LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
docs/post_process_html.py
docs/source/conf.py
examples/analytic_example/Albanian.tree.152tax.nwk
examples/analytic_example/Anolis.tre
examples/analytic_example/demo2.tree
examples/analytic_example/demo2_ls.tsv
examples/analytic_example/demo_acr_ls.sh
examples/analytic_example/metadata_tab.csv
examples/analytic_example/metadata_tab_ls.csv
examples/analytic_example/show_tree_props.py
examples/analytic_example/svl.csv
examples/automatic_query/basic_example1.nw
examples/automatic_query/basic_example1_metadata1.tsv
examples/automatic_query/collapse_demo.sh
examples/automatic_query/color.config.collapsed
examples/automatic_query/color.config.query
examples/automatic_query/color.config.template
examples/automatic_query/highlight_demo.sh
examples/automatic_query/prune_demo.sh
examples/basic_example0/boolean.tsv
examples/basic_example0/categorical.tsv
examples/basic_example0/categorical_ancestor.tsv
examples/basic_example0/categorical_duplicated.tsv
examples/basic_example0/data.array
examples/basic_example0/demo1.tree
examples/basic_example0/numerical.tsv
examples/basic_example0/run_demo.sh
examples/basic_example0/show_tree_props.py
examples/basic_example0/show_tree_props_ancestor.py
examples/basic_example1/basic_example1.nw
examples/basic_example1/basic_example1_metadata.tsv
examples/basic_example1/basic_example1_metadata1.tsv
examples/basic_example1/basic_example1_metadata2.tsv
examples/basic_example1/example1_demo.sh
examples/basic_example2/FluA_H3_AA.fas
examples/basic_example2/MCC_FluA_H3.nw
examples/basic_example2/MCC_FluA_H3_Genotype.txt
examples/basic_example2/diauxic.array
examples/basic_example2/diauxic.nw
examples/basic_example2/example2_demo.sh
examples/custom_color/basic_example1.nw
examples/custom_color/basic_example1_metadata1.tsv
examples/custom_color/basic_example1_metadata2.tsv
examples/custom_color/color.boolean.config
examples/custom_color/color.categorical.config
examples/custom_color/color.config.template
examples/custom_color/color.datamatrix.config
examples/custom_color/color.numerical.config
examples/custom_color/color.numerical2.config
examples/custom_color/color.numerical3.config
examples/custom_color/data_1col.array
examples/custom_color/data_2col.array
examples/custom_color/data_nan.array
examples/custom_color/demo1.tree
examples/pratical_example/emapper/7955.ENSDARP00000116736.aln.faa
examples/pratical_example/emapper/7955.ENSDARP00000116736.nw
examples/pratical_example/emapper/7955.out.emapper.annotations
examples/pratical_example/emapper/7955.out.emapper.pfam
examples/pratical_example/emapper/7955.out.emapper.smart.out
examples/pratical_example/emapper/emapper_demo.sh
examples/pratical_example/emapper/nifH.faa.aln
examples/pratical_example/emapper/nifH.nw
examples/pratical_example/emapper/nifH.out.emapper.annotations
examples/pratical_example/emapper/nifH.out.emapper.pfam
examples/pratical_example/gtdb_r202/ar122_metadata_r202_lite.tar.gz
examples/pratical_example/gtdb_r202/bac120_metadata_r202_lite.tar.gz
examples/pratical_example/gtdb_r202/gtdbv202.nw
examples/pratical_example/gtdb_r202/gtdbv202_annotated.ete.tar.gz
examples/pratical_example/gtdb_r202/gtdbv202full_demo.sh
examples/pratical_example/gtdb_r202/gtdbv202lite_demo.sh
examples/pratical_example/gtdb_r202/merge_gtdbtree.py
examples/pratical_example/gtdb_r202/progenome3.tar.gz
examples/supporting_information/figure1.zip
examples/supporting_information/figure2.zip
examples/supporting_information/figure3.zip
examples/taxonomy_example/archaea.nw
examples/taxonomy_example/archaea_annotated.nw
examples/taxonomy_example/demo3.tree
examples/taxonomy_example/demo3.tsv
examples/taxonomy_example/demo4.tree
examples/taxonomy_example/demo4.tsv
examples/taxonomy_example/gtdb_v202.tree
