├── .gitignore ├── LICENSE ├── README.md ├── docs ├── .nojekyll ├── _sources │ ├── analysis.rst.txt │ ├── extractor.rst.txt │ ├── hyphy.rst.txt │ ├── index.rst.txt │ └── modules.rst.txt ├── _static │ ├── ajax-loader.gif │ ├── alert_info_32.png │ ├── alert_warning_32.png │ ├── basic.css │ ├── bg-page.png │ ├── bullet_orange.png │ ├── comment-bright.png │ ├── comment-close.png │ ├── comment.png │ ├── doctools.js │ ├── documentation_options.js │ ├── down-pressed.png │ ├── down.png │ ├── file.png │ ├── haiku.css │ ├── jquery-3.1.0.js │ ├── jquery-3.2.1.js │ ├── jquery.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore-1.3.1.js │ ├── underscore.js │ ├── up-pressed.png │ ├── up.png │ └── websupport.js ├── analysis.html ├── extractor.html ├── genindex.html ├── hyphy.html ├── index.html ├── modules.html ├── objects.inv ├── py-modindex.html ├── search.html └── searchindex.js ├── examples ├── absrel_selection.tre ├── json-fields.pdf ├── visualize_feature_tree_ete3.py └── visualize_feature_tree_ggtree.R ├── paper ├── paper.bib └── paper.md ├── rawdocs ├── Makefile ├── _build │ ├── doctrees │ │ ├── analysis.doctree │ │ ├── environment.pickle │ │ ├── extractor.doctree │ │ ├── hyphy.doctree │ │ ├── index.doctree │ │ └── modules.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _sources │ │ ├── analysis.rst.txt │ │ ├── extractor.rst.txt │ │ ├── hyphy.rst.txt │ │ ├── index.rst.txt │ │ └── modules.rst.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alert_info_32.png │ │ ├── alert_warning_32.png │ │ ├── basic.css │ │ ├── bg-page.png │ │ ├── bullet_orange.png │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── haiku.css │ │ ├── jquery-3.1.0.js │ │ ├── jquery-3.2.1.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── analysis.html │ │ ├── extractor.html │ │ ├── genindex.html │ │ ├── hyphy.html │ │ ├── index.html │ │ ├── modules.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── analysis.rst ├── conf.py ├── extractor.rst ├── hyphy.rst ├── index.rst ├── make.bat └── modules.rst ├── setup.cfg ├── setup.py ├── src ├── __init__.py ├── analysis.py ├── extractor.py └── hyphy.py └── tests ├── __init__.py ├── phyphy_test.py └── test_data ├── AAgamma.LEISR.json ├── AAnoRV.LEISR.json ├── ABSREL.json ├── BUSTED.json ├── FEL.json ├── FEL_multipartitions.json ├── FUBAR.json ├── LEISR_deprecated.json ├── MEME.json ├── NucNoRV.LEISR.json ├── RELAX.json ├── SLAC.json ├── aa.fasta ├── aa.fna ├── absrel_hyphy_names.csv ├── absrel_original_names.csv ├── codon.fasta ├── codon.fna ├── codon.nexus ├── codon_relax_onelabel.fna ├── codon_relax_twolabels.fna ├── fel.csv ├── fel_multipartitions.csv ├── fubar.csv ├── leisr_v0.23.csv ├── leisr_v0.4.csv ├── lysin.nex ├── lysin.tre ├── lysin_treeless.nex ├── meme.csv ├── sim.py ├── slac_averaged.csv ├── slac_resolved.csv ├── test.tre ├── v0.23.LEISR.json └── v0.4.LEISR.json /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/phyphy/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/phyphy/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/phyphy/HEAD/README.md -------------------------------------------------------------------------------- /docs/.nojekyll: 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