.clang-format
.gitignore
.gitmodules
CHANGELOG.md
CITATION.md
LICENSE
MANIFEST.in
Makefile
README.md
algorithms.py
asv.conf.json
codecov.yml
lwt_interface
msp_dev.py
mspms_dev.py
prek.toml
pyproject.toml
setup.py
stress_lowlevel.py
uv.lock
verification.py
.github/zizmor.yml
.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/.clang-format
git-submodules/tskit/.codecov.yml
git-submodules/tskit/.gitignore
git-submodules/tskit/.pre-commit-config.yaml
git-submodules/tskit/CONTRIBUTING.md
git-submodules/tskit/LICENSE
git-submodules/tskit/README.md
git-submodules/tskit/.circleci/config.yml
git-submodules/tskit/.circleci/images/32bit/Dockerfile
git-submodules/tskit/.github/PULL_REQUEST_TEMPLATE.md
git-submodules/tskit/.github/workflows/docs.yml
git-submodules/tskit/.github/workflows/release.yml
git-submodules/tskit/.github/workflows/tests.yml
git-submodules/tskit/.github/workflows/wheels.yml
git-submodules/tskit/.github/workflows/docker/buildwheel.sh
git-submodules/tskit/.github/workflows/docker/shared.env
git-submodules/tskit/c/.gitignore
git-submodules/tskit/c/CHANGELOG.rst
git-submodules/tskit/c/VERSION.txt
git-submodules/tskit/c/meson.build
git-submodules/tskit/c/meson_options.txt
git-submodules/tskit/c/tskit.h
git-submodules/tskit/c/examples/Makefile
git-submodules/tskit/c/examples/api_structure.c
git-submodules/tskit/c/examples/cpp_sorting_example.cpp
git-submodules/tskit/c/examples/error_handling.c
git-submodules/tskit/c/examples/haploid_wright_fisher.c
git-submodules/tskit/c/examples/multichrom_wright_fisher.c
git-submodules/tskit/c/examples/multichrom_wright_fisher_singlethreaded.c
git-submodules/tskit/c/examples/streaming.c
git-submodules/tskit/c/examples/take_ownership.c
git-submodules/tskit/c/examples/tree_iteration.c
git-submodules/tskit/c/examples/tree_traversal.c
git-submodules/tskit/c/subprojects/kastore/README.md
git-submodules/tskit/c/subprojects/kastore/VERSION.txt
git-submodules/tskit/c/subprojects/kastore/kastore.c
git-submodules/tskit/c/subprojects/kastore/kastore.h
git-submodules/tskit/c/subprojects/kastore/meson.build
git-submodules/tskit/c/tests/test_convert.c
git-submodules/tskit/c/tests/test_core.c
git-submodules/tskit/c/tests/test_file_format.c
git-submodules/tskit/c/tests/test_genotypes.c
git-submodules/tskit/c/tests/test_haplotype_matching.c
git-submodules/tskit/c/tests/test_minimal_cpp.cpp
git-submodules/tskit/c/tests/test_stats.c
git-submodules/tskit/c/tests/test_tables.c
git-submodules/tskit/c/tests/test_trees.c
git-submodules/tskit/c/tests/testlib.c
git-submodules/tskit/c/tests/testlib.h
git-submodules/tskit/c/tests/meson-subproject/example.c
git-submodules/tskit/c/tests/meson-subproject/meson.build
git-submodules/tskit/c/tests/meson-subproject/subprojects/tskit
git-submodules/tskit/c/tskit/convert.c
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.c
git-submodules/tskit/c/tskit/haplotype_matching.h
git-submodules/tskit/c/tskit/stats.c
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
git-submodules/tskit/docs/.gitignore
git-submodules/tskit/docs/Makefile
git-submodules/tskit/docs/_config.yml
git-submodules/tskit/docs/_toc.yml
git-submodules/tskit/docs/build.sh
git-submodules/tskit/docs/c-api.rst
git-submodules/tskit/docs/changelogs.rst
git-submodules/tskit/docs/citation.md
git-submodules/tskit/docs/cli.md
git-submodules/tskit/docs/convert_changelog.py
git-submodules/tskit/docs/data-model.md
git-submodules/tskit/docs/development.md
git-submodules/tskit/docs/export.md
git-submodules/tskit/docs/favicon.ico
