treesak 1.53.3__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- TreeSAK/ALE.py +63 -0
- TreeSAK/ALE1.py +268 -0
- TreeSAK/ALE2.py +168 -0
- TreeSAK/ALE2RTC.py +30 -0
- TreeSAK/ALE3.py +205 -0
- TreeSAK/ALE4.py +636 -0
- TreeSAK/ALE5.py +210 -0
- TreeSAK/ALE6.py +401 -0
- TreeSAK/ALE7.py +126 -0
- TreeSAK/ALE_backup.py +1081 -0
- TreeSAK/AssessCVG.py +128 -0
- TreeSAK/AssessMarker.py +306 -0
- TreeSAK/AssessMarkerDeltaLL.py +257 -0
- TreeSAK/AssessMarkerPA.py +317 -0
- TreeSAK/AssessPB.py +113 -0
- TreeSAK/BMGE.jar +0 -0
- TreeSAK/BMGE.py +49 -0
- TreeSAK/C60SR4.nex +127 -0
- TreeSAK/CompareMCMC.py +138 -0
- TreeSAK/ConcateMSA.py +111 -0
- TreeSAK/ConvertMSA.py +135 -0
- TreeSAK/Dir.rb +82 -0
- TreeSAK/ExtractMarkerSeq.py +263 -0
- TreeSAK/FastRoot.py +1175 -0
- TreeSAK/FastRoot_backup.py +1122 -0
- TreeSAK/FigTree.py +34 -0
- TreeSAK/GTDB_tree.py +76 -0
- TreeSAK/GeneTree.py +142 -0
- TreeSAK/KEGG_Luo17.py +807 -0
- TreeSAK/LcaToLeaves.py +66 -0
- TreeSAK/MarkerRef2Tree.py +616 -0
- TreeSAK/MarkerRef2Tree_backup.py +628 -0
- TreeSAK/MarkerSeq2Tree.py +299 -0
- TreeSAK/MarkerSeq2Tree_backup.py +259 -0
- TreeSAK/ModifyTopo.py +116 -0
- TreeSAK/Newick_tree_plotter.py +79 -0
- TreeSAK/OMA.py +170 -0
- TreeSAK/OMA2.py +212 -0
- TreeSAK/OneLineAln.py +50 -0
- TreeSAK/PB.py +155 -0
- TreeSAK/PMSF.py +115 -0
- TreeSAK/PhyloBiAssoc.R +84 -0
- TreeSAK/PhyloBiAssoc.py +167 -0
- TreeSAK/PlotMCMC.py +41 -0
- TreeSAK/PlotMcmcNode.py +152 -0
- TreeSAK/PlotMcmcNode_old.py +252 -0
- TreeSAK/RootTree.py +101 -0
- TreeSAK/RootTreeGTDB.py +371 -0
- TreeSAK/RootTreeGTDB214.py +288 -0
- TreeSAK/RootTreeGTDB220.py +300 -0
- TreeSAK/SequentialDating.py +16 -0
- TreeSAK/SingleAleHGT.py +157 -0
- TreeSAK/SingleLinePhy.py +50 -0
- TreeSAK/SliceMSA.py +142 -0
- TreeSAK/SplitScore.py +21 -0
- TreeSAK/SplitScore1.py +177 -0
- TreeSAK/SplitScore1OMA.py +148 -0
- TreeSAK/SplitScore2.py +608 -0
- TreeSAK/TaxaCountStats.R +256 -0
- TreeSAK/TaxonTree.py +47 -0
- TreeSAK/TreeSAK_config.py +32 -0
- TreeSAK/VERSION +164 -0
- TreeSAK/VisHPD95.R +45 -0
- TreeSAK/VisHPD95.py +200 -0
- TreeSAK/__init__.py +0 -0
- TreeSAK/ale_parser.py +74 -0
- TreeSAK/ale_splitter.py +63 -0
- TreeSAK/alignment_pruner.pl +1471 -0
- TreeSAK/assessOG.py +45 -0
- TreeSAK/batch_itol.py +171 -0
- TreeSAK/catfasta2phy.py +140 -0
- TreeSAK/cogTree.py +185 -0
- TreeSAK/compare_trees.R +30 -0
- TreeSAK/compare_trees.py +255 -0
- TreeSAK/dating.py +264 -0
- TreeSAK/dating_ss.py +361 -0
- TreeSAK/deltall.py +82 -0
- TreeSAK/do_rrtc.rb +464 -0
- TreeSAK/fa2phy.py +42 -0
- TreeSAK/filter_rename_ar53.py +118 -0
- TreeSAK/format_leaf_name.py +70 -0
- TreeSAK/gap_stats.py +38 -0
- TreeSAK/get_SCG_tree.py +742 -0
- TreeSAK/get_arCOG_seq.py +97 -0
- TreeSAK/global_functions.py +222 -0
- TreeSAK/gnm_leaves.py +43 -0
- TreeSAK/iTOL.py +791 -0
- TreeSAK/iTOL_gene_tree.py +80 -0
- TreeSAK/itol_msa_stats.py +56 -0
- TreeSAK/keep_highest_rrtc.py +37 -0
- TreeSAK/koTree.py +194 -0
- TreeSAK/label_gene_tree_by_gnm.py +34 -0
- TreeSAK/label_tree.R +75 -0
- TreeSAK/label_tree.py +121 -0
- TreeSAK/mad.py +708 -0
- TreeSAK/mcmc2tree.py +58 -0
- TreeSAK/mcmcTC copy.py +92 -0
- TreeSAK/mcmcTC.py +104 -0
- TreeSAK/mcmctree_vs_reltime.R +44 -0
- TreeSAK/mcmctree_vs_reltime.py +252 -0
- TreeSAK/merge_pdf.py +32 -0
- TreeSAK/pRTC.py +56 -0
