.flake8
.travis.yml
CHANGELOG.rst
LICENSE.txt
MANIFEST.in
README.rst
pytest.ini
setup.py
test.bash
test_requirements.txt
docs/ExpCM.rst
docs/Makefile
docs/README.rst
docs/acknowledgments.rst
docs/auxiliary_progs.rst
docs/conf.py
docs/howtouse.rst
docs/implementation.rst
docs/index.rst
docs/indices_and_tables.rst
docs/installation.rst
docs/phydms_comprehensive_prog.rst
docs/phydms_logoplot.rst
docs/phydms_prepalignment.rst
docs/phydms_prog.rst
docs/phydmslib.rst
docs/plot_diffprefs_prior.py
docs/weblinks.txt
docs/_static/BloomLogo.jpg
docs/_static/SUMO1_alignment.jpg
docs/_static/custom.css
docs/_static/diffprefs_logoplot.jpg
docs/_static/diffprefs_logoplot.pdf
docs/_static/diffprefs_prior_plot.png
docs/_static/implementation_tree_example.jpg
docs/_static/omegaoverlay_logoplot.jpg
docs/_static/omegaoverlay_logoplot.pdf
docs/_static/prefs_logoplot.jpg
docs/_static/prefs_logoplot.pdf
phydms.egg-info/PKG-INFO
phydms.egg-info/SOURCES.txt
phydms.egg-info/dependency_links.txt
phydms.egg-info/requires.txt
phydms.egg-info/top_level.txt
phydmslib/__init__.py
phydmslib/_metadata.py
phydmslib/_weblogo_template.eps
phydmslib/constants.py
phydmslib/file_io.py
phydmslib/models.py
phydmslib/numutils.c
phydmslib/numutils.pyx
phydmslib/parsearguments.py
phydmslib/simulate.py
phydmslib/treelikelihood.py
phydmslib/utils.py
phydmslib/weblogo.py
scripts/phydms
scripts/phydms_comprehensive
scripts/phydms_divpressure
scripts/phydms_logoplot
scripts/phydms_prepalignment
tests/README.rst
tests/profile_phydms.py
tests/run_tests.py
tests/run_time_test.err
tests/run_time_test.out
tests/run_time_test.py
tests/test_YNGKPM0.py
tests/test_alignmentSimulation.py
tests/test_alignmentSimulationRandomSeed.py
tests/test_alignmentSimulation_divpressure.py
tests/test_branchScale.py
tests/test_brlenderivatives.py
tests/test_brlenoptimize.py
tests/test_diffprefsbysite.py
tests/test_doctests.py
tests/test_expcm.py
tests/test_expcm_divpressure.py
tests/test_expcm_empirical_phi.py
tests/test_expcm_fitprefs.py
tests/test_expcm_fitprefs_invquadraticprior.py
tests/test_gammadistributedbeta_model.py
tests/test_gammadistributedomega_model.py
tests/test_omegabysite.py
tests/test_phydms_comprehensive.py
tests/test_phydms_divpressure.py
tests/test_phydms_logoplot.py
tests/test_prepalignment.py
tests/test_prepalignment_prealigned.py
tests/test_readDivPressure.py
tests/test_readprefs.py
tests/test_spielmanwr.py
tests/test_treelikelihood.py
tests/test_treelikelihood_fitprefs.py
tests/test_underflow.py
tests/time_test_results.csv
tests/NP_data/NP_alignment.fasta
tests/NP_data/NP_alignment_short.fasta
tests/NP_data/NP_prefs-dms_tools_format.txt
tests/NP_data/NP_prefs.csv
tests/NP_data/NP_prefs.tsv
tests/NP_data/NP_prefs_short.csv
tests/NP_data/NP_tree.newick
tests/NP_data/NP_tree_short.newick
tests/NP_data/README.rst
tests/divpressure_tests/NP_prefs.txt
tests/divpressure_tests/NP_tree.newick
tests/divpressure_tests/divpressure.csv
tests/divpressure_tests/divpressure.tsv
tests/divpressure_tests/divpressure.txt
tests/divpressure_tests/divpressure2.csv
tests/divpressure_tests/simulated_NP.fasta
tests/expected_NP_test_results/ExpCM_NP_prefs_short_diffprefsbysite.txt
tests/expected_NP_test_results/ExpCM_NP_prefs_short_loglikelihood.txt
tests/expected_NP_test_results/ExpCM_NP_prefs_short_modelparams.txt
