Skip to main content

Infer tree sequences from genetic variation data.

Project description


CircleCI Build Status Docs Build codecov

Infer a tree sequence from genetic variation data

The documentation contains details of how to use this software, including installation instructions.

The algorithm, its rationale, and results from testing on simulated and real data are described in the following Nature Genetics paper:

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

Please cite this if you use tsinfer in your work. Code to reproduce the results in the paper is present in a separate GitHub repository.

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.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

tsinfer-0.3.1.tar.gz (703.5 kB view hashes)

Uploaded source

Built Distributions

tsinfer-0.3.1-cp310-cp310-win_amd64.whl (129.9 kB view hashes)

Uploaded cp310

tsinfer-0.3.1-cp39-cp39-win_amd64.whl (129.9 kB view hashes)

Uploaded cp39

tsinfer-0.3.1-cp38-cp38-win_amd64.whl (129.9 kB view hashes)

Uploaded cp38

tsinfer-0.3.1-cp37-cp37m-win_amd64.whl (129.7 kB view hashes)

Uploaded cp37

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page