git-submodules/tskit/docs/file-formats.md
git-submodules/tskit/docs/glossary.md
git-submodules/tskit/docs/ibd.md
git-submodules/tskit/docs/installation.md
git-submodules/tskit/docs/introduction.md
git-submodules/tskit/docs/logo.svg
git-submodules/tskit/docs/metadata.md
git-submodules/tskit/docs/numba.md
git-submodules/tskit/docs/provenance.md
git-submodules/tskit/docs/python-api.md
git-submodules/tskit/docs/quickstart.md
git-submodules/tskit/docs/stats.md
git-submodules/tskit/docs/topological-analysis.md
git-submodules/tskit/docs/_static/README
git-submodules/tskit/docs/_static/bespoke.css
git-submodules/tskit/docs/_static/four_leaf_tree_shapes.png
git-submodules/tskit/docs/_static/tskit_logo_pale.svg
git-submodules/tskit/docs/data/basic_tree_seq.trees
git-submodules/tskit/docs/doxygen/Doxyfile
git-submodules/tskit/docs/substitutions/linear_traversal_warning.rst
git-submodules/tskit/docs/substitutions/table_edit_warning.rst
git-submodules/tskit/docs/substitutions/table_keep_rows_main.rst
git-submodules/tskit/docs/substitutions/tree_array_warning.rst
git-submodules/tskit/docs/substitutions/virtual_root_array_note.rst
git-submodules/tskit/python/.flake8
git-submodules/tskit/python/.gitignore
git-submodules/tskit/python/CHANGELOG.rst
git-submodules/tskit/python/LICENSE
git-submodules/tskit/python/MANIFEST.in
git-submodules/tskit/python/Makefile
git-submodules/tskit/python/README.rst
git-submodules/tskit/python/_tskitmodule.c
git-submodules/tskit/python/development.yml
git-submodules/tskit/python/lib
git-submodules/tskit/python/pyproject.toml
git-submodules/tskit/python/setup.py
git-submodules/tskit/python/stress_lowlevel.py
git-submodules/tskit/python/benchmark/config.yaml
git-submodules/tskit/python/benchmark/run-for-all-releases.py
git-submodules/tskit/python/benchmark/run.py
git-submodules/tskit/python/lwt_interface/CHANGELOG.rst
git-submodules/tskit/python/lwt_interface/Makefile
git-submodules/tskit/python/lwt_interface/README.md
git-submodules/tskit/python/lwt_interface/dict_encoding_testlib.py
git-submodules/tskit/python/lwt_interface/example_c_module.c
git-submodules/tskit/python/lwt_interface/setup.py
git-submodules/tskit/python/lwt_interface/test_example_c_module.py
git-submodules/tskit/python/lwt_interface/tskit_lwt_interface.h
git-submodules/tskit/python/lwt_interface/cython_example/Makefile
git-submodules/tskit/python/lwt_interface/cython_example/_lwtc.c
git-submodules/tskit/python/lwt_interface/cython_example/example.pyx
git-submodules/tskit/python/lwt_interface/cython_example/pyproject.toml
git-submodules/tskit/python/lwt_interface/cython_example/setup.py
git-submodules/tskit/python/tests/__init__.py
git-submodules/tskit/python/tests/conftest.py
git-submodules/tskit/python/tests/ibd.py
git-submodules/tskit/python/tests/simplify.py
git-submodules/tskit/python/tests/test_avl_tree.py
git-submodules/tskit/python/tests/test_balance_metrics.py
git-submodules/tskit/python/tests/test_cli.py
git-submodules/tskit/python/tests/test_coalrate.py
git-submodules/tskit/python/tests/test_combinatorics.py
git-submodules/tskit/python/tests/test_dict_encoding.py
git-submodules/tskit/python/tests/test_distance_metrics.py
git-submodules/tskit/python/tests/test_divmat.py
git-submodules/tskit/python/tests/test_drawing.py
git-submodules/tskit/python/tests/test_extend_haplotypes.py
git-submodules/tskit/python/tests/test_file_format.py
git-submodules/tskit/python/tests/test_fileobj.py
git-submodules/tskit/python/tests/test_genotype_matching.py
git-submodules/tskit/python/tests/test_genotypes.py
