├── .gitignore ├── LICENSE.txt ├── README.md ├── docs ├── Makefile ├── _build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── evolver.doctree │ │ ├── genetics.doctree │ │ ├── index.doctree │ │ ├── matrix_builder.doctree │ │ ├── model.doctree │ │ ├── modules.doctree │ │ ├── newick.doctree │ │ ├── partition.doctree │ │ └── state_freqs.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _sources │ │ ├── evolver.txt │ │ ├── genetics.txt │ │ ├── index.txt │ │ ├── matrix_builder.txt │ │ ├── model.txt │ │ ├── modules.txt │ │ ├── newick.txt │ │ ├── partition.txt │ │ └── state_freqs.txt │ │ ├── _static │ │ ├── agogo.css │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── bgfooter.png │ │ ├── bgtop.png │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── jquery-1.11.1.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── pyvolve_favicon.ico │ │ ├── pyvolve_logo.png │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── evolver.html │ │ ├── genetics.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── matrix_builder.html │ │ ├── model.html │ │ ├── modules.html │ │ ├── newick.html │ │ ├── objects.inv │ │ ├── partition.html │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── state_freqs.html ├── agogo_sjs │ ├── layout.html │ ├── static │ │ ├── agogo.css_t │ │ ├── bgfooter.png │ │ └── bgtop.png │ └── theme.conf ├── conf.py ├── evolver.rst ├── genetics.rst ├── haiku_sjs │ ├── layout.html │ ├── static │ │ ├── alert_info_32.png │ │ ├── alert_warning_32.png │ │ ├── bg-page.png │ │ ├── bullet_orange.png │ │ └── haiku.css_t │ └── theme.conf ├── index.rst ├── make.bat ├── matrix_builder.rst ├── model.rst ├── modules.rst ├── newick.rst ├── partition.rst ├── pyvolve_favicon.ico ├── pyvolve_favicon.idraw ├── pyvolve_logo.idraw ├── pyvolve_logo.png └── state_freqs.rst ├── examples ├── README.md ├── aminoacid_site_heterogeneity.py ├── codon_site_heterogeneity.py ├── custom_aminoacid.py ├── custom_code.py ├── custom_codon.py ├── custom_codon_mutsel.py ├── custom_nucleotide.py ├── custom_nucleotide_mutsel.py ├── file_with_tree.tre ├── nucleotide_branch_heterogeneity.py ├── nucleotide_multipartition.py ├── nucleotide_site_heterogeneity.py ├── simple_aminoacid.py ├── simple_codon.py ├── simple_codon_mutsel.py ├── simple_ecm.py ├── simple_nucleotide.py └── simple_nucleotide_mutsel.py ├── helper_scripts ├── README.md ├── compute_dnds_from_mutsel.py └── count_simulated_dnds.py ├── setup.cfg ├── setup.py ├── src ├── .gitignore ├── __init__.py ├── empirical_matrices.py ├── evolver.py ├── genetics.py ├── matrix_builder.py ├── model.py ├── newick.py ├── paml_models │ ├── AB.paml │ ├── BLOSUM62.paml │ ├── DAYHOFF.paml │ ├── DAYHOFFDCMUT.paml │ ├── FLU.paml │ ├── HIVB.paml │ ├── HIVW.paml │ ├── JTT.paml │ ├── JTTDCMUT.paml │ ├── LG.paml │ ├── MtZoa.paml │ ├── PMB.paml │ ├── VT.paml │ ├── WAG.paml │ ├── convert_empirical_matrices.py │ ├── converted.txt │ ├── cpREV.paml │ ├── mtArt.paml │ ├── mtInv.paml │ ├── mtMAM.paml │ ├── mtMet.paml │ ├── mtREV24.paml │ ├── mtVer.paml │ └── rtREV.paml ├── parameters_sanity.py ├── partition.py └── state_freqs.py ├── tests ├── __init__.py ├── evolFiles │ ├── expected_sim_seed.fasta │ ├── single_part_no_het_rates.txt │ └── two_part_no_het_rates.txt ├── evolver_test.py ├── freqFiles │ ├── testFreq_amino_aln.fasta │ └── testFreq_codon_aln.fasta ├── matrixFiles │ ├── scaled_matrix_homo_gy_w0.5.txt │ └── scaled_matrix_homo_mg_w0.5.txt ├── matrix_builder_test.py ├── modelFiles │ ├── WAG.paml │ ├── scaled_matrix_hetcodon_uneven_w0.2.txt │ ├── scaled_matrix_hetcodon_uneven_w0.8.txt │ ├── scaled_matrix_hetcodon_w0.2.txt │ ├── scaled_matrix_hetcodon_w0.8.txt │ ├── true_ecmrest_matrix.txt │ ├── true_ecmunrest_matrix.txt │ ├── true_gy_matrix.txt │ ├── true_mg_matrix.txt │ ├── true_mutsel_aafit_matrix.txt │ ├── true_mutsel_codonfit_matrix.txt │ ├── true_mutsel_codonfreq_matrix.txt │ ├── true_mutsel_nucfit_matrix.txt │ ├── true_mutsel_nucfreq_matrix.txt │ ├── true_nucleotide_matrix.txt │ └── true_wag_matrix.txt ├── model_test.py ├── newickFiles │ ├── printed_labeledroot.txt │ ├── printed_nodenames.txt │ ├── printed_nodenames_nopropflags.txt │ ├── printed_nodenames_propflags.txt │ ├── printed_noflags.txt │ ├── printed_noflags_scaled.txt │ ├── printed_nopropflags.txt │ ├── printed_propflags.txt │ └── test_tree.tre ├── newick_test.py ├── parameters_sanity_test.py └── state_freqs_test.py └── user_manual ├── citations.bib ├── compare_scaling_results.csv ├── plot_scaling_results.R ├── pyvolve_logo_manual.png ├── pyvolve_manual.pdf ├── pyvolve_manual.tex ├── scaling_schemes.py ├── script.py ├── treeflags_colors.pdf └── yang_neutral_scaling.pdf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /docs/_build/doctrees/evolver.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/evolver.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/genetics.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/genetics.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/matrix_builder.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/matrix_builder.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/model.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/model.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/modules.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/modules.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/newick.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/newick.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/partition.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/partition.doctree -------------------------------------------------------------------------------- /docs/_build/doctrees/state_freqs.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/doctrees/state_freqs.doctree -------------------------------------------------------------------------------- /docs/_build/html/.buildinfo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/.buildinfo -------------------------------------------------------------------------------- /docs/_build/html/_sources/evolver.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/evolver.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/genetics.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/genetics.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/index.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/index.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/matrix_builder.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/matrix_builder.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/model.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/model.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/modules.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/modules.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/newick.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/newick.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/partition.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/partition.txt -------------------------------------------------------------------------------- /docs/_build/html/_sources/state_freqs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_sources/state_freqs.txt -------------------------------------------------------------------------------- /docs/_build/html/_static/agogo.