:0.53980275,0_2525:1.97236025):0.28629425,2_2038:0.21805655);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3413944f41715cbdc0ada276a2d26afaf38f3a52
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001895_tree_id.txt
@@ -0,0 +1,2 @@
+(2_697:1.26156290,(0_2197:0.19363775,2_2069:0.23404125):1.20744025,2_385:1.05135010);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cb27de4e6fa3d8d9205078331f2256a0785bf0d3
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001897_tree_id.txt
@@ -0,0 +1,2 @@
+(4_567:0.16083100,(0_2223:-0.00021925,2_1786:0.00898025):0.00021925,3_307:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b032de2b449fd6d22d3ccf549edc831c7e6bf1a9
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+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001900_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2247:0.02828300,(4_609:0.00000000,3_385:0.00000000):0.00190700,1_639:0.00737100);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8fe60b98223db07e205d5c3e0db9cb60e406f100
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001901_tree_id.txt
@@ -0,0 +1,2 @@
+(3_383:0.00000000,(0_2250:0.03916700,1_637:0.00213000):0.00264600,4_607:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..23dcf542a03031e00f2fd68efe045dd567bfb0ec
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001902_tree_id.txt
@@ -0,0 +1,2 @@
+(1_621:0.00545750,(4_591:-0.00046575,0_2266:0.26318375):0.00349825,3_367:-0.00061450);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b850af882b7fa626184547a48eb37a0c00d195ba
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001906_tree_id.txt
@@ -0,0 +1,2 @@
+(0_2300:0.56156008,(1_557:0.28887325,3_299:0.04302775):0.17537225,4_558:0.09324192);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0c2a5eba31241735db760ab01019eec4bf36448c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001910_tree_id.txt
@@ -0,0 +1,2 @@
+(1_348:0.03021800,(3_73:0.00000000,4_355:0.00000000):0.04741900,0_2342:1.74451700);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9822d3c5978b26772e14973c5ba60847bdd65310
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001912_tree_id.txt
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+(4_513:0.00641214,(2_2244:0.39303775,0_2363:0.15553525):0.14190525,3_243:0.00331986);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..54213313da260768969e9029040d242482521c2f
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001914_tree_id.txt
@@ -0,0 +1,2 @@
+(1_500:0.00648852,(2_2255:0.18952025,0_2373:0.19748975):0.20750275,4_500:0.00312048);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d2cc62649cc83e155701cf4935deb63ee1fc8ae3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001915_tree_id.txt
@@ -0,0 +1,2 @@
+(4_413:0.01000075,(0_2470:0.34070825,1_410:0.02249775):0.00488375,3_140:0.00445325);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..18ad28f0e17d419072dd9459057ca89886cc4494
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001916_tree_id.txt
@@ -0,0 +1,2 @@
+((4_375:0.01063325,3_102:-0.00191525):0.00191525,0_2510:0.46259900,1_369:0.00000000);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9c5f8772340ee4af04fd975c17f16291a8ca8c94
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001917_tree_id.txt
@@ -0,0 +1,2 @@
+(4_334:0.01026100,(3_52:0.00206300,1_327:-0.00018100):0.01767400,0_2565:0.12478700);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66946cc5c83fbc8e385546bd4ed9f2ac5ac5c979
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001920_tree_id.txt
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+((3_2033:0.04257217,2_247:1.17513583):0.02008475,1_69:0.03343275,4_63:0.01581625);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6c5e8fddfe29c187b8889807c0193b85b5b3ac95
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001921_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25f31ff5c7e844697831f49c68862384239bfc74
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001922_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2d690a8b10d59ca58828af3788a6c04b6abdb46a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001923_tree_id.txt
@@ -0,0 +1,2 @@
+((1_219:-0.00031650,4_220:0.00485150):0.00031650,3_2183:-0.00031650,2_101:0.02093050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..0471e984c11119b27215c0bdfe5d9e8fce30e49e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001924_tree_id.txt
@@ -0,0 +1,2 @@
+((3_2201:0.00654200,2_82:0.19840800):0.00560950,4_238:0.00610932,1_238:0.00847068);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..2420843a32f926f153612619471e158252c4fe14
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001927_tree_id.txt
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+((3_107:-0.00094900,1_374:0.00459800):0.00423500,2_2377:0.35973800,4_380:0.00328600);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52f5e5b142f955649d35952f7f913f4004210055
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001931_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2206:0.23141800,1_545:0.07538200):0.02164900,3_278:0.03389044,4_547:0.03854856);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d5b9110d386413e536754b9052f0b11d9d63d67b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001933_tree_id.txt
@@ -0,0 +1,2 @@
+((2_2133:0.10456775,3_361:-0.03195675):0.07907725,4_584:-0.03009825,1_615:1.08293225);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f72582948d460276746b09bea83651bd53015b1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001936_tree_id.txt
@@ -0,0 +1,2 @@
+((3_556:0.01005725,2_1927:0.25844175):0.00682175,4_784:0.00274725,1_825:0.00471675);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cf4c87fd935366162e83b9d8bfcdbba12de227a7
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001938_tree_id.txt
@@ -0,0 +1,2 @@
+(2_1801:0.48178800,(1_957:0.00970375,3_680:0.00428225):0.00368925,4_900:0.01484300);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cba397327f10695014b028c5a9c108cff6c2dad3
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001943_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1114:0.00349000,(3_842:0.00000000,4_1064:0.00000000):0.00454100,2_1595:0.88181700);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..bf61a85ce0b64b1588e07a039a51af05a8b11985
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001944_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1165:0.01302995,(3_893:0.00675400,2_1542:0.19926400):0.00320900,4_1122:0.00316705);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..da1c524625d8c2c76f33a0019d10402c062f9253
