Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 24, Issue 8, Pages 1586-1591Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msm088
Keywords
codon models; likelihood; PAML; phylogenetic analysis; software
Funding
- Natural Environment Research Council [NE/C509974/1] Funding Source: researchfish
Ask authors/readers for more resources
PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at http://abacus.gene.ucl.ac.uk/ software/paml.html.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available