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Make scripts and data available #1

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849d4e2
initial upload of scripts and data
adw96 Aug 21, 2026
0974971
README and MSA
adw96 Aug 21, 2026
2040268
state provenance of gene alignments
adw96 Aug 24, 2026
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1 change: 1 addition & 0 deletions data/COG0436.treefile
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1 change: 1 addition & 0 deletions data/PF01000.treefile
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1 change: 1 addition & 0 deletions data/PF07541.treefile
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1 change: 1 addition & 0 deletions data/TIGR01040.treefile
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1 change: 1 addition & 0 deletions data/arCOG00042.treefile
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1 change: 1 addition & 0 deletions data/arCOG00063.treefile
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1 change: 1 addition & 0 deletions data/arCOG00081.treefile
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1 change: 1 addition & 0 deletions data/arCOG00109.treefile
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1 change: 1 addition & 0 deletions data/arCOG00352.treefile
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1 change: 1 addition & 0 deletions data/arCOG00410.treefile
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1 change: 1 addition & 0 deletions data/arCOG00415.treefile
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1 change: 1 addition & 0 deletions data/arCOG00570.treefile
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1 change: 1 addition & 0 deletions data/arCOG00675.treefile
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1 change: 1 addition & 0 deletions data/arCOG00678.treefile
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1 change: 1 addition & 0 deletions data/arCOG00780.treefile
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1 change: 1 addition & 0 deletions data/arCOG00781.treefile
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(DZ3M.111:0.4989771884,((((((Eukarya_Bodo_saltans:0.2065803623,Eukarya_Naegleria_gruberi:0.9665839615)81.2/73:0.1499012612,Eukarya_Dictyostelium_discoideum:0.2273407779)97.7/77:0.2576638359,Eukarya_Homo_sapiens:0.0714759013)12/32:0.0544599092,Eukarya_Capsaspora_owczarzaki:0.2964211333)100/100:0.7241645416,Kariarchaeaceae_B11T1B5_GCA_022574115:0.4128894563)65.5/34:0.1515496162,((Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.3817570855,(Hodarchaeales_LC_3_GCA_001940645:0.6254168435,Hodarchaeales_S146_22_GCA_015520535:0.2949950261)35.6/61:0.0608976626)88.2/61:0.1456676182,(Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.3568117244,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.4234317648)20/32:0.0927877659)66.5/33:0.0538776851)38.1/55:0.1638236765,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:0.5020982273);
1 change: 1 addition & 0 deletions data/arCOG00785.treefile
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(DZ3M.111:0.9663146916,(((((DZ3M.326:0.2793026382,Hodarchaeales_S146_22_GCA_015520535:0.7470001769)37.4/59:0.0883682782,Hodarchaeales_LC_3_GCA_001940645:0.5191838130)83.4/72:0.1729731016,((Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.6221072991,Kariarchaeaceae_B11T1B5_GCA_022574115:0.4260052628)0/63:0.0000023598,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:1.1507631670)75.2/40:0.1777471582)59.1/30:0.1268986228,Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.5700275656)20.8/35:0.1394171574,Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.5643951589)79.2/74:0.1997067897,(((Eukarya_Bodo_saltans:0.5961267377,Eukarya_Homo_sapiens:0.1226926852)77.9/41:0.1156533422,Eukarya_Capsaspora_owczarzaki:0.5606330982)54.9/36:0.1125805543,Eukarya_Naegleria_gruberi:0.5955188219)94.3/97:0.5375323169);
