Infer tree sequences from genetic variation data.

Project description

tsinfer

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

Release history Release notifications | RSS feed

This version

0.3.1

Apr 19, 2023

0.3.0

Oct 25, 2022

0.2.3

Apr 8, 2022

0.2.2

Feb 23, 2022

0.2.1

May 26, 2021

0.2.0

Dec 18, 2020

0.1.4

Dec 12, 2018

0.1.3

Nov 2, 2018

0.1.2

Jun 20, 2018

0.1.1

May 12, 2018

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

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

Uploaded Apr 19, 2023 cp310

tsinfer-0.3.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (275.2 kB view hashes)

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tsinfer-0.3.1-cp310-cp310-macosx_11_0_x86_64.whl (148.7 kB view hashes)

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

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tsinfer-0.3.1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (275.0 kB view hashes)

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tsinfer-0.3.1-cp39-cp39-macosx_11_0_x86_64.whl (148.7 kB view hashes)

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tsinfer-0.3.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (277.1 kB view hashes)

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

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tsinfer-0.3.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (273.4 kB view hashes)

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Hashes for tsinfer-0.3.1-cp38-cp38-win_amd64.whl
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Hashes for tsinfer-0.3.1-cp37-cp37m-win_amd64.whl
Algorithm	Hash digest
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Algorithm	Hash digest
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Algorithm	Hash digest
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