A program for generation time serial samples under an infinite sites model

The program COMPASS generates serial samples collected at various points in time. The samples are generated using coalescence simulations permitting various demographic scenarios. COMPASS uses an infinite sites model to generate polymorphism data for the samples. By generating serially sampled population-genetic data, COMPASS provide means of investigating the properties of data that has been collected at different time-points, and potentially, aid in interpreting the results from empirical data, for example polymorphism data collected from both present-day samples and historic samples. The program is written in C++ and it is freely available. A program note describing COMPASS was published in Bioinformatics.

Version 1.0.1 (March 17, 2010)
[Download software for UNIX (incl. manual)]
[Download software for Windows (incl. manual)]
[Download software for Mac OSX (incl. manual)]
[Download only manual]

If you are interested in previous versions of the software, please email Mattias Jakobsson.

To use the the UNIX version, unzip and untar the files in an appropriate directory using

tar xvzf filename.tar.gz

where “filename.tar.gz” is the downloaded file. Run the program by typing

./COMPASS [options — see manual]

In windows, open a command prompt and move to the location of the program. Run the program by typing

COMPASS [options — see manual]

If you run the program without options, a short summary of available options will be printed to the screen. If you have comments or problems with COMPASS send Mattias Jakobsson an e-mail.

Software history:

  • March 2010, release of version 1.0.1 (minor printing bug fix from version 1.0 — see manual for more info)
  • Nov 2009, release of version 1.0 (minor bug fixes from version 0.9 — see manual for more info)
  • Sept 2009, program note published in Bioinformatics
  • June 2009, upload of pre-compiled Mac OSX executable (version 0.9)
  • April 2009, upload of software, beta version 0.9