Hi Anna, See the package phangorn: recent versions implement codon-based models.
Cheers, Emmanuel Anna Syme wrote on 28/06/2012 08:42:
Hi all, I was wondering if there are any packages in R that can detect positive selection, comparable to programs such as PAML. I have two gene copies (each copy in multiple species), and want to see whether either copy has been subject to positive selection since divergence. Thanks, Anna *Dr Anna Syme* Molecular Systematist, National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Private Bag 2000, Birdwood Avenue, South Yarra, 3141, Australia. Phone (03) 9252 2328, Fax (03) 9252 2413. anna.s...@rbg.vic.gov.au <mailto:anna.s...@rbg.vic.gov.au> www.rbg.vic.gov.au <http://www.rbg.vic.gov.au/> -- This email and any attachments may contain information that is personal, confidential, legally privileged and/or copyright. No part of it should be reproduced, adapted or communicated without the prior written consent of the sender and/or copyright owner. It is the responsibility of the recipient to check for and remove viruses. If you have received this email in error, please notify the sender by return email, delete it from your system and destroy any copies. You are not authorised to use, communicate or rely on the information contained in this email. Please consider the environment before printing this email. This email was Anti Virus checked by RBG Astaro Mail Gateway. _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
-- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
