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.