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001945_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1199:0.00391700,(1_1242:0.00000000,3_970:0.00000000):0.00994000,2_692:0.21881200);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..29b9a18812817a2b956e1248f082600b0e0c9b6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001946_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1452:0.90308000,4_1215:0.01204100):0.01526250,3_990:0.00000050,1_1258:0.00000050);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9dd3b0649e7e20b1ad127934c756ee36a4c98ca0
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001949_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1095:0.00000000,4_1305:0.00000000):0.00377350,2_1373:0.26085150,1_1356:0.00079250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55b318f3343e01573dc255c8a9a13a81fa5d7b26
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001950_tree_id.txt
@@ -0,0 +1,2 @@
+((2_1368:0.15856025,4_1309:0.00272875):0.00153525,1_1360:0.01341608,3_1099:0.00372492);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d64aadf5d48e11ee7efced831db3e57ec0fca5f5
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001951_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1310:0.32309138,(1_1361:0.34820950,2_1367:0.54147950):0.14310450,3_1100:-0.10263238);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..477b01db6d48c9c301e3638907bcc04d78faa91a
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001952_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1311:0.00175313,(2_1366:0.39236500,3_1101:0.21528300):0.06504000,1_1362:0.00394987);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..86838a9e9d939bfe0076e60cdf3c927d7517ca13
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001954_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1142:0.00099150,(4_1350:-0.00167800,1_1401:0.00587100):0.00487950,2_1324:0.05272750);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b884f24d32d8a041eb719b352e5f0978a16074b6
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001955_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1418:0.02350671,(3_1159:0.04004475,2_1306:0.38512425):0.02350125,4_1367:0.02062529);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f3a60431be9b19ff72b18f39cfde28e611fc8cd
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001956_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1165:0.00000000,1_1424:0.00000000):0.00000000,4_1373:0.00000000,2_1300:0.00995200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b4d3082a24e1cefb5d420049dce117c82a0abc68
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001958_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1453:0.12875650,(2_1709:0.00000000,2_2184:0.00000000):0.08104050,2_623:0.24833250);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d22c51f3098ef160a99737b6c49eb7b8c01392a8
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001959_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1260:0.00157400,(2_1197:0.30823250,4_1465:0.00102150):0.00435850,1_1538:0.00337200);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9becca286647a8a41f4ecf605b32c37b1d01b2f9
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001961_tree_id.txt
@@ -0,0 +1,2 @@
+(3_1439:-0.00122627,(4_1651:0.00898425,2_1001:0.39050275):0.03213125,1_1722:0.00651427);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..64426a4cf91daa437282c3cf7a4d97f92afc6438
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001964_tree_id.txt
@@ -0,0 +1,2 @@
+((3_1559:0.00012600,4_1773:0.00249400):0.00764950,2_864:0.13131157,1_1852:0.00944343);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..146d17672755d28a79ea326340c5a0ade3484308
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001967_tree_id.txt
@@ -0,0 +1,2 @@
+(1_1856:0.00804070,(4_1777:0.01020475,2_860:0.36019225):0.00621675,3_1563:0.00145130);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17cc316c23440ea83fa53e6843139627db78bc60
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001968_tree_id.txt
@@ -0,0 +1,2 @@
+((2_859:0.10268550,4_1778:0.00278250):0.00079600,3_1564:0.00456237,1_1857:0.00054263);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..884389665c58240b8a5988e1adf2e47266542742
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001969_tree_id.txt
@@ -0,0 +1,2 @@
+(2_779:0.32329800,(3_1640:0.00000000,1_1935:0.00000000):0.00857600,4_1862:0.01399700);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..166be7120822410bf50d707223cd14f12e07d291
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001970_tree_id.txt
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+(2_778:0.89557837,(3_1641:0.01665025,4_1863:0.02075775):0.00537075,1_1936:0.01365963);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..12393d19227918f47ae048f0da8f29cd545648a1
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001972_tree_id.txt
@@ -0,0 +1,2 @@
+(4_1922:0.00392433,(1_1987:0.00100925,3_1704:0.00799775):0.00193075,2_714:0.31536567);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..511963f31b5efbc9461bc556d6a8179be3e025ff
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001973_tree_id.txt
@@ -0,0 +1,2 @@
+(2_713:0.19433068,(4_1923:0.00095475,1_1988:0.00290425):0.00420825,3_1705:0.00499932);
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..b2dd349437abbf1b73a590a8c972892163fdec6e
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001974_tree_id.txt
@@ -0,0 +1,2 @@
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diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e5cce0e4facfca870473b3ed2f4e1660e290c989
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001975_tree_id.txt
@@ -0,0 +1,2 @@
+(1_2063:-0.00020400,(4_2002:0.00837450,3_1782:0.00475950):0.01837400,2_556:0.02309900);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..61a0c20829cb95a7f66abcff9918272c0afbdf3c
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001977_tree_id.txt
@@ -0,0 +1,2 @@
+((1_2157:0.00228125,3_1881:0.00316475):0.01289075,4_2097:0.00443573,2_456:0.59056127);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4f5c0ca960f3ff724ddac87eaaaa14154b132b2b
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001978_tree_id.txt
@@ -0,0 +1,2 @@
+(2_444:0.12995810,(4_2101:0.00374375,3_1888:0.01060225):0.00078375,1_2161:0.00002590);
+
diff --git a/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc51aad44565f0be4aa9337e79b41b761962ac19
--- /dev/null
+++ b/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135806/orthofinder_output/Results_May15/WorkingDirectory/Trees_ids/OG0001982_tree_id.txt
@@ -0,0 +1,2 @@
+((2_392:1.18538150,2_638:1.26865750):0.25628450,2_1736:0.88935448,2_296:-0.29496448);
+