CHANGELOG.md
LICENSE
MANIFEST.in
README.md
RELEASE_NOTES_0.5.0.md
RELEASE_NOTES_0.6.0.md
pyproject.toml
setup.py
src/Alphabet.py
src/BiMarkers.py
src/BirthDeath.py
src/GTR.py
src/GeneTrees.py
src/GraphUtils.py
src/IO.py
src/Logger.py
src/MSA.py
src/Matrix.py
src/MetropolisHastings.py
src/ModelGraph.py
src/ModelMove.py
src/ModelSelection.py
src/Network.py
src/Newick.py
src/PopulationGenetics.py
src/ReticulationComparison.py
src/SNPSimulator.py
src/State.py
src/Validation.py
src/__init__.py
src/_chain_analysis.py
src/_engines.py
src/_infer_mp_allop.py
src/_infernetworkml.py
src/_mcmc_gt.py
src/_mcmc_seq.py
src/_mpl.py
src/_msnc_density.py
src/_network_moves.py
src/_network_optimizations.py
src/_optimize.py
src/_registry.py
src/_search_flags.py
src/_seq_likelihood.py
src/_sim_markers.py
src/_sim_seq.py
src/_simulate.py
src/_snp_model.py
src/_units.py
src/_version.py
src/infer.py
src/criteria/__init__.py
src/criteria/_objectives.py
src/cython/__init__.py
src/cython/graph_core_cy.pyx
src/cython/gt_msc_cy.pyx
src/cython/mpl_engine_cy.pyx
src/cython/seq_engine_cy.pyx
src/data/__init__.py
src/data/_base.py
src/data/_genetrees.py
src/data/_sequence.py
src/models/__init__.py
src/models/_processes.py