tests/expected_NP_test_results/ExpCM_NP_prefs_short_omegabysite.txt
tests/expected_NP_test_results/ExpCM_NP_prefs_short_tree.newick
tests/expected_NP_test_results/YNGKP_M0_loglikelihood.txt
tests/expected_NP_test_results/YNGKP_M0_modelparams.txt
tests/expected_NP_test_results/YNGKP_M0_omegabysite.txt
tests/expected_NP_test_results/YNGKP_M0_tree.newick
tests/expected_NP_test_results/YNGKP_M5_loglikelihood.txt
tests/expected_NP_test_results/YNGKP_M5_modelparams.txt
tests/expected_NP_test_results/YNGKP_M5_omegabysite.txt
tests/expected_NP_test_results/YNGKP_M5_tree.newick
tests/expected_NP_test_results/averaged_ExpCM_NP_prefs_short_diffprefsbysite.txt
tests/expected_NP_test_results/averaged_ExpCM_NP_prefs_short_loglikelihood.txt
tests/expected_NP_test_results/averaged_ExpCM_NP_prefs_short_modelparams.txt
tests/expected_NP_test_results/averaged_ExpCM_NP_prefs_short_omegabysite.txt
tests/expected_NP_test_results/averaged_ExpCM_NP_prefs_short_tree.newick
tests/expected_NP_test_results/modelcomparison.md
tests/expected_divpressure_test_results/modelcomparison.csv
tests/expected_divpressure_test_results/modelcomparison.md
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.6_minuniqueness2_purgeseqs_keepseqs.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness1_purgeseqs_keepseqs.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqsFcat_keepseqstest_keepseqsfile.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqs_keepseqs.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqs_keepseqsPanuGgor.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqs_keepseqstest_keepseqsfile.fasta
tests/prepalignment_tests/expected_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqstest_purgeseqsfile_keepseqsPanuGgor.fasta
tests/prepalignment_tests/expected_unaligned_SUMO1_alignment_minidentity0.7_minuniqueness2_purgeseqs_keepseqs.fasta
tests/prepalignment_tests/prealigned_SUMO1_orthologs.fasta
tests/prepalignment_tests/unaligned_SUMO1_orthologs.fasta
tutorial/HA_prefs_avg.csv
tutorial/phydms_tutorial.Rmd
tutorial/phydms_tutorial.html
tutorial/HA/ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA/ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA/ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA/ExpCM_HA_prefs_Thyagarajan_loglikelihood.txt
tutorial/HA/ExpCM_HA_prefs_Thyagarajan_modelparams.txt
tutorial/HA/ExpCM_HA_prefs_Thyagarajan_tree.newick
tutorial/HA/ExpCM_HA_prefs_avg_loglikelihood.txt
tutorial/HA/ExpCM_HA_prefs_avg_modelparams.txt
tutorial/HA/ExpCM_HA_prefs_avg_tree.newick
tutorial/HA/RAxML_tree.newick
tutorial/HA/YNGKP_M0_loglikelihood.txt
tutorial/HA/YNGKP_M0_modelparams.txt
tutorial/HA/YNGKP_M0_tree.newick
tutorial/HA/YNGKP_M5_loglikelihood.txt
tutorial/HA/YNGKP_M5_modelparams.txt
tutorial/HA/YNGKP_M5_tree.newick
tutorial/HA/averaged_ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA/averaged_ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA/averaged_ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA/averaged_ExpCM_HA_prefs_Thyagarajan_loglikelihood.txt
tutorial/HA/averaged_ExpCM_HA_prefs_Thyagarajan_modelparams.txt
tutorial/HA/averaged_ExpCM_HA_prefs_Thyagarajan_tree.newick
tutorial/HA/averaged_ExpCM_HA_prefs_avg_loglikelihood.txt
tutorial/HA/averaged_ExpCM_HA_prefs_avg_modelparams.txt
tutorial/HA/averaged_ExpCM_HA_prefs_avg_tree.newick
