├── .gitignore ├── LICENSE ├── README.md ├── doc ├── Makefile ├── _build │ ├── doctrees │ │ ├── advanced.doctree │ │ ├── calc_qstats.doctree │ │ ├── environment.pickle │ │ ├── faq.doctree │ │ ├── index.doctree │ │ ├── install.doctree │ │ ├── installation.doctree │ │ ├── intro.doctree │ │ ├── merge_output.doctree │ │ ├── output.doctree │ │ ├── outputs.doctree │ │ ├── part2.doctree │ │ ├── prog_desc.doctree │ │ ├── qs.doctree │ │ ├── quartet_sampling.doctree │ │ ├── query_tree.doctree │ │ ├── releases.doctree │ │ └── usage.doctree │ ├── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _sources │ │ │ ├── calc_qstats.rst.txt │ │ │ ├── faq.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── installation.rst.txt │ │ │ ├── intro.rst.txt │ │ │ ├── merge_output.rst.txt │ │ │ ├── output.rst.txt │ │ │ ├── prog_desc.rst.txt │ │ │ ├── qs.rst.txt │ │ │ ├── quartet_sampling.rst.txt │ │ │ ├── query_tree.rst.txt │ │ │ ├── releases.rst.txt │ │ │ └── usage.rst.txt │ │ ├── _static │ │ │ ├── ajax-loader.gif │ │ │ ├── alabaster.css │ │ │ ├── basic.css │ │ │ ├── comment-bright.png │ │ │ ├── comment-close.png │ │ │ ├── comment.png │ │ │ ├── custom.css │ │ │ ├── doctools.js │ │ │ ├── down-pressed.png │ │ │ ├── down.png │ │ │ ├── file.png │ │ │ ├── jquery-3.1.0.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 │ │ ├── calc_qstats.html │ │ ├── faq.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── intro.html │ │ ├── merge_output.html │ │ ├── objects.inv │ │ ├── output.html │ │ ├── prog_desc.html │ │ ├── qs.html │ │ ├── quartet_sampling.html │ │ ├── query_tree.html │ │ ├── releases.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── usage.html │ └── latex │ │ ├── LICRcyr2utf8.xdy │ │ ├── LICRlatin2utf8.xdy │ │ ├── LatinRules.xdy │ │ ├── Makefile │ │ ├── footnotehyper-sphinx.sty │ │ ├── latexmkjarc │ │ ├── latexmkrc │ │ ├── logo.png │ │ ├── make.bat │ │ ├── pdflatex31266.fls │ │ ├── python.ist │ │ ├── quartetsampling.aux │ │ ├── quartetsampling.fdb_latexmk │ │ ├── quartetsampling.fls │ │ ├── quartetsampling.idx │ │ ├── quartetsampling.ilg │ │ ├── quartetsampling.ind │ │ ├── quartetsampling.out │ │ ├── quartetsampling.pdf │ │ ├── quartetsampling.tex │ │ ├── quartetsampling.toc │ │ ├── sphinx.sty │ │ ├── sphinx.xdy │ │ ├── sphinxhighlight.sty │ │ ├── sphinxhowto.cls │ │ ├── sphinxmanual.cls │ │ └── sphinxmulticell.sty ├── calc_qstats.rst ├── conf.py ├── faq.rst ├── index.rst ├── intro.rst ├── logo.png ├── makeargparse.py ├── merge_output.rst ├── output.rst ├── prog_desc.rst ├── quartet_sampling.rst ├── query_tree.rst └── releases.rst ├── pysrc ├── __init__.py ├── alignment.py ├── merge_output.py ├── paramset.py ├── phylo │ ├── __init.py__ │ ├── node.py │ ├── tree_reader.py │ └── tree_utils.py ├── quartet_sampling.py ├── query_tree.py ├── rep_data.py ├── tree_data.py └── utils │ ├── calc_qstats.py │ └── fasta2phy.py ├── quartetsampling.pdf └── test ├── cyp ├── RAxML_fastTreeSH_Support.SH ├── RAxML_info.SH ├── cyp.phy ├── cyp.tre └── test.config ├── run_single_test.py ├── run_tests.py ├── test_2 ├── test.config ├── test.phy └── test.tre ├── test_amino ├── .test.config.swp ├── test.config ├── test.phy └── test.tre ├── test_bigger_balanced ├── test.config ├── test.phy └── test.tre ├── test_paup ├── test.config ├── test.phy └── test.tre ├── test_simple ├── test.config ├── test.phy └── test.tre ├── test_simple_iqtree ├── test.config ├── test.phy └── test.tre └── test_simple_ng ├── test.config ├── test.phy └── test.tre /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FePhyFoFum/quartetsampling/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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