Source code

We do not distribute binaries at this time, but you are welcome to download and compile the source code. The download contains a README file with compilation instructions and an example directory (SampleData) with the ADH case study from our paper.

This code has compiled on Centos 5 (x86, 32 and 64 bit), Ubuntu Hardy Heron (x86, 32 bit), and Mac OS (10.4.5 and 10.4.11).

Important! To analyze the output from PrIME-GSR, you also need mcmc_analysis, a Perl script for summarizing the MCMC samples.

Preview of next version

You can try out a binary of our next release, PrIME-GSRf ("f" is for "fast"). This binary is compiled for a 64 bit system using GNU/Linux 2.6.9.

Important: This build uses the Xerces library and you might need to point the LD_LIBRARY_PATH to where the lib-files are, if not available right away in your installation.

Manual

Dependencies

The code base depends on the following:
  • Bison, the GNU parser generator.
  • Flex, a lexical analyzer.
  • LAPACK and BLAS, for fast linear algebra.
All of these dependencies are commonly available as RPM and APT packages in (at least) Linux and should be very easy to download and install.

Notes on usage

The command and option used in the Åkerborg et al. manuscript are:
primeGSR -o <mcmc output file> -i 1000000 -t 100 -Sm JTT -Bp 0.1 0.1 -Bt 1.0  -Ed Gamma -Hi <species tree file> <sequence data file> <gene-to-species leaf map (gs) file>