A reimplementation of Hudson's classical ms simulator for modern data sets.
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.circleci Update CI. May 8, 2018
data Removed unused get_ms_commandline method. Mar 14, 2017
docs Document flags reserved and unreserved status. Aug 24, 2018
lib Fix overallocation for node metadata. Sep 20, 2018
msprime Implement xi-beta lambda coalescent Sep 11, 2018
requirements Initial version of provenance schema. Aug 24, 2018
tests Updated test to work on newer glibc. Sep 15, 2018
.codecov.yml Bumped up Python coverage target. Jan 25, 2017
.gitignore Ignore automated version files Oct 30, 2017
.gitmodules Initial addition of the kastore submodule. May 8, 2018
.travis.yml Turn back on OSX travis builds. Jun 18, 2018
CHANGELOG.rst CHANGELOG updates for version 0.6.1. Aug 25, 2018
CITATION.rst Added citation text to docs and CLI help. May 9, 2016
LICENSE Changed license to GPLv3. Sep 15, 2014
MANIFEST.in Initial version of provenance schema. Aug 24, 2018
Makefile Added some 'retrict's to sample_count path. Aug 14, 2018
README.md Update badges to refer to tskit-dev. Jun 3, 2018
README.rst Modernised setup.py, and change README to rst. Feb 2, 2018
UI_update.md Test apis for SparseTree Nov 2, 2016
_msprimemodule.c Working-ish versions of most things. Aug 24, 2018
algorithms.py Tidy up algorithm code. Aug 24, 2018
appveyor.yml Basic tests for kastore functionality. May 8, 2018
ez_setup.py Initial module infrastructure. Sep 22, 2014
large-example.py Fixed up CLI for edges. Sep 27, 2017
msp_dev.py Initial framework. Nov 5, 2015
mspms_dev.py Initial framework. Nov 5, 2015
setup.py Initial version of provenance schema. Aug 24, 2018
stress_lowlevel.py Cleared out some more HDF5 cruft. May 8, 2018
verification.py Implement xi-beta lambda coalescent Sep 11, 2018

README.md

msprime

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msprime is a Python API and command line interface for simulating the coalescent with recombination. Please see the documentation for further information and installation instructions.

If you would like to help make msprime better, please see the developer documentation to get started.

If you are looking for help on a specific issue or would like to ask a question to fellow msprime users, please send an email to the mailing list. By asking questions on the mailing list, you can help to build a searchable knowledge base.

If you use msprime in your work, please cite the PLOS Computational Biology paper. See here for full citation details.