Downloading primeGEM

Source code

This is a very preliminary release of the source code of primeGEM. Presently, only the program primeGEM is available, and the release is only tested on MacOSX 10.5; we aim to remedy this asap. Compilation of the program is done under a unix shell by:

tar -xvzf primeGEM_v.tgz
cd primeGEM_v

We are grateful for any reports of problem compiling the source code. For running the program, please refer to the instructions under Binaries.

Source Code tested on MacOSX 10.5
primeGEM sources


The programs primeGEM, primeGEM-generator and xprimeGEM-enum a command-line tool and should be run from within a terminal window. For a brief usage description, try typing, e.g., 'primeGEM -h' (the binary may download as 'primeGEM.exe', if this causes trouble, please rename file to 'primeGEM'). While all program should be considered experimental, the starting 'x' in xprimeGEM-enum, indicates that this program is even more so. We are grateful for any reports of problems with these binaries.

A typical run of primeGEM could be:

primeGEM -Go -o orthology.mcmc -i 10000 -t 1 mhc.g MHCIYang2003.S mhc.gsmap

Alternatively, we can first save the posterior distribution Pr[G,\lambda,\mu|S] in the file postDistr.mcmc, which can then be used in a second run to estimate orthology. In certain cases this may save computation time.

primeGEM -o postDistr.mcmc -i 10000 -t 1 mhc.g MHCIYang2003.S mhc.gsmap
primeGEM -Go -o orthology.mcmc -u postDistr.mcmc mhc.g MHCIYang2003.S mhc.gsmap

The result in file orthology output can now be investigated using mcmc_analysis:
mcmc_analysis orthology.mcmc

-The maximum likelihood implementation is untested
-The current version of primeGEM requires the times in the species tree to be given as floating point numbers rather than integers (i.e., 59.0 instead of 59). This will be fixed in future releases.
-We have noted occasional program failures due to precision problems when the divergence times in the species tree are very high. For the time being the simple remedy is to rescale the species tree divergence times (we recommend a total root-to-leaf time in the range 1-10 to be on the safe side).

Linux (ix86) binaries tested on Centos

MacOSX ppc binaries tested on MacOSX 10.4

MacOSX intel binaries tested on MacOSX 10.5

Cygwin_ix86 binaries tested on Windows 2000/XP/Vista

perl script for analysis of MCMC output Should be platform independent, but requires that perl is installed.

Old releases

primeGEM was previously available as 'troyo'
Linux binaries

MacOSX binaries


Version history: v0.2 Changed integers to floats in Species trees.
v0.1 First relaease

Test data MHC class I data and ABC-transporter subfamily A data used in Sennblad and Lagergren, Probabilistic orthology analysis, submitted