sampletrees and Rsampletrees

A Markov chain Monte Carlo algorithm for sampling gene genealogies conditional on either phased or unphased SNP genotype data. The algorithm has been implemented in C++ by Kelly Burkett. For details, see Burkett et al. (2013a) and Burkett et al. (2013b). For an application to genetic association mapping, see Burkett et al. (2013c).

In addition to the sampletrees C++ program, the R package Rsampletrees is available to assist users with (i) creating the input files needed by sampletrees, and (ii) processing and plotting the results of a sampletrees run. Most users of sampletrees will also want Rsampletrees.

The C++ program and R interface are described in Burkett et al. (2016).

Installing sampletrees

For the C++ program, Mac and Linux users need to install from source, but Windows users can download pre-compiled versions.

  • From source: Download the C++ source code and documentation as a gzipped tar file and follow the instructions for installing from source
  • Compiled versions for Windows: Download compiled versions for 32 bit Windows or for 64 bit Windows. (Note: Before using one of these pre-compiled versions you may wish to change its name from sampletreesXX.exe, where XX is 32 or 64, to sampletrees.exe to match the documentation.)

Installing Rsampletrees

Rsampletrees is now available on CRAN. Install from within R using

install.packages("Rsampletrees")

Documentation for sampletrees

Documentation for the C++ program is available in the combined sampletrees/Rsampletrees documentation. Please be aware that the software is under active development, with improvements to the user interface in progress. As a result, the documentation may be out of date in some places.

Documentation for Rsampletrees

See the combined sampletrees/Rsampletrees documentation. In addition, the help pages for all functions in the package (also known as the reference manual) is available here. A package vignette is currently under development.