LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
treesapp/HMMER_domainTblParser.py
treesapp/MCC_calculator.py
treesapp/__init__.py
treesapp/__main__.py
treesapp/annotate_extra.py
treesapp/assign.py
treesapp/auto_itol_colours_style.py
treesapp/clade_exclusion_evaluator.py
treesapp/classy.py
treesapp/commands.py
treesapp/create_refpkg.py
treesapp/entish.py
treesapp/entrez_utils.py
treesapp/external_command_interface.py
treesapp/extract_tree_clade.py
treesapp/fasta.py
treesapp/file_parsers.py
treesapp/jplace_utils.py
treesapp/lca_calculations.py
treesapp/phylo_dist.py
treesapp/placement_trainer.py
treesapp/treesapp_args.py
treesapp/update_refpkg.py
treesapp/utilities.py
treesapp/wrapper.py
treesapp.egg-info/PKG-INFO
treesapp.egg-info/SOURCES.txt
treesapp.egg-info/dependency_links.txt
treesapp.egg-info/entry_points.txt
treesapp.egg-info/requires.txt
treesapp.egg-info/top_level.txt
treesapp/data/.DS_Store
treesapp/data/ref_build_parameters.tsv
treesapp/data/alignment_data/DsrAB.fa
treesapp/data/alignment_data/GH101.fa
treesapp/data/alignment_data/GH163.fa
treesapp/data/alignment_data/GH20.fa
treesapp/data/alignment_data/GH94.fa
treesapp/data/alignment_data/HydA.fa
treesapp/data/alignment_data/McrA.fa
treesapp/data/alignment_data/McrB.fa
treesapp/data/alignment_data/McrG.fa
treesapp/data/alignment_data/NirK.fa
treesapp/data/alignment_data/NorB.fa
treesapp/data/alignment_data/NrfA.fa
treesapp/data/alignment_data/NxrA.fa
treesapp/data/alignment_data/NxrB.fa
treesapp/data/alignment_data/PF00380.fa
treesapp/data/alignment_data/PF00410.fa
treesapp/data/alignment_data/PF00687.fa
treesapp/data/alignment_data/PF00750.fa
treesapp/data/alignment_data/PF00900.fa
treesapp/data/alignment_data/PF01015.fa
treesapp/data/alignment_data/PF01092.fa
treesapp/data/alignment_data/PF01157.fa
treesapp/data/alignment_data/PF01200.fa
treesapp/data/alignment_data/PF01280.fa
treesapp/data/alignment_data/PF01409.fa
treesapp/data/alignment_data/PF01655.fa
treesapp/data/alignment_data/PF01866.fa
treesapp/data/alignment_data/PF04919.fa
treesapp/data/alignment_data/RadA.fa
treesapp/data/alignment_data/RecA.fa
treesapp/data/alignment_data/RpoB.fa
treesapp/data/alignment_data/mcrG.fa
treesapp/data/alignment_data/napA.fa
treesapp/data/alignment_data/narG.fa
treesapp/data/alignment_data/nifD.fa
treesapp/data/alignment_data/nifH.fa
treesapp/data/alignment_data/nirA.fa
treesapp/data/alignment_data/nirK.fa
treesapp/data/alignment_data/nirS.fa
treesapp/data/alignment_data/nosZ.fa
treesapp/data/alignment_data/p_amoA.fa
treesapp/data/hmm_data/DsrAB.hmm
treesapp/data/hmm_data/GH101.hmm
treesapp/data/hmm_data/GH163.hmm
treesapp/data/hmm_data/GH20.hmm
treesapp/data/hmm_data/GH94.hmm
treesapp/data/hmm_data/HydA.hmm
treesapp/data/hmm_data/McrA.hmm
treesapp/data/hmm_data/McrB.hmm
treesapp/data/hmm_data/McrG.hmm
treesapp/data/hmm_data/NirK.hmm
treesapp/data/hmm_data/NorB.hmm
treesapp/data/hmm_data/NrfA.hmm
treesapp/data/hmm_data/NxrA.hmm
treesapp/data/hmm_data/NxrB.hmm
treesapp/data/hmm_data/PF00380.hmm
treesapp/data/hmm_data/PF00410.hmm
treesapp/data/hmm_data/PF00687.hmm
treesapp/data/hmm_data/PF00750.hmm
treesapp/data/hmm_data/PF00900.hmm
treesapp/data/hmm_data/PF01015.hmm
treesapp/data/hmm_data/PF01092.hmm
treesapp/data/hmm_data/PF01157.hmm
treesapp/data/hmm_data/PF01200.hmm
treesapp/data/hmm_data/PF01280.hmm
treesapp/data/hmm_data/PF01409.hmm
treesapp/data/hmm_data/PF01655.hmm
treesapp/data/hmm_data/PF01866.hmm
treesapp/data/hmm_data/PF04919.hmm
treesapp/data/hmm_data/RadA.hmm