- TreeSAK/parse_mcmctree.py +198 -0
- TreeSAK/parse_reltime.py +141 -0
- TreeSAK/phy2fa.py +37 -0
- TreeSAK/plot_distruibution_th.py +165 -0
- TreeSAK/prep_mcmctree_ctl.py +92 -0
- TreeSAK/print_leaves.py +32 -0
- TreeSAK/pruneMSA.py +63 -0
- TreeSAK/recode.py +73 -0
- TreeSAK/remove_bias.R +112 -0
- TreeSAK/rename_leaves.py +78 -0
- TreeSAK/replace_clade.py +55 -0
- TreeSAK/root_with_out_group.py +84 -0
- TreeSAK/run_TaxaCountStats_R_s1.py +455 -0
- TreeSAK/subsample_drep_gnms.py +74 -0
- TreeSAK/subset.py +69 -0
- TreeSAK/subset_tree_stupid_old_way.py +193 -0
- TreeSAK/supertree.py +330 -0
- TreeSAK/tmp_1.py +19 -0
- TreeSAK/tmp_2.py +19 -0
- TreeSAK/tmp_3.py +120 -0
- TreeSAK/tmp_4.py +43 -0
- TreeSAK/tmp_5.py +12 -0
- TreeSAK/weighted_rand.rb +23 -0
- treesak-1.53.3.data/scripts/TreeSAK +955 -0
- treesak-1.53.3.dist-info/LICENSE +674 -0
- treesak-1.53.3.dist-info/METADATA +27 -0
- treesak-1.53.3.dist-info/RECORD +131 -0
- treesak-1.53.3.dist-info/WHEEL +5 -0
- treesak-1.53.3.dist-info/top_level.txt +1 -0
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Metadata-Version: 2.1
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Name: treesak
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Version: 1.53.3
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Summary: BioSAK
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Home-page: https://github.com/songweizhi/TreeSAK
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Author: Weizhi Song
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Author-email: songwz03@gmail.com
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License: GPL3+
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Keywords: Bioinformatics
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License-File: LICENSE
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Requires-Dist: biopython
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Requires-Dist: matplotlib
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Requires-Dist: numpy
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Requires-Dist: scipy
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Requires-Dist: itolapi
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Requires-Dist: networkx
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Requires-Dist: seaborn
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Requires-Dist: lxml
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Requires-Dist: beautifulsoup4
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Requires-Dist: ete3
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Requires-Dist: arviz
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Requires-Dist: plotly
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Requires-Dist: kaleido
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Requires-Dist: PyPDF3
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Requires-Dist: dendropy
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TreeSAK v1.53.3
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TreeSAK/ALE.py,sha256=Gv5BxwLR6-t0uz6TcKIgQB6wFDB6jlOntBV_0h7tKPU,4499
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TreeSAK/ALE1.py,sha256=gkrO88QP5h2WYyuaFWh66Cr7IEuASqdaVEGwLGn23SM,12426
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TreeSAK/ALE2.py,sha256=WNpYgGJQCWWP2CLLMJ6UeuX9E5SmXtqtpcBg5mbvEjI,7109