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(DZ3M.111:0.5709767356,(((((((DZ3M.326:0.2849209838,Hodarchaeales_YT1_057_GCA_016839955:0.3498033086)96.4/90:0.0894466394,(Hodarchaeales_S146_22_GCA_015520535:0.3365203190,Kariarchaeaceae_B11T1B5_GCA_022574115:0.6843617585)96.3/69:0.0949855090)20.6/41:0.0521680281,Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.5679252176)99.6/98:0.1458856117,Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.4653159546)45.1/64:0.0660269881,Hodarchaeales_LC_3_GCA_001940645:0.6581825126)82.2/81:0.1179367825,(Eukarya_Bodo_saltans:0.5147591077,((Eukarya_Dictyostelium_discoideum:0.3944961279,Eukarya_Homo_sapiens:0.3503685493)96.7/95:0.1100429452,Eukarya_Naegleria_gruberi:0.4460115330)95.3/96:0.1102142603)100/100:0.7476757607)98.3/99:0.3275322061,Eukarya_Capsaspora_owczarzaki:3.0738720446)19/56:0.1588924271,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.4762714440);
1 change: 1 addition & 0 deletions data/arCOG00833.treefile
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(DZ3M.111:0.4499379569,((DZ3M.326:0.4147039575,Hodarchaeales_S146_22_GCA_015520535:0.4434670688)0/13:0.0000024301,((((((Eukarya_Bodo_saltans:0.5007063570,Eukarya_Dictyostelium_discoideum:0.2024989923)65.2/56:0.1026068187,Eukarya_Naegleria_gruberi:0.3907493136)69.1/54:0.0719211194,(Eukarya_Capsaspora_owczarzaki:0.1244308503,Eukarya_Homo_sapiens:0.1574419572)59/69:0.0694171667)99.9/100:0.7822537837,Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.0500316561)79.6/56:0.1535121417,((Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.4247590060,Kariarchaeaceae_B11T1B5_GCA_022574115:0.4580768393)0/37:0.0000028385,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.6376893301)92.8/76:0.3279803323)72.9/31:0.0489690721,(Hodarchaeales_LC_3_GCA_001940645:0.0000020508,Hodarchaeales_YT1_057_GCA_016839955:1.9107857718)29.4/60:0.3829282446)81.6/12:0.1035404399)79.4/40:0.1875415205,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:0.4793591376);
1 change: 1 addition & 0 deletions data/arCOG00972.treefile
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(DZ3M.111:0.7560859539,(((DZ3M.326:0.1629844502,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.5509108268)84.3/51:0.1213070166,(((Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.2808268217,Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.3348468634)56.2/72:0.0545243019,Kariarchaeaceae_B11T1B5_GCA_022574115:0.7044767075)69/71:0.1290587407,Hodarchaeales_YT1_057_GCA_016839955:0.4800095977)84.3/53:0.1582441519)37.1/31:0.1274309535,(Hodarchaeales_LC_3_GCA_001940645:0.4763040523,Hodarchaeales_S146_22_GCA_015520535:0.3217286610)60.1/31:0.0689611816)84/71:0.5075023374,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:0.9701009354);
1 change: 1 addition & 0 deletions data/arCOG00976.treefile
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(DZ3M.111:0.5356608976,((((((DZ3M.326:0.3564503002,Hodarchaeales_YT1_057_GCA_016839955:0.3673465511)99.9/98:0.0907304848,Hodarchaeales_S146_22_GCA_015520535:0.5777507208)28.5/52:0.0421527596,Hodarchaeales_LC_3_GCA_001940645:0.6693796082)100/99:0.1171094240,((Eukarya_Bodo_saltans:0.8342052655,Eukarya_Naegleria_gruberi:0.3413379010)100/100:0.2397518854,((Eukarya_Capsaspora_owczarzaki:0.2108934132,Eukarya_Homo_sapiens:0.2982704656)99.7/99:0.0827788240,Eukarya_Dictyostelium_discoideum:0.3610041841)100/99:0.1092557731)100/100:0.7238590232)86.1/81:0.0495807075,((Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.3966248822,Kariarchaeaceae_B11T1B5_GCA_022574115:0.5871376578)100/100:0.2491120558,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.4558303947)99.8/100:0.0926245073)99/92:0.0681737556,Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.4556679578)100/100:0.2400236424,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:0.4982286320);
1 change: 1 addition & 0 deletions data/arCOG00987.treefile
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(DZ3M.111:0.5413660719,((((DZ3M.326:0.4044115678,Hodarchaeales_LC_3_GCA_001940645:0.5692434364)85.7/66:0.1143460246,(((((Eukarya_Bodo_saltans:0.3255631722,Eukarya_Naegleria_gruberi:0.3668255977)51.9/27:0.0718102900,Eukarya_Capsaspora_owczarzaki:0.0716970059)23.1/23:0.0349111764,Eukarya_Homo_sapiens:0.1035984159)95.2/57:0.1201005764,Eukarya_Dictyostelium_discoideum:0.0843602572)100/100:0.8173740926,Hodarchaeales_S146_22_GCA_015520535:0.4192686887)91/70:0.1521467460)75.2/47:0.0590463149,Gerdarchaeales_SZ_4_bin5.60_GCA_011364945:0.6128820759)37.3/35:0.0742259251,Lokiarchaeia_AS27yjCOA_147_GCA_012798355:0.3928305830)47.8/43:0.0947853658,(Heimdallarchaeia_PIR-30_metabat2_scaf2bin.046_GCA_027061945:0.5978584835,Heimdasllarchaeaceae_HM4_B3_GCA_018238585:0.4255538352)87.2/81:0.1072691717);
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