treesapp/data/hmm_data/RecA.hmm
treesapp/data/hmm_data/RpoB.hmm
treesapp/data/hmm_data/mcrG.hmm
treesapp/data/hmm_data/napA.hmm
treesapp/data/hmm_data/narG.hmm
treesapp/data/hmm_data/nifD.hmm
treesapp/data/hmm_data/nifH.hmm
treesapp/data/hmm_data/nirA.hmm
treesapp/data/hmm_data/nirK.hmm
treesapp/data/hmm_data/nirS.hmm
treesapp/data/hmm_data/nosZ.hmm
treesapp/data/hmm_data/p_amoA.hmm
treesapp/data/iTOL_data/DsrAB_Gene.txt
treesapp/data/iTOL_data/DsrAB_colour_strip.txt
treesapp/data/iTOL_data/DsrAB_colours_style.txt
treesapp/data/iTOL_data/GH101_colour_strip.txt
treesapp/data/iTOL_data/GH101_colours_style.txt
treesapp/data/iTOL_data/GH109_colour_strip.txt
treesapp/data/iTOL_data/GH109_colours_style.txt
treesapp/data/iTOL_data/GH163_colour_strip.txt
treesapp/data/iTOL_data/GH163_colours_style.txt
treesapp/data/iTOL_data/GH31_colours_style.txt
treesapp/data/iTOL_data/GH36_Clusters.txt
treesapp/data/iTOL_data/GH36_Clusters_strip.txt
treesapp/data/iTOL_data/GH36_colour_strip.txt
treesapp/data/iTOL_data/GH36_colours_style.txt
treesapp/data/iTOL_data/HydA_colour_strip.txt
treesapp/data/iTOL_data/HydA_colours_style.txt
treesapp/data/iTOL_data/McrA_Metabolism.txt
treesapp/data/iTOL_data/McrA_colour_strip.txt
treesapp/data/iTOL_data/McrA_colours_style.txt
treesapp/data/iTOL_data/MtrA_colour_strip.txt
treesapp/data/iTOL_data/MtrA_colours_style.txt
treesapp/data/iTOL_data/MtrC_colour_strip.txt
treesapp/data/iTOL_data/MtrC_colours_style.txt
treesapp/data/iTOL_data/MtrH_colour_strip.txt
treesapp/data/iTOL_data/MtrH_colours_style.txt
treesapp/data/iTOL_data/NorB_colour_strip.txt
treesapp/data/iTOL_data/NorB_colours_style.txt
treesapp/data/iTOL_data/NrfA_colour_strip.txt
treesapp/data/iTOL_data/NrfA_colours_style.txt
treesapp/data/iTOL_data/NxrB_Gene.txt
treesapp/data/iTOL_data/hzao_Function.txt
treesapp/data/iTOL_data/mcrA_colour_strip.txt
treesapp/data/iTOL_data/mcrA_colours_style.txt
treesapp/data/iTOL_data/mcrB_colour_strip.txt
treesapp/data/iTOL_data/mcrB_colours_style.txt
treesapp/data/iTOL_data/mcrG_colour_strip.txt
treesapp/data/iTOL_data/mcrG_colours_style.txt
treesapp/data/iTOL_data/napA_colour_strip.txt
treesapp/data/iTOL_data/napA_colours_style.txt
treesapp/data/iTOL_data/narG_colour_strip.txt
treesapp/data/iTOL_data/narG_colours_style.txt
treesapp/data/iTOL_data/nirK_colour_strip.txt
treesapp/data/iTOL_data/nirK_colours_style.txt
treesapp/data/iTOL_data/nirS_colour_strip.txt
treesapp/data/iTOL_data/nirS_colours_style.txt
treesapp/data/iTOL_data/norC_colour_strip.txt
treesapp/data/iTOL_data/norC_colours_style.txt
treesapp/data/iTOL_data/nosZ_colour_strip.txt
treesapp/data/iTOL_data/nosZ_colours_style.txt
treesapp/data/iTOL_data/p_amoA_Function.txt
treesapp/data/iTOL_data/p_amoA_Function_strip.txt
treesapp/data/iTOL_data/p_amoA_colour_strip.txt
treesapp/data/iTOL_data/p_amoA_colours_style.txt
treesapp/data/tree_data/.DS_Store
treesapp/data/tree_data/DsrAB_bipartitions.txt
treesapp/data/tree_data/DsrAB_tree.txt
treesapp/data/tree_data/GH101_tree.txt
treesapp/data/tree_data/GH163_tree.txt
treesapp/data/tree_data/GH20_tree.txt
treesapp/data/tree_data/GH94_tree.txt
treesapp/data/tree_data/HydA_tree.txt
treesapp/data/tree_data/McrA_bipartitions.txt
treesapp/data/tree_data/McrA_tree.txt
treesapp/data/tree_data/McrB_bipartitions.txt
treesapp/data/tree_data/McrB_tree.txt
treesapp/data/tree_data/McrG_bipartitions.txt
treesapp/data/tree_data/McrG_tree.txt
treesapp/data/tree_data/NirK_tree.txt
treesapp/data/tree_data/NorB_tree.txt