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TreeSAK/ALE2RTC.py,sha256=qeXHQFdg9Bv26ZahTMxsbBaLIhxg_-ueWCAPvrvvbQY,779
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TreeSAK/ALE3.py,sha256=ngSmKqPfuWqe0fPOYZleOAUoOmGuwNygT4ABnU6L7dM,8763
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TreeSAK/ALE4.py,sha256=xtIqxPRyBYYa7WDjaq07XPnCM3SVj9--vn6ZYsNileY,33507
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TreeSAK/ALE5.py,sha256=IEK8fxYFARbTIo4G57vn6uM_swDaUlZ-1365a4XQRPQ,8361
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TreeSAK/ALE6.py,sha256=HCk0KFUEeTVdnO0FHYstpGrHFBi8fh7fI6TJuTcNxrk,18775
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TreeSAK/ALE7.py,sha256=w3ju99fleKKDEISpO_AlOMyXkBLIJzH2BTDnvDdDQO0,4997
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TreeSAK/ALE_backup.py,sha256=FU6SiPgvlsyaxH5Oc77tMqiCHWde25iJGDFKbBPVxz8,56120
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TreeSAK/AssessCVG.py,sha256=jMI59pFFDAJ-1pbcq_-ygpy-3EobS6E1_DcLEpypFro,4893
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TreeSAK/AssessMarker.py,sha256=QT2WTzTzWPO8YLjab2TA2Qce4WdzzUjoVTrDkEIdiCY,15774
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TreeSAK/AssessMarkerDeltaLL.py,sha256=SYOK0cql1d5275G4QX1KhvdUR3orXYRvJZJchb1sFx8,12086
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TreeSAK/AssessMarkerPA.py,sha256=1B6Qp-gB1j4Aqiy980O8q_tdjFogSivS_FyJNnXUxvk,15180
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TreeSAK/AssessPB.py,sha256=Hk55l7Nsc2Mpj5sKYQYVt9gAghBaLpiAlHPBXxBlAEY,5076
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TreeSAK/BMGE.jar,sha256=iF4oq7nKklc9EYJP0KQkcc9huf7hOVk2wDnEqRhlTKw,105670
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TreeSAK/BMGE.py,sha256=LBKGKz_L45JTGPMT5Y-s9SMNCrmCd4oLm2KGK2VfJqo,1550
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TreeSAK/C60SR4.nex,sha256=oqGkmURHF1W1I8b5mDuY98lfpEJvEf25tjnLJdU6hiY,4867
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TreeSAK/CompareMCMC.py,sha256=Al8-zPmDxY_Hm0SWiHU8Ik-eypGcJiwZyHZFB5yb8F0,5287
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TreeSAK/ConcateMSA.py,sha256=4CFLSaLpmmyKk9OCYKjXiMzJfE66-WEs0zLYGHx3R44,4126
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TreeSAK/ConvertMSA.py,sha256=DTbEGoA0y1xeMdfkigXMp6zasQNkwolS9_IrGfntFVI,5871
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TreeSAK/Dir.rb,sha256=sTtyfFK9HXTmkUP5DklthCuvEdtYr_-AbubYBwZ82Rk,1862
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TreeSAK/ExtractMarkerSeq.py,sha256=0i8grE7akeU8CO-cmb1Ivxf0mxxapeDfizLRaiIX5Jg,11988
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TreeSAK/FastRoot.py,sha256=tR1d9jEP-yUGN4VlooBeO4SjY5E2yvIaQliZS6jMIjs,45554
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TreeSAK/FastRoot_backup.py,sha256=REYWct6FtmJUJVzSinUn8COMqyUivmYoGx9PkF--lEE,43646
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TreeSAK/FigTree.py,sha256=7WC-hfOZY6P7zfzNZzxoQ0Be_4UR2b3GR_L4w1NxNC8,1153
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TreeSAK/GTDB_tree.py,sha256=h2HaOYDf3RIiPB_V2DGqaHNvcJt5CPC0NlsDndewdfQ,3944
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TreeSAK/GeneTree.py,sha256=kXZf-54X4ejTaRBumP3WOWi9cXvEZILR7W-umSMpUrI,5356
