LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
cherryml/__init__.py
cherryml/__main__.py
cherryml/_cherryml_public_api.py
cherryml/_siterm_public_api.py
cherryml/config.py
cherryml/constants_neurips.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/__init__.py
cherryml/_siterm/_cherryml_vectorized.py
cherryml/_siterm/_learn_site_rate_matrix.py
cherryml/_siterm/_site_specific_rate_matrix.py
cherryml/_siterm/_utils.py
cherryml/_siterm/fast_site_rates.cpp
cherryml/_siterm/fast_site_rates.pyx
cherryml/_siterm/_data/__init__.py
cherryml/_siterm/_maximum_parsimony/maximum_parsimony.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_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/_str.py
cherryml/io/_transitions.py
cherryml/io/_transitions_log_likelihood.py
cherryml/io/_transitions_log_likelihood_per_site.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_cherries.py
cherryml/phylogeny_estimation/_fast_tree.py
cherryml/phylogeny_estimation/_gt_tree_estimator.py
cherryml/phylogeny_estimation/_phyml.py
cherryml/phylogeny_estimation/phylogeny_estimator.py
cherryml/phylogeny_estimation/FastCherries/Makefile
cherryml/phylogeny_estimation/FastCherries/branch_length_estimation.cpp
cherryml/phylogeny_estimation/FastCherries/branch_length_estimation.h
cherryml/phylogeny_estimation/FastCherries/fast_cherries.cpp
cherryml/phylogeny_estimation/FastCherries/io_helpers.cpp
cherryml/phylogeny_estimation/FastCherries/io_helpers.h
cherryml/phylogeny_estimation/FastCherries/pairing_algorithms.cpp
cherryml/phylogeny_estimation/FastCherries/pairing_algorithms.h
cherryml/phylogeny_estimation/FastCherries/test_write.txt
cherryml/phylogeny_estimation/FastCherries/types.h
cherryml/phylogeny_estimation/FastCherries/build/branch_length_estimation.o
cherryml/phylogeny_estimation/FastCherries/build/c8lib.o
cherryml/phylogeny_estimation/FastCherries/build/fast_cherries
cherryml/phylogeny_estimation/FastCherries/build/fast_cherries.o
cherryml/phylogeny_estimation/FastCherries/build/io_helpers.o
cherryml/phylogeny_estimation/FastCherries/build/matrix_exponential.o
cherryml/phylogeny_estimation/FastCherries/build/pairing_algorithms.o
cherryml/phylogeny_estimation/FastCherries/build/r8lib.o
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/c8lib.cpp
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/c8lib.hpp
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/matrix_exponential.cpp
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/matrix_exponential.hpp
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/r8lib.cpp
cherryml/phylogeny_estimation/FastCherries/matrix_exponential/r8lib.hpp
cherryml/phylogeny_estimation/FastCherries/tests/Aln0000_txt-gb_phyml.txt
cherryml/phylogeny_estimation/FastCherries/tests/lg.txt
cherryml/phylogeny_estimation/FastCherries/tests/test_branch_length_estimation.cpp
cherryml/phylogeny_estimation/FastCherries/tests/test_io_helpers.cpp
cherryml/phylogeny_estimation/FastCherries/tests/test_pairing_algorithms.cpp
cherryml/simulation/__init__.py
cherryml/simulation/_simulate_msas.py
cherryml/simulation/simulate.cpp
tests/__init__.py
tests/utils.py