Detecting selection

[Sean.Maceachern at nre.vic.gov.au]

Hello, I have just commenced a PhD and am interested in detecting selection
in a large subset of genes between two species. Owing to the large number
of samples that I am analysing I need to find a program that I can automate
through command line. To date I have not been able to find a program on
EMBOSS that will detect ratios between synonymous and nonsynonymous
mutations in a method analagous to GCG's Diverge. Does anyone know of a
program on EMBOSS that will calculate these ratios or can anyone suggest a
reliable program that would be easy to automate via command line that i can
source from the web
Thank you

Sean MacEachern
PhD Student
Sean.Maceachern at nre.vic.gov.au