Cited by 13,879Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsEvolution and Paleontology Studies

PAML 4: Phylogenetic Analysis by Maximum Likelihood

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Yang, Z.·2007·Molecular Biology and Evolution

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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  • Two-branch and branch-site models identified 467, 331, and 281 genes putatively shaped by positive selection in the carnivore, felid, and domestic cat ancestral lineages, respectively.

    “Two-branch and branch-site models (17) collectively identified 467, 331, and 281 genes that were putatively shaped by positive selection in the carnivore, felid, and domestic cat (subfamily Felinae) ancestral lineages, respectively (S1.1-S1.3 in Dataset S1).”

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Authors
Yang, Z.
Affiliations
University College London (GB)
Corresponding author
Yang, Z.
Venue
Molecular Biology and Evolution
Published
2007-04-18
Volume
24
Issue
8
Pages
1586-1591
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
OpenAlex
W2110335151
Cited by
13,879
References
103
Citations by year
2026: 864 · 2025: 1024 · 2024: 1124 · 2023: 999 · 2022: 1223 · 2021: 1188 · 2020: 974 · 2019: 838 · 2018: 723 · 2017: 656 · 2016: 663 · 2015: 595 · 2014: 609 · 2013: 570 · 2012: 526
FWCI
111.59
Type
journal article
Language
en
Open access
Locations
  • Molecular Biology and Evolution (publishedVersion)
  • PubMed (publishedVersion)
  • UCL Discovery (University College London) (submittedVersion)
Funders
  • Directorate for Biological Sciences
  • Biotechnology and Biological Sciences Research Council
  • Natural Environment Research Council (NE/C509974/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
PAML, maximum likelihood phylogeny, sequence evolution models, synonymous and nonsynonymous substitution rates, positive selection, ancestral sequence reconstruction, fossil calibration, divergence time estimation, protein-coding genes
MeSH terms
Animals, Computer Simulation, Models, Genetic, Phylogeny, Selection, Genetic, Software, Species Specificity, Genetic Variation, Likelihood Functions

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