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      PAML 4: phylogenetic analysis by maximum likelihood.

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      Molecular biology and evolution

      Oxford University Press (OUP)

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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 (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).

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          Author and article information

          Journal
          Mol. Biol. Evol.
          Molecular biology and evolution
          Oxford University Press (OUP)
          0737-4038
          0737-4038
          Aug 2007
          : 24
          : 8
          Affiliations
          [1 ] Department of Biology, Galton Laboratory, University College London, London, UK. z.yang@ucl.ac.uk
          msm088
          10.1093/molbev/msm088
          17483113

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