.clang-format
.gitignore
.gitmodules
CHANGELOG.md
CITATION.md
LICENSE
MANIFEST.in
Makefile
README.md
algorithms.py
asv.conf.json
codecov.yml
msp_dev.py
mspms_dev.py
prek.toml
pyproject.toml
setup.py
stress_lowlevel.py
uv.lock
verification.py
.github/workflows/docs.yml
.github/workflows/lint.yml
.github/workflows/tests.yml
.github/workflows/wheels.yml
benchmarks/__init__.py
benchmarks/benchmarks.py
benchmarks/check_asv.sh
benchmarks/version_hashes.txt
data/.gitignore
data/Makefile
data/run_old_msprime.py
data/msHOTdir/Makefile
data/msHOTdir/README
data/msHOTdir/eca_funcsHOTmulti.h
data/msHOTdir/ms.h
data/msHOTdir/msGCHOT.c
data/msHOTdir/rand1.c
data/msHOTdir/rand1t.c
data/msHOTdir/rand2.c
data/msHOTdir/rand2t.c
data/msHOTdir/streecGCHOT.c
data/msdir/Makefile
data/msdir/README
data/msdir/ms.c
data/msdir/ms.h
data/msdir/rand1.c
data/msdir/sample_stats.c
data/msdir/streec.c
data/msdir/tajd.c
docs/.gitignore
docs/CHANGELOG.md
docs/CITATION.md
docs/Makefile
docs/_config.yml
docs/_toc.yml
docs/ancestry.md
docs/api.md
docs/build.sh
docs/cli.md
docs/demes_example_01.yaml
docs/demography.md
docs/development.md
docs/favicon.ico
docs/installation.md
docs/intro.md
docs/legacy.md
docs/likelihoods.md
docs/logging.md
docs/msprime_logo.svg
docs/mutations.md
docs/pedigrees.md
docs/quickstart.md
docs/rate_maps.md
docs/replication.md
docs/switch_from_other_simulators.md
docs/utilities.md
docs/_static/.README
docs/_static/Gutenkunst_OOA_diagram.svg
docs/_static/primates.svg
docs/_static/slim_alleles.svg
docs/_templates/.README
git-submodules/tskit/c/tskit.h
git-submodules/tskit/c/subprojects/kastore/kastore.c
git-submodules/tskit/c/subprojects/kastore/kastore.h
git-submodules/tskit/c/tskit/convert.h
git-submodules/tskit/c/tskit/core.c
git-submodules/tskit/c/tskit/core.h
git-submodules/tskit/c/tskit/genotypes.c
git-submodules/tskit/c/tskit/genotypes.h
git-submodules/tskit/c/tskit/haplotype_matching.h
git-submodules/tskit/c/tskit/stats.h
git-submodules/tskit/c/tskit/tables.c
git-submodules/tskit/c/tskit/tables.h
git-submodules/tskit/c/tskit/trees.c
git-submodules/tskit/c/tskit/trees.h
lib/avl.c
lib/avl.h
lib/fenwick.c
lib/fenwick.h
lib/likelihood.c
lib/likelihood.h
lib/meson.build
lib/msprime.c
lib/msprime.h
lib/mutgen.c
lib/object_heap.c
lib/object_heap.h
lib/rate_map.c
lib/rate_map.h
lib/util.c
lib/util.h
lib/subprojects/tskit.wrap
lib/tests/test_ancestry.c
lib/tests/test_core.c
lib/tests/test_fenwick.c
lib/tests/test_likelihood.c
lib/tests/test_mutations.c
lib/tests/test_pedigrees.c
lib/tests/test_rate_map.c
lib/tests/test_sweeps.c
lib/tests/testlib.c
lib/tests/testlib.h
lwt_interface/tskit_lwt_interface.h
msprime/__init__.py
msprime/_msprimemodule.c
msprime/_version.py
msprime/ancestry.py
msprime/cli.py
msprime/core.py
msprime/demography.py
msprime/intervals.py
msprime/likelihood.py
msprime/mutations.py
msprime/pedigrees.py
msprime/provenance.py
msprime/species_trees.py
msprime.egg-info/PKG-INFO
msprime.egg-info/SOURCES.txt
msprime.egg-info/dependency_links.txt
msprime.egg-info/entry_points.txt
msprime.egg-info/requires.txt
msprime.egg-info/top_level.txt
tests/__init__.py
tests/conftest.py
tests/test_algorithms.py
tests/test_ancestry.py
tests/test_cli.py
tests/test_core.py
tests/test_demes.py
tests/test_demography.py
tests/test_deprecation.py
tests/test_dict_encoding.py
tests/test_imports_star.py
tests/test_intervals.py
tests/test_likelihood.py
tests/test_matrix_exponential.py
tests/test_models.py
tests/test_mutations.py
tests/test_pedigree.py
tests/test_provenance.py
tests/test_python_c.py
tests/test_recombination_map.py
tests/test_simulate_from.py
tests/test_species_tree_parsing.py
tests/test_threads.py
tests/tsutil.py
tests/wright_fisher.py
tests/data/SLiM/README
tests/data/SLiM/minimal-example.trees
tests/data/SLiM/minimal-example.txt
tests/data/SLiM/single-locus-example.trees
tests/data/SLiM/single-locus-example.txt
tests/data/species_trees/101g_nucl_conc_unconst.combined.nwk.tre
tests/data/species_trees/91genes_species_rev.tre