PAML 4: Phylogenetic Analysis by Maximum Likelihood
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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).”
From Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication (2014) · cites this paper as [17]
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- Authors
- Yang, Z.
- Affiliations
- University College London (GB)
- Corresponding author
- Yang, Z.
- ORCID
- Yang, Z.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-04-18
- Volume
- 24
- Issue
- 8
- Pages
- 1586-1591
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2110335151
- Semantic Scholar
- da7ab2f1b6278472f3671a7430c9a72bad07781f
- 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
- bronze
- doi.org
- 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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