tutorial/HA/modelcomparison.md
tutorial/HA/ramxl_output.txt
tutorial/HA/raxml_output.txt
tutorial/HA_diffprefs/ExpCM_HA_prefs_Doud_diffprefsbysite.txt
tutorial/HA_diffprefs/ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA_diffprefs/ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA_diffprefs/ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA_diffprefs/RAxML_tree.newick
tutorial/HA_diffprefs/YNGKP_M0_loglikelihood.txt
tutorial/HA_diffprefs/YNGKP_M0_modelparams.txt
tutorial/HA_diffprefs/YNGKP_M0_tree.newick
tutorial/HA_diffprefs/YNGKP_M5_loglikelihood.txt
tutorial/HA_diffprefs/YNGKP_M5_modelparams.txt
tutorial/HA_diffprefs/YNGKP_M5_tree.newick
tutorial/HA_diffprefs/averaged_ExpCM_HA_prefs_Doud_diffprefsbysite.txt
tutorial/HA_diffprefs/averaged_ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA_diffprefs/averaged_ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA_diffprefs/averaged_ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA_diffprefs/modelcomparison.md
tutorial/HA_diffprefs/ramxl_output.txt
tutorial/HA_diffprefs/raxml_output.txt
tutorial/HA_omegabysite/ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA_omegabysite/ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA_omegabysite/ExpCM_HA_prefs_Doud_omegabysite.txt
tutorial/HA_omegabysite/ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA_omegabysite/RAxML_tree.newick
tutorial/HA_omegabysite/YNGKP_M0_loglikelihood.txt
tutorial/HA_omegabysite/YNGKP_M0_modelparams.txt
tutorial/HA_omegabysite/YNGKP_M0_omegabysite.txt
tutorial/HA_omegabysite/YNGKP_M0_tree.newick
tutorial/HA_omegabysite/YNGKP_M5_loglikelihood.txt
tutorial/HA_omegabysite/YNGKP_M5_modelparams.txt
tutorial/HA_omegabysite/YNGKP_M5_omegabysite.txt
tutorial/HA_omegabysite/YNGKP_M5_tree.newick
tutorial/HA_omegabysite/averaged_ExpCM_HA_prefs_Doud_loglikelihood.txt
tutorial/HA_omegabysite/averaged_ExpCM_HA_prefs_Doud_modelparams.txt
tutorial/HA_omegabysite/averaged_ExpCM_HA_prefs_Doud_omegabysite.txt
tutorial/HA_omegabysite/averaged_ExpCM_HA_prefs_Doud_tree.newick
tutorial/HA_omegabysite/modelcomparison.md
tutorial/HA_omegabysite/ramxl_output.txt
tutorial/HA_omegabysite/raxml_output.txt
tutorial/betaLactamase/ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase/ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase/ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase/RAxML_bestTree.betaLactamase_alignment
tutorial/betaLactamase/RAxML_tree.newick
tutorial/betaLactamase/YNGKP_M0_loglikelihood.txt
tutorial/betaLactamase/YNGKP_M0_modelparams.txt
tutorial/betaLactamase/YNGKP_M0_tree.newick
tutorial/betaLactamase/YNGKP_M5_loglikelihood.txt
tutorial/betaLactamase/YNGKP_M5_modelparams.txt
tutorial/betaLactamase/YNGKP_M5_tree.newick
tutorial/betaLactamase/averaged_ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase/averaged_ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase/averaged_ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase/modelcomparison.md
tutorial/betaLactamase/ramxl_output.txt
tutorial/betaLactamase/raxml_output.txt
tutorial/betaLactamase_diffprefs/ExpCM_betaLactamase_prefs_diffprefsbysite.txt
tutorial/betaLactamase_diffprefs/ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase_diffprefs/ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase_diffprefs/ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase_diffprefs/RAxML_tree.newick