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TreeSAK/KEGG_Luo17.py,sha256=lUdQ6TxtbEtHgGrTAlvblz5ytMJO642HR3iDzxJOhMg,44627
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TreeSAK/LcaToLeaves.py,sha256=d_qP116AzUDtpfrGg-ZhYExF-o4GRVrBvs67bQ1kdWs,2236
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TreeSAK/MarkerRef2Tree.py,sha256=u0KWqD9s0vIf4F1ZbqjQPUsbcEu6Xu6gUrnnp6paDhY,28454
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TreeSAK/MarkerRef2Tree_backup.py,sha256=BLhPLd2V1SdfwkdLaF-hMekiRgFJixRKojwIsozmQ1o,31526
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TreeSAK/MarkerSeq2Tree.py,sha256=_L3J2zgiJx5CMDp56aFItFciUaBr7RuKPtXKC1QiYjA,13197
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TreeSAK/MarkerSeq2Tree_backup.py,sha256=XR4XP6v1nntyEAWNM3qefLPtiYfzi7zspr6XY2lF1Aw,10980
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TreeSAK/ModifyTopo.py,sha256=HzXrz8EqewmQLajLnNXlGNj32GMwWdAwRIntyOSr2a8,3939
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TreeSAK/Newick_tree_plotter.py,sha256=PSx2ywJ3wOE_7Di9_VQDsteOt6bu2-1_YMVDCOmkiNs,3713
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TreeSAK/OMA.py,sha256=X404rVJ5tZCrnp2G1d41C00sYXLAn07xMqC9KD-qeAA,5981
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TreeSAK/OMA2.py,sha256=gX47w4Lzk2MaWiI2mf_u3Mmkyb3c7arBzeBOT11d8fM,8388
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TreeSAK/OneLineAln.py,sha256=Odo-gVxa6zvhZB-0QzOKg3oG90NiYdmkI0Lp2Wcc73E,1679
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TreeSAK/PB.py,sha256=urPYxUuFa3dFArLaDSbcZVLvmAES-3Ho6k9lExT55iU,6826
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TreeSAK/PMSF.py,sha256=dcsbXUObIxfXJBM6FjBScv_-lMT8CY1x4LD7YxDaJWg,5049
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TreeSAK/PhyloBiAssoc.R,sha256=QQOqXaySFwmD0x0kQ0-1OHRaKvY2VCXssIgyMn0YXq8,3080
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TreeSAK/PhyloBiAssoc.py,sha256=9svrQRBiMYFxbdO44967rD2-B97JROMfE44Y6_QpSh4,6917
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TreeSAK/PlotMCMC.py,sha256=4n8w4_sEMOxgpYHsbX2FO4PK2KMp58wmQaAjI0tzYpI,1292
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TreeSAK/PlotMcmcNode.py,sha256=Emb3BaXdNJf3Rlj5rgozy5mGJ-kOG08fjztt4aQIiy0,5139
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TreeSAK/PlotMcmcNode_old.py,sha256=KLqqcRrVIIljuDB4mXAgHNgZR_rGnjU6g5U8_P9uYEQ,9026
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TreeSAK/RootTree.py,sha256=R4ij_DRGEE-zcOnlzPvkkaff4Btyjj_lyoam-Qt6LB0,4178
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TreeSAK/RootTreeGTDB.py,sha256=JotR2xVu8_SjppYb9t4HRvdFzBrImWdT-qnArGN0tYs,16092
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TreeSAK/RootTreeGTDB214.py,sha256=IYn7ceFEwH5HXFQam_-qHvwqLMg5iiTI5oChjsfjgSQ,11761
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TreeSAK/RootTreeGTDB220.py,sha256=Msa8oRAgXftY7_aq7nFmriPPl63bSGsAZqiq13Fxawc,12758
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TreeSAK/SequentialDating.py,sha256=8irBgNH9Tj_3TK5ApwUyzaeQVusmFQrRvRFud7HD1EY,289
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TreeSAK/SingleAleHGT.py,sha256=4YSuSnYgSxdYWKEPnsZ1lRvfYmWVT9JmIILpGPdpkG0,9164
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TreeSAK/SingleLinePhy.py,sha256=CsW8eDhO2-4sUBYfpPDvI8qrMxI4vFn83lDr7Hl7MmY,1418