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/agogo.css -------------------------------------------------------------------------------- /docs/_build/html/_static/ajax-loader.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/ajax-loader.gif -------------------------------------------------------------------------------- /docs/_build/html/_static/basic.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/basic.css -------------------------------------------------------------------------------- /docs/_build/html/_static/bgfooter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/bgfooter.png -------------------------------------------------------------------------------- /docs/_build/html/_static/bgtop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/bgtop.png -------------------------------------------------------------------------------- /docs/_build/html/_static/comment-bright.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/comment-bright.png -------------------------------------------------------------------------------- /docs/_build/html/_static/comment-close.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/comment-close.png -------------------------------------------------------------------------------- /docs/_build/html/_static/comment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/comment.png -------------------------------------------------------------------------------- /docs/_build/html/_static/doctools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/doctools.js -------------------------------------------------------------------------------- /docs/_build/html/_static/down-pressed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/down-pressed.png -------------------------------------------------------------------------------- /docs/_build/html/_static/down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/down.png -------------------------------------------------------------------------------- /docs/_build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/file.png -------------------------------------------------------------------------------- /docs/_build/html/_static/jquery-1.11.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/jquery-1.11.1.js -------------------------------------------------------------------------------- /docs/_build/html/_static/jquery.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/jquery.js -------------------------------------------------------------------------------- /docs/_build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/minus.png -------------------------------------------------------------------------------- /docs/_build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/plus.png -------------------------------------------------------------------------------- /docs/_build/html/_static/pygments.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/pygments.css -------------------------------------------------------------------------------- /docs/_build/html/_static/pyvolve_favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/pyvolve_favicon.ico -------------------------------------------------------------------------------- /docs/_build/html/_static/pyvolve_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/pyvolve_logo.png -------------------------------------------------------------------------------- /docs/_build/html/_static/searchtools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/searchtools.js -------------------------------------------------------------------------------- /docs/_build/html/_static/underscore-1.3.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/underscore-1.3.1.js -------------------------------------------------------------------------------- /docs/_build/html/_static/underscore.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/underscore.js -------------------------------------------------------------------------------- /docs/_build/html/_static/up-pressed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/up-pressed.png -------------------------------------------------------------------------------- /docs/_build/html/_static/up.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/up.png -------------------------------------------------------------------------------- /docs/_build/html/_static/websupport.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/_static/websupport.js -------------------------------------------------------------------------------- /docs/_build/html/evolver.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/evolver.html -------------------------------------------------------------------------------- /docs/_build/html/genetics.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/genetics.html -------------------------------------------------------------------------------- /docs/_build/html/genindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/genindex.html -------------------------------------------------------------------------------- /docs/_build/html/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/index.html -------------------------------------------------------------------------------- /docs/_build/html/matrix_builder.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/matrix_builder.html -------------------------------------------------------------------------------- /docs/_build/html/model.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/model.html -------------------------------------------------------------------------------- /docs/_build/html/modules.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/modules.html -------------------------------------------------------------------------------- /docs/_build/html/newick.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/newick.html -------------------------------------------------------------------------------- /docs/_build/html/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/objects.inv -------------------------------------------------------------------------------- /docs/_build/html/partition.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/partition.html -------------------------------------------------------------------------------- /docs/_build/html/py-modindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/py-modindex.html -------------------------------------------------------------------------------- /docs/_build/html/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/search.html -------------------------------------------------------------------------------- /docs/_build/html/searchindex.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/searchindex.js -------------------------------------------------------------------------------- /docs/_build/html/state_freqs.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/_build/html/state_freqs.html -------------------------------------------------------------------------------- /docs/agogo_sjs/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/agogo_sjs/layout.html -------------------------------------------------------------------------------- /docs/agogo_sjs/static/agogo.css_t: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/agogo_sjs/static/agogo.css_t -------------------------------------------------------------------------------- /docs/agogo_sjs/static/bgfooter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/agogo_sjs/static/bgfooter.png -------------------------------------------------------------------------------- /docs/agogo_sjs/static/bgtop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/agogo_sjs/static/bgtop.png -------------------------------------------------------------------------------- /docs/agogo_sjs/theme.