Metadata-Version: 2.1
Name: tsdate
Version: 0.2.1
Summary: Infer node ages from a tree sequence topology.
Home-page: http://pypi.python.org/pypi/tsdate
Author: Tskit Developers
Author-email: admin@tskit.dev
License: MIT
Project-URL: Documentation, https://tskit.dev/tsdate/docs/
Project-URL: Changelog, https://github.com/tskit-dev/tsdate/blob/main/CHANGELOG.rst
Project-URL: Bug Tracker, https://github.com/tskit-dev/tsdate/issues
Project-URL: GitHub, https://github.com/tskit-dev/tsdate
Keywords: population genetics,tree sequence,ancestral recombination graph,evolutionary tree,inference,dating,tsdate
Platform: POSIX
Platform: Windows
Platform: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
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: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: tskit >=0.5.8
Requires-Dist: scipy >=1.13.0
Requires-Dist: numba >=0.58.1
Requires-Dist: mpmath
Requires-Dist: tqdm
Requires-Dist: appdirs

# tsdate <img align="right" width="145" height="90" src="https://github.com/tskit-dev/tsdate/blob/main/docs/tsdate_logo.svg">

[![CircleCI](https://circleci.com/gh/tskit-dev/tsdate.svg?style=svg)](https://circleci.com/gh/tskit-dev/tsdate)
[![codecov](https://codecov.io/gh/tskit-dev/tsdate/branch/master/graph/badge.svg)](https://codecov.io/gh/tskit-dev/tsdate)

``tsdate`` is a scalable method for estimating the age of ancestral nodes in a 
[tree sequence](https://tskit.dev/tutorials/what_is.html). The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").

The method is frequently combined with the [tsinfer](https://tsinfer.readthedocs.io/en/latest/) algorithm, which efficiently infers tree sequence *topologies* from large genetic datasets.

Please refer to the [documentation](https://tskit.dev/tsdate/docs/latest/) for information on installing and using the software.

The algorithms for the original `inside_outside` and `maximization` [methods](https://tskit.dev/tsdate/docs/latest/methods.html) are described [in this Science paper](https://www.science.org/doi/10.1126/science.abi8264) (citation below, preprint [here](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2), evaluations in [another repository](https://github.com/awohns/unified_genealogy_paper)). The new `variational_gamma` method, the default from version 0.2 onwards, has not yet been described in print. For the moment, please cite this github repository if you need a citable reference.

The citation to use for the original tsdate algorithms is:

> 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; doi: https://doi.org/10.1126/science.abi8264