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TreeSAK/SliceMSA.py,sha256=qaFbV54csd946WO7w96VYSssqGH0EfbmGX01RMf12VE,5660
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TreeSAK/SplitScore.py,sha256=nmGPEGKtZxqUp5dg6WNbXGk-fA4sNuEKkrHtIoQWGyQ,996
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TreeSAK/SplitScore1.py,sha256=5_epfAhv2qXqj1G_JZiMuWhJoec7MGobVPtJhjhMfs8,8083
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TreeSAK/SplitScore1OMA.py,sha256=iyoIGCieen0IZYiNNoPZailyRzRwU4exX1cSAl6-Ako,7225
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TreeSAK/SplitScore2.py,sha256=I5jt96ZD04bDaA49HFAxuZUYrVxDD4sy6sr5gDztwKQ,28691
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TreeSAK/TaxaCountStats.R,sha256=ICZ4k7zwQbXNr8SY0t7Ku5TvtzZbUupXhyMvkYRvpek,13027
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TreeSAK/TaxonTree.py,sha256=uihyjlHeFdAr8uHpfnHaURBwDO79zr0iasCwaX-rFz8,1540
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TreeSAK/TreeSAK_config.py,sha256=lclcRmKDFZlLCCNWoXiqHxAmQdz-nGfpw9EkgDmM0s8,2030
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TreeSAK/VERSION,sha256=FAPaziccIUC-6KfStiGeVpo-WZqE4SWA0nSsu54A6Lo,2165
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TreeSAK/VisHPD95.R,sha256=ant381eB_NwHae155BAOyuBEMvQekXBOwm186QoAHsY,2593
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TreeSAK/VisHPD95.py,sha256=lCITnoaD_ZMrmXVWjrKTskB2MZAoJj3CW55llmSpeS4,7566
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TreeSAK/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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TreeSAK/ale_parser.py,sha256=liXahFch_0gGMj8Ja7MzoRnOv3-hWEgxpB0QbHzjPcE,2672
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TreeSAK/ale_splitter.py,sha256=_XaTxdsiiKoXOLR_H9xRuNi-jY26xJ_nxARnu1wvfcY,2493
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TreeSAK/alignment_pruner.pl,sha256=lO5eO8vPsZ-bVGnbWS6yDB4_kvrgdO9YT6XnloQpgGQ,40925
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TreeSAK/assessOG.py,sha256=Kbc1izl3tl1mvuhSWkdbfFEjEjWUJXMlXvpqpBVsgRk,1341
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TreeSAK/batch_itol.py,sha256=gqxV-xQU7cfjAxGGmstncwEIhuO8qa-giOcQr-3Ur5Y,8341
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TreeSAK/catfasta2phy.py,sha256=7kcRUaFXa8DYDynK3Dc6tDjEbgK6eOIdoOtI2LB_A9A,5472
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TreeSAK/cogTree.py,sha256=U2HVaTZnDgZkJ82OwMobrvfcXmtyF6Y-lhJnnULB04I,8039
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TreeSAK/compare_trees.R,sha256=Zs7LJO9NY1g9ovuj2sI8IvDMQTyXQxkX_X2o5RqMu4w,1076
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TreeSAK/compare_trees.py,sha256=x5wUX_5F4hKLB7RbxCj5C44oAAUQ8BqKaL8Oj_qaeJU,10641
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TreeSAK/dating.py,sha256=yxnICZjpExeGne25COF5G9r6sTqDQb5re5pmQ1IiIu4,13132
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TreeSAK/dating_ss.py,sha256=QsfUJPCXn1z_BS5MzLWfj_RDmpsf5y9v9eclbUZa3ck,21377
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TreeSAK/deltall.py,sha256=_smZSb699Wb2pZkPQOIm_CGz7kDUuWcFh3qBDorEByc,3294
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TreeSAK/do_rrtc.rb,sha256=X1kycUd8_nkaT39cvZzUomAqTg3lDgekfYyyRAFtknA,12753
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