LICENSE
MANIFEST.in
README.md
setup.py
cherryml/__init__.py
cherryml/__main__.py
cherryml/_cherryml_public_api.py
cherryml/global_vars.py
cherryml/types.py
cherryml/utils.py
cherryml.egg-info/PKG-INFO
cherryml.egg-info/SOURCES.txt
cherryml.egg-info/dependency_links.txt
cherryml.egg-info/requires.txt
cherryml.egg-info/top_level.txt
cherryml/_siterm/fast_site_rates.cpp
cherryml/benchmarking/__init__.py
cherryml/benchmarking/globals.py
cherryml/benchmarking/lg_paper.py
cherryml/benchmarking/pfam_15k.py
cherryml/benchmarking/_contact_generation/ContactMatrix.py
cherryml/benchmarking/_contact_generation/__init__.py
cherryml/caching/__init__.py
cherryml/caching/_cached.py
cherryml/caching/_cached_computation.py
cherryml/caching/_cached_parallel_computation.py
cherryml/caching/_common.py
cherryml/counting/__init__.py
cherryml/counting/_count_co_transitions.cpp
cherryml/counting/_count_co_transitions.py
cherryml/counting/_count_transitions.cpp
cherryml/counting/_count_transitions.py
cherryml/estimation/__init__.py
cherryml/estimation/_em_lg.py
cherryml/estimation/_em_lg_xrate.py
cherryml/estimation/_jtt_ipw.py
cherryml/estimation/_quantized_transitions_mle.py
cherryml/estimation/_ratelearn/__init__.py
cherryml/estimation/_ratelearn/rate.py
cherryml/estimation/_ratelearn/ratelearner.py
cherryml/estimation/_ratelearn/simulate.py
cherryml/estimation/_ratelearn/trainer.py
cherryml/estimation/historian/src/ECMrest.cpp
cherryml/estimation/historian/src/ECMunrest.cpp
cherryml/estimation/historian/src/alignpath.cpp
cherryml/estimation/historian/src/ctok.cpp
cherryml/estimation/historian/src/dayhoff.cpp
cherryml/estimation/historian/src/diagenv.cpp
cherryml/estimation/historian/src/fastseq.cpp
cherryml/estimation/historian/src/forward.cpp
cherryml/estimation/historian/src/gamma.cpp
cherryml/estimation/historian/src/gason.cpp
cherryml/estimation/historian/src/jc.cpp
cherryml/estimation/historian/src/jcrna.cpp
cherryml/estimation/historian/src/jones.cpp
cherryml/estimation/historian/src/jsonutil.cpp
cherryml/estimation/historian/src/knhx.cpp
cherryml/estimation/historian/src/lg.cpp
cherryml/estimation/historian/src/logger.cpp
cherryml/estimation/historian/src/logsumexp.cpp
cherryml/estimation/historian/src/memsize.cpp
cherryml/estimation/historian/src/model.cpp
cherryml/estimation/historian/src/nexus.cpp
cherryml/estimation/historian/src/optparser.cpp
cherryml/estimation/historian/src/pairhmm.cpp
cherryml/estimation/historian/src/presets.cpp
cherryml/estimation/historian/src/profile.cpp
cherryml/estimation/historian/src/quickalign.cpp
cherryml/estimation/historian/src/recon.cpp
cherryml/estimation/historian/src/refiner.cpp
cherryml/estimation/historian/src/sampler.cpp
cherryml/estimation/historian/src/seqgraph.cpp
cherryml/estimation/historian/src/simulator.cpp
cherryml/estimation/historian/src/span.cpp
cherryml/estimation/historian/src/stockholm.cpp
cherryml/estimation/historian/src/sumprod.cpp
cherryml/estimation/historian/src/tree.cpp
cherryml/estimation/historian/src/util.cpp
cherryml/estimation/historian/src/wag.cpp
cherryml/estimation/historian/t/testaligncount.cpp
cherryml/estimation/historian/t/testbackward.cpp
cherryml/estimation/historian/t/testcountio.cpp
cherryml/estimation/historian/t/testforward.cpp
cherryml/estimation/historian/t/testlogsumexp.cpp
cherryml/estimation/historian/t/testmatexp.cpp
cherryml/estimation/historian/t/testmerge.cpp
cherryml/estimation/historian/t/testnexus.cpp
cherryml/estimation/historian/t/testnj.cpp
cherryml/estimation/historian/t/testnullforward.cpp
cherryml/estimation/historian/t/testnumsubcount.cpp
cherryml/estimation/historian/t/testquickalign.cpp
cherryml/estimation/historian/t/testrateio.cpp
cherryml/estimation/historian/t/testregex.cpp
cherryml/estimation/historian/t/testseqio.cpp
cherryml/estimation/historian/t/testseqprofile.cpp
cherryml/estimation/historian/t/testspan.cpp
cherryml/estimation/historian/t/teststockholm.cpp
cherryml/estimation/historian/t/testsubcount.cpp
cherryml/estimation/historian/t/testsumprod.cpp
cherryml/estimation/historian/t/testtreeio.cpp
cherryml/estimation/historian/t/testupgma.cpp
cherryml/estimation/historian/target/historian.cpp
cherryml/estimation_end_to_end/__init__.py
cherryml/estimation_end_to_end/_cherry.py
cherryml/estimation_end_to_end/_em.py
cherryml/evaluation/__init__.py
cherryml/evaluation/__main__.py
cherryml/evaluation/_evaluation_public_api.py
cherryml/evaluation/_likelihood.py
cherryml/evaluation/_maximal_matching.py
cherryml/evaluation/_metrics.py
cherryml/io/__init__.py
cherryml/io/_contact_map.py
cherryml/io/_count_matrices.py
cherryml/io/_log_likelihood.py
cherryml/io/_msa.py
cherryml/io/_pickle.py
cherryml/io/_rate_matrix.py
cherryml/io/_site_rates.py
cherryml/io/_sites_subset.py
cherryml/io/_tree.py
cherryml/markov_chain/__init__.py
cherryml/markov_chain/_markov_chain.py
cherryml/phylogeny_estimation/__init__.py
cherryml/phylogeny_estimation/_common.py
cherryml/phylogeny_estimation/_fast_tree.py
cherryml/phylogeny_estimation/_gt_tree_estimator.py
cherryml/phylogeny_estimation/_phyml.py
cherryml/simulation/__init__.py
cherryml/simulation/_simulate_msas.py
cherryml/simulation/simulate.cpp
tests/__init__.py
tests/utils.py