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/agogo_sjs/theme.conf -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/evolver.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/evolver.rst -------------------------------------------------------------------------------- /docs/genetics.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/genetics.rst -------------------------------------------------------------------------------- /docs/haiku_sjs/layout.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/layout.html -------------------------------------------------------------------------------- /docs/haiku_sjs/static/alert_info_32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/static/alert_info_32.png -------------------------------------------------------------------------------- /docs/haiku_sjs/static/alert_warning_32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/static/alert_warning_32.png -------------------------------------------------------------------------------- /docs/haiku_sjs/static/bg-page.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/static/bg-page.png -------------------------------------------------------------------------------- /docs/haiku_sjs/static/bullet_orange.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/static/bullet_orange.png -------------------------------------------------------------------------------- /docs/haiku_sjs/static/haiku.css_t: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/static/haiku.css_t -------------------------------------------------------------------------------- /docs/haiku_sjs/theme.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/haiku_sjs/theme.conf -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/matrix_builder.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/matrix_builder.rst -------------------------------------------------------------------------------- /docs/model.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/model.rst -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/modules.rst -------------------------------------------------------------------------------- /docs/newick.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/newick.rst -------------------------------------------------------------------------------- /docs/partition.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/partition.rst -------------------------------------------------------------------------------- /docs/pyvolve_favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/pyvolve_favicon.ico -------------------------------------------------------------------------------- /docs/pyvolve_favicon.idraw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/pyvolve_favicon.idraw -------------------------------------------------------------------------------- /docs/pyvolve_logo.idraw: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/pyvolve_logo.idraw -------------------------------------------------------------------------------- /docs/pyvolve_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/pyvolve_logo.png -------------------------------------------------------------------------------- /docs/state_freqs.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/docs/state_freqs.rst -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/README.md -------------------------------------------------------------------------------- /examples/aminoacid_site_heterogeneity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/aminoacid_site_heterogeneity.py -------------------------------------------------------------------------------- /examples/codon_site_heterogeneity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/codon_site_heterogeneity.py -------------------------------------------------------------------------------- /examples/custom_aminoacid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_aminoacid.py -------------------------------------------------------------------------------- /examples/custom_code.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_code.py -------------------------------------------------------------------------------- /examples/custom_codon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_codon.py -------------------------------------------------------------------------------- /examples/custom_codon_mutsel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_codon_mutsel.py -------------------------------------------------------------------------------- /examples/custom_nucleotide.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_nucleotide.py -------------------------------------------------------------------------------- /examples/custom_nucleotide_mutsel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/custom_nucleotide_mutsel.py -------------------------------------------------------------------------------- /examples/file_with_tree.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/file_with_tree.tre -------------------------------------------------------------------------------- /examples/nucleotide_branch_heterogeneity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/nucleotide_branch_heterogeneity.py -------------------------------------------------------------------------------- /examples/nucleotide_multipartition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/nucleotide_multipartition.py -------------------------------------------------------------------------------- /examples/nucleotide_site_heterogeneity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/nucleotide_site_heterogeneity.py -------------------------------------------------------------------------------- /examples/simple_aminoacid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_aminoacid.py -------------------------------------------------------------------------------- /examples/simple_codon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_codon.py -------------------------------------------------------------------------------- /examples/simple_codon_mutsel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_codon_mutsel.py -------------------------------------------------------------------------------- /examples/simple_ecm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_ecm.py -------------------------------------------------------------------------------- /examples/simple_nucleotide.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_nucleotide.py -------------------------------------------------------------------------------- /examples/simple_nucleotide_mutsel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/examples/simple_nucleotide_mutsel.py -------------------------------------------------------------------------------- /helper_scripts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/helper_scripts/README.md -------------------------------------------------------------------------------- /helper_scripts/compute_dnds_from_mutsel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/helper_scripts/compute_dnds_from_mutsel.py -------------------------------------------------------------------------------- /helper_scripts/count_simulated_dnds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/helper_scripts/count_simulated_dnds.