.gitignore
LICENSE
MANIFEST.in
README.md
setup.py
TreeSAK/AssessCVG.py
TreeSAK/AssessMarker.py
TreeSAK/AssessMarkerDeltaLL.py
TreeSAK/AssessMarkerPA.py
TreeSAK/CompareMCMC.py
TreeSAK/ConvertMSA.py
TreeSAK/Dating.py
TreeSAK/FastRoot.py
TreeSAK/FastRoot_backup.py
TreeSAK/KEGG_Luo17.py
TreeSAK/MCMCtreeR.py
TreeSAK/Marker2Tree.py
TreeSAK/ModifyTopo.py
TreeSAK/OneLineAln.py
TreeSAK/PMSF.py
TreeSAK/PlotMcmcNode.py
TreeSAK/SingleLinePhy.py
TreeSAK/SliceMSA.py
TreeSAK/SplitScore.py
TreeSAK/TaxaCountStats.R
TreeSAK/TreeSAK_config copy.py
TreeSAK/TreeSAK_config.py
TreeSAK/VERSION
TreeSAK/VisHPD95.R
TreeSAK/VisHPD95.py
TreeSAK/__init__.py
TreeSAK/compare_trees.R
TreeSAK/compare_trees.py
TreeSAK/deltaLL_gene_removal.ipynb
TreeSAK/fa2phy.py
TreeSAK/format_leaf_name.py
TreeSAK/get_arCOG_seq.py
TreeSAK/global_functions.py
TreeSAK/iTOL.py
TreeSAK/parse_deltall_stdout.py
TreeSAK/plot_distruibution_th.py
TreeSAK/prep_mcmctree_ctl.py
TreeSAK/rename_leaves.py
TreeSAK/replace_clades.py
TreeSAK/root_with_out_group.py
TreeSAK/run_TaxaCountStats_R_s1.py
TreeSAK/subset_tree.py
TreeSAK/subset_tree_stupid_old_way.py
TreeSAK/test_1.py
TreeSAK/test_2.py
TreeSAK/tmp_3.py
TreeSAK.egg-info/PKG-INFO
TreeSAK.egg-info/SOURCES.txt
TreeSAK.egg-info/dependency_links.txt
TreeSAK.egg-info/requires.txt
TreeSAK.egg-info/top_level.txt
bin/TreeSAK
bin/__init__.py
example_data/PlotMcmcNode/nodes.txt
example_data/PlotMcmcNode/y_label.txt
example_data/VisHPD95/M1_HPD95.pdf
example_data/VisHPD95/M1_HPD95.pdf.txt
example_data/VisHPD95/label.txt
example_data/VisHPD95/nodes.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_100_clock2_nsample500000_out.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_100_clock3_nsample500000_out.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_50_clock2_nsample500000_out.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_50_clock3_nsample500000_out.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_75_clock2_nsample500000_out.txt
example_data/VisHPD95/mcmc_out/M1_PA_75_DeltaLL_75_clock3_nsample500000_out.txt
images/Bioinformatics.jpg
images/windows_cmds.docx
images/windows_cmds.pdf