bms_runner is a free script written by Daniel Barker and Mark Pagel. bms_runner uses the separate program BayesTraits to predict functional links among genes, on the basis of correlated gain and loss of genes from species’ genomes.

bms_runner helps configure BayesTraits on the basis of known, user-supplied data, and launches BayesTraits repeatedly to seek correlated gain and loss within pairs of genes.

The current version is bms_runner 1.4.


Linux and Mac OS X users download BMS_Runner_Script_1_4.tar.gz


Click to download pdf

Citing bms_runner

Please cite this paper if you use bms_runner:

Barker, D., Meade, A. and Pagel, M. 2007. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics23, 14-20.

Since bms_runner uses BayesTraits, please also cite BayesTraits. See the manual of either program for details.


Please send questions and bug reports to:


We are grateful to the Biotechnology and Biological Sciences Research Council and Research Councils UK for financial support.