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/setup.py -------------------------------------------------------------------------------- /src/.gitignore: -------------------------------------------------------------------------------- 1 | parser.py* -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/__init__.py -------------------------------------------------------------------------------- /src/empirical_matrices.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/empirical_matrices.py -------------------------------------------------------------------------------- /src/evolver.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/evolver.py -------------------------------------------------------------------------------- /src/genetics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/genetics.py -------------------------------------------------------------------------------- /src/matrix_builder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/matrix_builder.py -------------------------------------------------------------------------------- /src/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/model.py -------------------------------------------------------------------------------- /src/newick.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/newick.py -------------------------------------------------------------------------------- /src/paml_models/AB.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/AB.paml -------------------------------------------------------------------------------- /src/paml_models/BLOSUM62.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/BLOSUM62.paml -------------------------------------------------------------------------------- /src/paml_models/DAYHOFF.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/DAYHOFF.paml -------------------------------------------------------------------------------- /src/paml_models/DAYHOFFDCMUT.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/DAYHOFFDCMUT.paml -------------------------------------------------------------------------------- /src/paml_models/FLU.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/FLU.paml -------------------------------------------------------------------------------- /src/paml_models/HIVB.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/HIVB.paml -------------------------------------------------------------------------------- /src/paml_models/HIVW.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/HIVW.paml -------------------------------------------------------------------------------- /src/paml_models/JTT.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/JTT.paml -------------------------------------------------------------------------------- /src/paml_models/JTTDCMUT.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/JTTDCMUT.paml -------------------------------------------------------------------------------- /src/paml_models/LG.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/LG.paml -------------------------------------------------------------------------------- /src/paml_models/MtZoa.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/MtZoa.paml -------------------------------------------------------------------------------- /src/paml_models/PMB.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/PMB.paml -------------------------------------------------------------------------------- /src/paml_models/VT.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/VT.paml -------------------------------------------------------------------------------- /src/paml_models/WAG.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/WAG.paml -------------------------------------------------------------------------------- /src/paml_models/convert_empirical_matrices.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/convert_empirical_matrices.py -------------------------------------------------------------------------------- /src/paml_models/converted.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/converted.txt -------------------------------------------------------------------------------- /src/paml_models/cpREV.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/cpREV.paml -------------------------------------------------------------------------------- /src/paml_models/mtArt.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtArt.paml -------------------------------------------------------------------------------- /src/paml_models/mtInv.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtInv.paml -------------------------------------------------------------------------------- /src/paml_models/mtMAM.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtMAM.paml -------------------------------------------------------------------------------- /src/paml_models/mtMet.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtMet.paml -------------------------------------------------------------------------------- /src/paml_models/mtREV24.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtREV24.paml -------------------------------------------------------------------------------- /src/paml_models/mtVer.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/mtVer.paml -------------------------------------------------------------------------------- /src/paml_models/rtREV.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/paml_models/rtREV.paml -------------------------------------------------------------------------------- /src/parameters_sanity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/parameters_sanity.py -------------------------------------------------------------------------------- /src/partition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/partition.py -------------------------------------------------------------------------------- /src/state_freqs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/src/state_freqs.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/evolFiles/expected_sim_seed.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/evolFiles/expected_sim_seed.fasta -------------------------------------------------------------------------------- /tests/evolFiles/single_part_no_het_rates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/evolFiles/single_part_no_het_rates.txt -------------------------------------------------------------------------------- /tests/evolFiles/two_part_no_het_rates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/evolFiles/two_part_no_het_rates.txt -------------------------------------------------------------------------------- /tests/evolver_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/evolver_test.py -------------------------------------------------------------------------------- /tests/freqFiles/testFreq_amino_aln.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/freqFiles/testFreq_amino_aln.fasta -------------------------------------------------------------------------------- /tests/freqFiles/testFreq_codon_aln.