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Paml 4: Phylogenetic analysis by maximum likelihood (2007)
| Venue: | Mol. Biol. Evol |
| Citations: | 1199 - 28 self |
BibTeX
@ARTICLE{Yang07paml4:,
author = {Ziheng Yang},
title = {Paml 4: Phylogenetic analysis by maximum likelihood},
journal = {Mol. Biol. Evol},
year = {2007},
pages = {1586--1591}
}
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Abstract
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 (dN and dS) 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.
Keyphrases
maximum likelihood phylogenetic analysis phylogenetic tree positive darwinian selection nonsynonymous rate sequence evolution main strength extinct life form unix system mac osx phylogenetic comparison protein-coding gene protein sequence heterogeneous data set molecular restoration study protein-coding dna sequence uk software paml interesting biological hypothesis major application multiple gene locus fossil calibration example data set evolutionary model ancestral gene specie divergence time rich repertoire