git-submodules/tskit/python/tests/test_haplotype_matching.py
git-submodules/tskit/python/tests/test_highlevel.py
git-submodules/tskit/python/tests/test_ibd.py
git-submodules/tskit/python/tests/test_immutable_table_collection.py
git-submodules/tskit/python/tests/test_intervals.py
git-submodules/tskit/python/tests/test_jit.py
git-submodules/tskit/python/tests/test_ld_matrix.py
git-submodules/tskit/python/tests/test_lowlevel.py
git-submodules/tskit/python/tests/test_metadata.py
git-submodules/tskit/python/tests/test_ms.py
git-submodules/tskit/python/tests/test_parsimony.py
git-submodules/tskit/python/tests/test_phylo_formats.py
git-submodules/tskit/python/tests/test_provenance.py
git-submodules/tskit/python/tests/test_reference_sequence.py
git-submodules/tskit/python/tests/test_relatedness_vector.py
git-submodules/tskit/python/tests/test_stats.py
git-submodules/tskit/python/tests/test_table_transforms.py
git-submodules/tskit/python/tests/test_tables.py
git-submodules/tskit/python/tests/test_text_formats.py
git-submodules/tskit/python/tests/test_threads.py
git-submodules/tskit/python/tests/test_topology.py
git-submodules/tskit/python/tests/test_tree_positioning.py
git-submodules/tskit/python/tests/test_tree_stats.py
git-submodules/tskit/python/tests/test_util.py
git-submodules/tskit/python/tests/test_utilities.py
git-submodules/tskit/python/tests/test_vcf.py
git-submodules/tskit/python/tests/test_version.py
git-submodules/tskit/python/tests/test_wright_fisher.py
git-submodules/tskit/python/tests/tsutil.py
git-submodules/tskit/python/tests/data/SLiM/README
git-submodules/tskit/python/tests/data/SLiM/minimal-example.trees
git-submodules/tskit/python/tests/data/SLiM/minimal-example.txt
git-submodules/tskit/python/tests/data/SLiM/single-locus-example.trees
git-submodules/tskit/python/tests/data/SLiM/single-locus-example.txt
git-submodules/tskit/python/tests/data/dict-encodings/generate_msprime.py
git-submodules/tskit/python/tests/data/dict-encodings/msprime-0.7.4.pkl
git-submodules/tskit/python/tests/data/hdf5-formats/msprime-0.3.0_v2.0.hdf5
git-submodules/tskit/python/tests/data/hdf5-formats/msprime-0.4.0_v3.1.hdf5
git-submodules/tskit/python/tests/data/hdf5-formats/msprime-0.5.0_v10.0.hdf5
git-submodules/tskit/python/tests/data/old-formats/tskit-0.3.3.trees
git-submodules/tskit/python/tests/data/simplify-bugs/01-edges.txt
git-submodules/tskit/python/tests/data/simplify-bugs/01-mutations.txt
git-submodules/tskit/python/tests/data/simplify-bugs/01-nodes.txt
git-submodules/tskit/python/tests/data/simplify-bugs/01-sites.txt
git-submodules/tskit/python/tests/data/simplify-bugs/02-edges.txt
git-submodules/tskit/python/tests/data/simplify-bugs/02-mutations.txt
git-submodules/tskit/python/tests/data/simplify-bugs/02-nodes.txt
git-submodules/tskit/python/tests/data/simplify-bugs/02-sites.txt
git-submodules/tskit/python/tests/data/simplify-bugs/03-edges.txt
git-submodules/tskit/python/tests/data/simplify-bugs/03-mutations.txt
git-submodules/tskit/python/tests/data/simplify-bugs/03-nodes.txt
git-submodules/tskit/python/tests/data/simplify-bugs/03-sites.txt
git-submodules/tskit/python/tests/data/simplify-bugs/04-edges.txt
git-submodules/tskit/python/tests/data/simplify-bugs/04-mutations.txt
git-submodules/tskit/python/tests/data/simplify-bugs/04-nodes.txt
git-submodules/tskit/python/tests/data/simplify-bugs/04-sites.txt
git-submodules/tskit/python/tests/data/simplify-bugs/05-edges.txt
git-submodules/tskit/python/tests/data/simplify-bugs/05-mutations.txt
