Probabilistic orthology analysisprimeGEM is a program that performs probabilistic orthology analysis (Arvestad et al. 2003, 2004, submitted, Sennblad and Lagergren, 2009). It computes for a pair of genes the probability that they are orthologous (note that this correpsponds to the probability that their least common ancestor is a speciation). It is based on the gene evolution model which models gene duplication and loss using a generalized birth-death model with threee parameters. The parameters can be integrated over using MCMC or (soon) maximized over using ML.
If you use primeGEM, please cite:
Sennblad, Lagergren, 2009, Probabilistic orthology analysis, Systematic Biology (advance online acces, issue and pages pending).