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/freqFiles/testFreq_codon_aln.fasta -------------------------------------------------------------------------------- /tests/matrixFiles/scaled_matrix_homo_gy_w0.5.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/matrixFiles/scaled_matrix_homo_gy_w0.5.txt -------------------------------------------------------------------------------- /tests/matrixFiles/scaled_matrix_homo_mg_w0.5.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/matrixFiles/scaled_matrix_homo_mg_w0.5.txt -------------------------------------------------------------------------------- /tests/matrix_builder_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/matrix_builder_test.py -------------------------------------------------------------------------------- /tests/modelFiles/WAG.paml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/WAG.paml -------------------------------------------------------------------------------- /tests/modelFiles/scaled_matrix_hetcodon_uneven_w0.2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/scaled_matrix_hetcodon_uneven_w0.2.txt -------------------------------------------------------------------------------- /tests/modelFiles/scaled_matrix_hetcodon_uneven_w0.8.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/scaled_matrix_hetcodon_uneven_w0.8.txt -------------------------------------------------------------------------------- /tests/modelFiles/scaled_matrix_hetcodon_w0.2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/scaled_matrix_hetcodon_w0.2.txt -------------------------------------------------------------------------------- /tests/modelFiles/scaled_matrix_hetcodon_w0.8.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/scaled_matrix_hetcodon_w0.8.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_ecmrest_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_ecmrest_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_ecmunrest_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_ecmunrest_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_gy_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_gy_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mg_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mg_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mutsel_aafit_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mutsel_aafit_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mutsel_codonfit_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mutsel_codonfit_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mutsel_codonfreq_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mutsel_codonfreq_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mutsel_nucfit_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mutsel_nucfit_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_mutsel_nucfreq_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_mutsel_nucfreq_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_nucleotide_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_nucleotide_matrix.txt -------------------------------------------------------------------------------- /tests/modelFiles/true_wag_matrix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/modelFiles/true_wag_matrix.txt -------------------------------------------------------------------------------- /tests/model_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/model_test.py -------------------------------------------------------------------------------- /tests/newickFiles/printed_labeledroot.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_labeledroot.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_nodenames.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_nodenames.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_nodenames_nopropflags.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_nodenames_nopropflags.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_nodenames_propflags.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_nodenames_propflags.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_noflags.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_noflags.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_noflags_scaled.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_noflags_scaled.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_nopropflags.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_nopropflags.txt -------------------------------------------------------------------------------- /tests/newickFiles/printed_propflags.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/printed_propflags.txt -------------------------------------------------------------------------------- /tests/newickFiles/test_tree.tre: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newickFiles/test_tree.tre -------------------------------------------------------------------------------- /tests/newick_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/newick_test.py -------------------------------------------------------------------------------- /tests/parameters_sanity_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/parameters_sanity_test.py -------------------------------------------------------------------------------- /tests/state_freqs_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/tests/state_freqs_test.py -------------------------------------------------------------------------------- /user_manual/citations.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/citations.bib -------------------------------------------------------------------------------- /user_manual/compare_scaling_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/compare_scaling_results.csv -------------------------------------------------------------------------------- /user_manual/plot_scaling_results.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/plot_scaling_results.R -------------------------------------------------------------------------------- /user_manual/pyvolve_logo_manual.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/pyvolve_logo_manual.png -------------------------------------------------------------------------------- /user_manual/pyvolve_manual.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/pyvolve_manual.pdf -------------------------------------------------------------------------------- /user_manual/pyvolve_manual.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/pyvolve_manual.tex -------------------------------------------------------------------------------- /user_manual/scaling_schemes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/scaling_schemes.py -------------------------------------------------------------------------------- /user_manual/script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/script.py -------------------------------------------------------------------------------- /user_manual/treeflags_colors.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/treeflags_colors.pdf -------------------------------------------------------------------------------- /user_manual/yang_neutral_scaling.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sjspielman/pyvolve/HEAD/user_manual/yang_neutral_scaling.pdf --------------------------------------------------------------------------------