git-submodules/tskit/python/tests/data/simplify-bugs/05-nodes.txt
git-submodules/tskit/python/tests/data/simplify-bugs/05-sites.txt
git-submodules/tskit/python/tests/data/svg/internal_sample_ts.svg
git-submodules/tskit/python/tests/data/svg/tree.svg
git-submodules/tskit/python/tests/data/svg/tree_both_axes.svg
git-submodules/tskit/python/tests/data/svg/tree_muts.svg
git-submodules/tskit/python/tests/data/svg/tree_muts_all_edge.svg
git-submodules/tskit/python/tests/data/svg/tree_poly.svg
git-submodules/tskit/python/tests/data/svg/tree_poly_tracked.svg
git-submodules/tskit/python/tests/data/svg/tree_poly_tracked_collapse.svg
git-submodules/tskit/python/tests/data/svg/tree_simple_collapsed.svg
git-submodules/tskit/python/tests/data/svg/tree_subtree.svg
git-submodules/tskit/python/tests/data/svg/tree_subtrees_with_collapsed.svg
git-submodules/tskit/python/tests/data/svg/tree_timed_muts.svg
git-submodules/tskit/python/tests/data/svg/tree_x_axis.svg
git-submodules/tskit/python/tests/data/svg/tree_y_axis_rank.svg
git-submodules/tskit/python/tests/data/svg/ts.svg
git-submodules/tskit/python/tests/data/svg/ts_max_trees.svg
git-submodules/tskit/python/tests/data/svg/ts_max_trees_treewise.svg
git-submodules/tskit/python/tests/data/svg/ts_multiroot.svg
git-submodules/tskit/python/tests/data/svg/ts_mut_highlight.svg
git-submodules/tskit/python/tests/data/svg/ts_mut_times.svg
git-submodules/tskit/python/tests/data/svg/ts_mut_times_logscale.svg
git-submodules/tskit/python/tests/data/svg/ts_mut_times_titles.svg
git-submodules/tskit/python/tests/data/svg/ts_mutations_no_edges.svg
git-submodules/tskit/python/tests/data/svg/ts_mutations_timed_no_edges.svg
git-submodules/tskit/python/tests/data/svg/ts_no_axes.svg
git-submodules/tskit/python/tests/data/svg/ts_nonbinary.svg
git-submodules/tskit/python/tests/data/svg/ts_plain.svg
git-submodules/tskit/python/tests/data/svg/ts_plain_no_xlab.svg
git-submodules/tskit/python/tests/data/svg/ts_plain_y.svg
git-submodules/tskit/python/tests/data/svg/ts_rank.svg
git-submodules/tskit/python/tests/data/svg/ts_title.svg
git-submodules/tskit/python/tests/data/svg/ts_x_lim.svg
git-submodules/tskit/python/tests/data/svg/ts_xlabel.svg
git-submodules/tskit/python/tests/data/svg/ts_y_axis.svg
git-submodules/tskit/python/tests/data/svg/ts_y_axis_log.svg
git-submodules/tskit/python/tests/data/svg/ts_y_axis_regular.svg
git-submodules/tskit/python/tskit/__init__.py
git-submodules/tskit/python/tskit/__main__.py
git-submodules/tskit/python/tskit/_version.py
git-submodules/tskit/python/tskit/cli.py
git-submodules/tskit/python/tskit/combinatorics.py
git-submodules/tskit/python/tskit/drawing.py
git-submodules/tskit/python/tskit/exceptions.py
git-submodules/tskit/python/tskit/genotypes.py
git-submodules/tskit/python/tskit/intervals.py
git-submodules/tskit/python/tskit/metadata.py
git-submodules/tskit/python/tskit/metadata_schema.schema.json
git-submodules/tskit/python/tskit/provenance.py
git-submodules/tskit/python/tskit/provenance.schema.json
git-submodules/tskit/python/tskit/stats.py
git-submodules/tskit/python/tskit/tables.py
git-submodules/tskit/python/tskit/text_formats.py
git-submodules/tskit/python/tskit/trees.py
git-submodules/tskit/python/tskit/util.py
git-submodules/tskit/python/tskit/vcf.py
git-submodules/tskit/python/tskit/jit/__init__.py
git-submodules/tskit/python/tskit/jit/numba.py
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/scm_file_list.json
msprime.egg-info/scm_version.json
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