.gitignore
LICENSE
MANIFEST.in
README.md
setup.py
TreeSAK/ALE.py
TreeSAK/ALE1.py
TreeSAK/ALE2.py
TreeSAK/ALE3.py
TreeSAK/ALE4.py
TreeSAK/AssessCVG.py
TreeSAK/AssessMarker.py
TreeSAK/AssessMarkerDeltaLL.py
TreeSAK/AssessMarkerPA.py
TreeSAK/CompareMCMC.py
TreeSAK/ConvertMSA.py
TreeSAK/Dating.py
TreeSAK/ExtractMarkerSeq.py
TreeSAK/FastRoot.py
TreeSAK/FastRoot_backup.py
TreeSAK/GTDB_tree.py
TreeSAK/KEGG_Luo17.py
TreeSAK/MCMCtreeR.py
TreeSAK/MarkerRef2Tree.py
TreeSAK/MarkerSeq2Tree.py
TreeSAK/ModifyTopo.py
TreeSAK/OMA.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.py
TreeSAK/VERSION
TreeSAK/VisHPD95.R
TreeSAK/VisHPD95.py
TreeSAK/__init__.py
TreeSAK/ale_parser.py
TreeSAK/ale_splitter.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/print_leaves.py
TreeSAK/rename_leaves.py
TreeSAK/replace_clades.py
TreeSAK/root_with_out_group.py
TreeSAK/run_TaxaCountStats_R_s1.py
TreeSAK/subsample_drep_gnms.py
TreeSAK/subset_tree.py
TreeSAK/subset_tree_stupid_old_way.py
TreeSAK/test_1.py
TreeSAK/test_2.py
TreeSAK/tmp_1.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
TreeSAK_DateArTree/4.sampling_th.py
TreeSAK_DateArTree/AssessMarker.py
TreeSAK_DateArTree/combine_trees.py
TreeSAK_DateArTree/distribution_plot_Tianhua.py
TreeSAK_DateArTree/get_outgroup_gnms.py
TreeSAK_DateArTree/get_prokka_cmds.py
TreeSAK_DateArTree/iTOL_tree.py
TreeSAK_DateArTree/prototypeSelection.py
TreeSAK_DateArTree/s1_select_ar_gnm.py
TreeSAK_DateArTree/s2_psiblast.py
TreeSAK_DateArTree/s3_Prep_gnm_metadata.py
TreeSAK_DateArTree/s6_decorate_tree.py
TreeSAK_DateArTree/submit_cmds.py
TreeSAK_DateArTree/tmp_1.py
TreeSAK_DateArTree/tmp_2.py
TreeSAK_DateArTree/tmp_3.py
TreeSAK_DateArTree/tmp_4.py
TreeSAK_DateArTree/tmp_5.py
TreeSAK_DateArTree/HGT/runALE.py
TreeSAK_DateArTree/HGT/backup/HGT_ALE.py
TreeSAK_DateArTree/HGT/backup/HGT_MetaCHIP.py
TreeSAK_DateArTree/script_backup/Marker2Tree.py
TreeSAK_DateArTree/script_backup/ModifyTopo.py
TreeSAK_DateArTree/script_backup/Tianhua_deltaLL.py
TreeSAK_DateArTree/script_backup/Tianhua_main_deno100.py
TreeSAK_DateArTree/script_backup/batch_access_itol_Tianhua.py
TreeSAK_DateArTree/script_backup/deltaLL_gene_removal.ipynb
TreeSAK_DateArTree/script_backup/do_rrtc.rb
TreeSAK_DateArTree/script_backup/fit_mcmctree_posterior.R
TreeSAK_DateArTree/script_backup/itol_tree.py
TreeSAK_DateArTree/script_backup/merged_two_trees.py
TreeSAK_DateArTree/script_backup/plot_tree.py
TreeSAK_DateArTree/script_backup/s2_assess_markers.py
TreeSAK_DateArTree/script_backup/s2_select_assessed_marker.py
TreeSAK_DateArTree/script_backup/s4_get_dm_Mash.py
TreeSAK_DateArTree/script_backup/s4_get_dm_fastANI.py
TreeSAK_DateArTree/script_backup/tmp_1.py
TreeSAK_DateArTree/script_backup/tmp_2.py
TreeSAK_DateArTree/script_backup/tmp_3.py
TreeSAK_DateArTree/script_backup/true_by_prob.py
TreeSAK_DateArTree/scripts/dating_pro.py
TreeSAK_DateArTree/scripts/deltaLL.py
TreeSAK_DateArTree/scripts/final_params.py
TreeSAK_DateArTree/scripts/main_deno100.py
TreeSAK_DateArTree/scripts/multiple_sbatch.py
TreeSAK_DateArTree/scripts/untouched_backup/deltaLL.py
TreeSAK_DateArTree/scripts/untouched_backup/final_params.py
TreeSAK_DateArTree/scripts/untouched_backup/main_deno100.py
TreeSAK_DateArTree/scripts/untouched_backup/multiple_sbatch.py
TreeSAK_Sponge/extract_gnm_source.py
TreeSAK_Sponge/get_prokka_cmds.py
TreeSAK_Sponge/prep_metadata.py
TreeSAK_Sponge/tmp_1.py
bin/TreeSAK
bin/__init__.py
images/Bioinformatics.jpg
images/windows_cmds.docx
images/windows_cmds.pdf