tutorial/betaLactamase_diffprefs/YNGKP_M0_loglikelihood.txt
tutorial/betaLactamase_diffprefs/YNGKP_M0_modelparams.txt
tutorial/betaLactamase_diffprefs/YNGKP_M0_tree.newick
tutorial/betaLactamase_diffprefs/YNGKP_M5_loglikelihood.txt
tutorial/betaLactamase_diffprefs/YNGKP_M5_modelparams.txt
tutorial/betaLactamase_diffprefs/YNGKP_M5_tree.newick
tutorial/betaLactamase_diffprefs/averaged_ExpCM_betaLactamase_prefs_diffprefsbysite.txt
tutorial/betaLactamase_diffprefs/averaged_ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase_diffprefs/averaged_ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase_diffprefs/averaged_ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase_diffprefs/modelcomparison.md
tutorial/betaLactamase_diffprefs/ramxl_output.txt
tutorial/betaLactamase_diffprefs/raxml_output.txt
tutorial/betaLactamase_omegabysite/ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase_omegabysite/ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase_omegabysite/ExpCM_betaLactamase_prefs_omegabysite.txt
tutorial/betaLactamase_omegabysite/ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase_omegabysite/RAxML_tree.newick
tutorial/betaLactamase_omegabysite/YNGKP_M0_loglikelihood.txt
tutorial/betaLactamase_omegabysite/YNGKP_M0_modelparams.txt
tutorial/betaLactamase_omegabysite/YNGKP_M0_omegabysite.txt
tutorial/betaLactamase_omegabysite/YNGKP_M0_tree.newick
tutorial/betaLactamase_omegabysite/YNGKP_M5_loglikelihood.txt
tutorial/betaLactamase_omegabysite/YNGKP_M5_modelparams.txt
tutorial/betaLactamase_omegabysite/YNGKP_M5_omegabysite.txt
tutorial/betaLactamase_omegabysite/YNGKP_M5_tree.newick
tutorial/betaLactamase_omegabysite/averaged_ExpCM_betaLactamase_prefs_loglikelihood.txt
tutorial/betaLactamase_omegabysite/averaged_ExpCM_betaLactamase_prefs_modelparams.txt
tutorial/betaLactamase_omegabysite/averaged_ExpCM_betaLactamase_prefs_omegabysite.txt
tutorial/betaLactamase_omegabysite/averaged_ExpCM_betaLactamase_prefs_tree.newick
tutorial/betaLactamase_omegabysite/modelcomparison.md
tutorial/betaLactamase_omegabysite/ramxl_output.txt
tutorial/betaLactamase_omegabysite/raxml_output.txt
tutorial/example_data/HA_alignment.fasta
tutorial/example_data/HA_prefs_Doud.csv
tutorial/example_data/HA_prefs_Thyagarajan.csv
tutorial/example_data/betaLactamase_alignment.fasta
tutorial/example_data/betaLactamase_enrichmentScores.csv
tutorial/example_data/betaLactamase_prefs.csv
tutorial/logoplots/HA_prefs_Doud.pdf
tutorial/logoplots/HA_prefs_Doud.png
tutorial/logoplots/HA_prefs_Thyagarajan.pdf
tutorial/logoplots/HA_prefs_Thyagarajan.png
tutorial/logoplots/betaLactamase_prefs.pdf
tutorial/logoplots/betaLactamase_prefs.png
tutorial/logoplots/betaLactamase_prefs_beta0.pdf
tutorial/logoplots/betaLactamase_prefs_beta0.png
tutorial/logoplots/betaLactamase_prefs_beta1.pdf
tutorial/logoplots/betaLactamase_prefs_beta1.png
tutorial/logoplots/betaLactamase_prefs_beta3.pdf
tutorial/logoplots/betaLactamase_prefs_beta3.png
tutorial/logoplots/betaLactamase_prefs_diff.pdf
tutorial/logoplots/betaLactamase_prefs_diff.png
tutorial/logoplots/example_data/HA_prefs_Doud_short.csv
tutorial/logoplots/example_data/HA_prefs_Thyagarajan_short.csv
tutorial/logoplots/example_data/betaLactamase_prefs_short.csv