Metadata-Version: 2.1
Name: tsdate
Version: 0.1.4
Summary: Infer node ages from a tree sequence topology
Home-page: http://pypi.python.org/pypi/tsdate
Author: Anthony Wilder Wohns and Yan Wong
Author-email: awohns@gmail.com
License: UNKNOWN
Project-URL: Source, https://github.com/awohns/tsdate
Project-URL: Bug Reports, https://github.com/awohns/tsdate/issues
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.5
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Requires-Python: >=3.4
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: tskit (>=0.2.3)
Requires-Dist: scipy (>1.2.3)
Requires-Dist: numba (>=0.46.0)
Requires-Dist: tqdm
Requires-Dist: appdirs

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

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``tsdate`` is a scalable method for estimating the age of ancestral nodes in a 
[tree sequence](https://www.youtube.com/watch?v=X1GEuQrF1jQ). 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 designed to operate on the output of [tsinfer](https://tsinfer.readthedocs.io/en/latest/), which efficiently infers tree sequence *topologies* from large genetic datasets.

Please refer to the [documentation](https://tsdate.readthedocs.io/en/latest/) for information on installing and using the software.

The algorithm is described [in this BioRxiv preprint](https://www.biorxiv.org/content/10.1101/2021.02.16.431497v2). We also provide evaluations of the accuracy and computational requirements of the method using both simulated and real data. The code to reproduce these results can be found in [another repository](https://github.com/awohns/unified_genealogy_paper).

> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2021) _A unified genealogy of modern and ancient genomes_. bioRxiv 2021.02.16.431497; doi: https://doi.org/10.1101/2021.02.16.431497

Please cite this preprint if you use ``tsdate`` in published work.


