Source codeWe do not distribute binaries at this time, but you are welcome to download and compile the source code.
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 versionYou 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.
DependenciesThe code base depends on the following:
- Bison, the GNU parser generator.
- Flex, a lexical analyzer.
- LAPACK and BLAS, for fast linear algebra.
Notes on usageThe 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>