treesapp/data/tree_data/NrfA_tree.txt
treesapp/data/tree_data/NxrA_tree.txt
treesapp/data/tree_data/NxrB_tree.txt
treesapp/data/tree_data/PF00380_tree.txt
treesapp/data/tree_data/PF00410_tree.txt
treesapp/data/tree_data/PF00687_tree.txt
treesapp/data/tree_data/PF00750_tree.txt
treesapp/data/tree_data/PF00900_tree.txt
treesapp/data/tree_data/PF01015_tree.txt
treesapp/data/tree_data/PF01092_tree.txt
treesapp/data/tree_data/PF01157_tree.txt
treesapp/data/tree_data/PF01200_tree.txt
treesapp/data/tree_data/PF01280_tree.txt
treesapp/data/tree_data/PF01409_tree.txt
treesapp/data/tree_data/PF01655_tree.txt
treesapp/data/tree_data/PF01866_tree.txt
treesapp/data/tree_data/PF04919_tree.txt
treesapp/data/tree_data/RadA_tree.txt
treesapp/data/tree_data/RecA_bipartitions.txt
treesapp/data/tree_data/RecA_tree.txt
treesapp/data/tree_data/RpoB_tree.txt
treesapp/data/tree_data/mcrG_tree.txt
treesapp/data/tree_data/napA_bipartitions.txt
treesapp/data/tree_data/napA_tree.txt
treesapp/data/tree_data/narG_bipartitions.txt
treesapp/data/tree_data/narG_tree.txt
treesapp/data/tree_data/nifD_bipartitions.txt
treesapp/data/tree_data/nifD_tree.txt
treesapp/data/tree_data/nifH_bipartitions.txt
treesapp/data/tree_data/nifH_tree.txt
treesapp/data/tree_data/nirA_bipartitions.txt
treesapp/data/tree_data/nirA_tree.txt
treesapp/data/tree_data/nirK_bipartitions.txt
treesapp/data/tree_data/nirK_tree.txt
treesapp/data/tree_data/nirS_bipartitions.txt
treesapp/data/tree_data/nirS_tree.txt
treesapp/data/tree_data/nosZ_bipartitions.txt
treesapp/data/tree_data/nosZ_tree.txt
treesapp/data/tree_data/p_amoA_bipartitions.txt
treesapp/data/tree_data/p_amoA_tree.txt
treesapp/data/tree_data/tax_ids_DsrAB.txt
treesapp/data/tree_data/tax_ids_GH101.txt
treesapp/data/tree_data/tax_ids_GH163.txt
treesapp/data/tree_data/tax_ids_GH20.txt
treesapp/data/tree_data/tax_ids_GH94.txt
treesapp/data/tree_data/tax_ids_HydA.txt
treesapp/data/tree_data/tax_ids_McrA.txt
treesapp/data/tree_data/tax_ids_McrB.txt
treesapp/data/tree_data/tax_ids_McrG.txt
treesapp/data/tree_data/tax_ids_NirK.txt
treesapp/data/tree_data/tax_ids_NorB.txt
treesapp/data/tree_data/tax_ids_NrfA.txt
treesapp/data/tree_data/tax_ids_NxrA.txt
treesapp/data/tree_data/tax_ids_NxrB.txt
treesapp/data/tree_data/tax_ids_PF00380.txt
treesapp/data/tree_data/tax_ids_PF00410.txt
treesapp/data/tree_data/tax_ids_PF00687.txt
treesapp/data/tree_data/tax_ids_PF00750.txt
treesapp/data/tree_data/tax_ids_PF00900.txt
treesapp/data/tree_data/tax_ids_PF01015.txt
treesapp/data/tree_data/tax_ids_PF01092.txt
treesapp/data/tree_data/tax_ids_PF01157.txt
treesapp/data/tree_data/tax_ids_PF01200.txt
treesapp/data/tree_data/tax_ids_PF01280.txt
treesapp/data/tree_data/tax_ids_PF01409.txt
treesapp/data/tree_data/tax_ids_PF01655.txt
treesapp/data/tree_data/tax_ids_PF01866.txt
treesapp/data/tree_data/tax_ids_PF04919.txt
treesapp/data/tree_data/tax_ids_RadA.txt
treesapp/data/tree_data/tax_ids_RecA.txt
treesapp/data/tree_data/tax_ids_RpoB.txt
treesapp/data/tree_data/tax_ids_napA.txt
treesapp/data/tree_data/tax_ids_narG.txt
treesapp/data/tree_data/tax_ids_nifD.txt
treesapp/data/tree_data/tax_ids_nifH.txt
treesapp/data/tree_data/tax_ids_nirA.txt
treesapp/data/tree_data/tax_ids_nirK.txt
treesapp/data/tree_data/tax_ids_nirS.txt
treesapp/data/tree_data/tax_ids_nosZ.txt
treesapp/data/tree_data/tax_ids_p_amoA.txt
treesapp/extensions/fasta_reader.cpp
treesapp/extensions/tree_parsermodule.cpp
treesapp/include/fasta_reader.hpp
treesapp/sub_binaries/BMGE.jar