CHANGELOG.rst
LICENSE.txt
MANIFEST.in
README.rst
setup.py
docs/ExpCM.rst
docs/Makefile
docs/README.rst
docs/acknowledgments.rst
docs/api.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/modules.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
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