Metadata-Version: 2.1
Name: tsinfer
Version: 0.4.0a2
Summary: Infer tree sequences from genetic variation data.
Home-page: https://tskit.dev/tsinfer
Author: Tskit Developers
Author-email: Tskit Developers <admin@tskit.dev>
License: GNU GPLv3+
Project-URL: Homepage, https://tskit.dev/tsinfer
Project-URL: Documentation, https://tskit.dev/tsinfer/docs/stable
Project-URL: Changelog, https://tskit.dev/tsinfer/docs/stable/CHANGELOG.html
Project-URL: Bug Tracker, https://github.com/tskit-dev/tsinfer/issues
Project-URL: Source Code, https://github.com/tskit-dev/tsinfer/
Keywords: population genetics,tree sequence,ancestral recombination graph,evolutionary tree,inference,tsinfer
Platform: POSIX
Platform: Windows
Platform: MacOS X
Classifier: Programming Language :: C
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.23.5
Requires-Dist: six
Requires-Dist: tqdm
Requires-Dist: humanize
Requires-Dist: daiquiri
Requires-Dist: tskit>=0.5.3
Requires-Dist: numcodecs>=0.6
Requires-Dist: zarr!=2.11.0,!=2.11.1,!=2.11.2,<3,>=2.2
Requires-Dist: lmdb
Requires-Dist: sortedcontainers
Requires-Dist: attrs>=19.2.0
Requires-Dist: dask[array]
Requires-Dist: numba

# tsinfer <img align="right" width="145" height="90" src="https://raw.githubusercontent.com/tskit-dev/tsinfer/main/docs/tsinfer_logo.svg">

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Infer a tree sequence from genetic variation data

The [documentation](https://tskit.dev/tsinfer/docs/latest) contains details of how to use this software, including [installation instructions](https://tskit.dev/tsinfer/docs/latest/installation.html).

The initial algorithm, its rationale, and results from testing on simulated and real data are described in the following [Nature Genetics paper](https://doi.org/10.1038/s41588-019-0483-y):

> Jerome Kelleher, Yan Wong, Anthony W Wohns, Chaimaa Fadil, Patrick K Albers and Gil McVean (2019) *Inferring whole-genome histories in large population datasets*. Nature Genetics **51**: 1330-1338

_Tsinfer_ versions [0.2.0](https://github.com/tskit-dev/tsinfer/releases/tag/0.2.0) onwards allow missing data and provide a fully parameterised Li & Stephens matching algorithm (i.e. which allows mismatch). These improvements are described in the
following [Science paper](https://doi.org/10.1126/science.abi8264):

> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) A unified genealogy of modern and ancient genomes. Science 375: eabi8264

Please cite either or both of these if you use ``tsinfer`` in your work. Code to reproduce the results in the first paper is present in a [separate GitHub repository](https://github.com/mcveanlab/treeseq-inference).

Note that `tsinfer` does not attempt to infer node times (i.e. branch lengths of the
inferred trees). If you require a tree sequence where the dates of common ancestors
are expressed in calendar or generation times, you should post-process the ``tsinfer``
output using software such as [``tsdate``](https://github.com/tskit-dev/tsdate).