examples/taxonomy_example/missing_gtdb_v202.tree
examples/taxonomy_example/missing_ncbi.tree
examples/taxonomy_example/ncbi.tree
examples/taxonomy_example/show_tree_props.py
tests/.coverage
tests/data_matrix.tsv
tests/test_alignment.py
tests/test_analytic.py
tests/test_annotate.py
tests/test_emapper.py
tests/test_plot.py
tests/test_prune.py
tests/test_taxonomic.py
treeprofiler/__init__.py
treeprofiler/app.py
treeprofiler/main.py
treeprofiler/tree_annotate.py
treeprofiler/tree_image.py
treeprofiler/tree_plot.py
treeprofiler.egg-info/PKG-INFO
treeprofiler.egg-info/SOURCES.txt
treeprofiler.egg-info/dependency_links.txt
treeprofiler.egg-info/entry_points.txt
treeprofiler.egg-info/requires.txt
treeprofiler.egg-info/top_level.txt
treeprofiler/layouts/__init__.py
treeprofiler/layouts/conditional_layouts.py
treeprofiler/layouts/general_layouts.py
treeprofiler/layouts/pfam2color.json
treeprofiler/layouts/phylosignal_layouts.py
treeprofiler/layouts/profile_layouts.py
treeprofiler/layouts/select_layouts.py
treeprofiler/layouts/seq_layouts.py
treeprofiler/layouts/smart2color.json
treeprofiler/layouts/staple_layouts.py
treeprofiler/layouts/taxon_layouts.py
treeprofiler/layouts/text_layouts.py
treeprofiler/src/__init__.py
treeprofiler/src/acr_continuous.py
treeprofiler/src/ete_format.py
treeprofiler/src/ls.py
treeprofiler/src/phylosignal.py
treeprofiler/src/utils.py
treeprofiler/static/css/bootstrap-grid.css
treeprofiler/static/css/bootstrap-grid.css.map
treeprofiler/static/css/bootstrap-grid.min.css
treeprofiler/static/css/bootstrap-grid.min.css.map
treeprofiler/static/css/bootstrap-grid.rtl.css
treeprofiler/static/css/bootstrap-grid.rtl.css.map
treeprofiler/static/css/bootstrap-grid.rtl.min.css
treeprofiler/static/css/bootstrap-grid.rtl.min.css.map
treeprofiler/static/css/bootstrap-reboot.css
treeprofiler/static/css/bootstrap-reboot.css.map
treeprofiler/static/css/bootstrap-reboot.min.css
treeprofiler/static/css/bootstrap-reboot.min.css.map
treeprofiler/static/css/bootstrap-reboot.rtl.css
treeprofiler/static/css/bootstrap-reboot.rtl.css.map
treeprofiler/static/css/bootstrap-reboot.rtl.min.css
treeprofiler/static/css/bootstrap-reboot.rtl.min.css.map
treeprofiler/static/css/bootstrap-utilities.css
treeprofiler/static/css/bootstrap-utilities.css.map
treeprofiler/static/css/bootstrap-utilities.min.css
treeprofiler/static/css/bootstrap-utilities.min.css.map
treeprofiler/static/css/bootstrap-utilities.rtl.css
treeprofiler/static/css/bootstrap-utilities.rtl.css.map
treeprofiler/static/css/bootstrap-utilities.rtl.min.css
treeprofiler/static/css/bootstrap-utilities.rtl.min.css.map
treeprofiler/static/css/bootstrap.css
treeprofiler/static/css/bootstrap.css.map
treeprofiler/static/css/bootstrap.min.css
treeprofiler/static/css/bootstrap.min.css.map
treeprofiler/static/css/bootstrap.rtl.css
treeprofiler/static/css/bootstrap.rtl.css.map
treeprofiler/static/css/bootstrap.rtl.min.css
treeprofiler/static/css/bootstrap.rtl.min.css.map
treeprofiler/static/css/explore_tree.css
treeprofiler/static/js/bootstrap.bundle.js
treeprofiler/static/js/bootstrap.bundle.js.map
treeprofiler/static/js/bootstrap.bundle.min.js
treeprofiler/static/js/bootstrap.bundle.min.js.map
treeprofiler/static/js/bootstrap.esm.js
treeprofiler/static/js/bootstrap.esm.js.map
treeprofiler/static/js/bootstrap.esm.min.js
treeprofiler/static/js/bootstrap.esm.min.js.map
treeprofiler/static/js/bootstrap.js
treeprofiler/static/js/bootstrap.js.map
treeprofiler/static/js/bootstrap.min.js
treeprofiler/static/js/bootstrap.min.js.map
treeprofiler/static/js/explore_tree.js
treeprofiler/views/__init__.py
treeprofiler/views/explore_tree_v3.html
treeprofiler/views/job_running.html
treeprofiler/views/tree_details.html
treeprofiler/views/upload_tree.html