Relate estimates genome-wide genealogies in the form of trees that adapt to changes in local ancestry caused by recombination. The method, which is scalable to thousands of samples, is described in the following paper. Please cite this paper if you use our software in your study.
Citation: Leo Speidel, Marie Forest, Sinan Shi, Simon Myers. A method for estimating genome-wide genealogies for thousands of samples. Nature Genetics 51: 1321-1329, 2019.
Relate is available for academic use. To see rules for non-academic use, please read the LICENCE file, which is included with each software download.
Alternatively, you can compile your own version by downloading the source code from this github repository.
In the downloaded directory, we have included a toy data set. You can try out Relate using this toy data set by following the instructions on our getting started page.
If you have any problems getting the program to work on your machine or would like to request an executable for a platform not shown here, please send a message to leo.speidel [at] outlook [dot] com.
We document changes to previous versions in a change-log.
We deposited Relate-estimated coalescence rates, allele ages, and p-values for evidence of positive selection for the 1000 Genomes Project here.
These were obtained by estimating the joint genealogy of all 1000 GP populations and then extracted the embedded genealogy for each population. For the genealogy of each population, we jointly estimated the population size history and branch lengths. Variants segregating in more than one population therefore have correlated but different allele ages in each population.
I made an R package for handling Relate output files (MIT license). It's still under development but the main functionality is working.You can install this package, e.g., using
I made a C++ library for handling Relate output files (MIT license). It's still under development but the main functionality is working.
This contains a binary for conversion of tree sequence format to anc/mut format and back. (Note that conversions are not loss-less).
relate_lib/bin/Convert --mode ConvertFromTreeSequence \ --anc example.anc.gz \ --mut example.mut.gz \ -i example
relate_lib/bin/Convert --mode ConvertToTreeSequence \ --anc example.anc.gz \ --mut example.mut.gz \ -o example