Summary: The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

Availability and implementation: sampletrees is implemented in C ++. The source code, documentation and test files are available at http://stat.sfu.ca/statgen/research/sampletrees.html. The R package Rsampletrees is available on CRAN http://cran.r-project.org/web/packages/Rsampletrees/index.html.

Contact: [email protected]

Supplementary information:  Supplementary data are available at Bioinformatics online.