MBE Advance Access published online on May 4, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm088
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
Department of Biology, Galton Laboratory, University College London, London, UK
Address for correspondence: Ziheng Yang, Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England, Tel: +44 (20) 7679 4379, Fax: +44 (20) 7679 7096, Email: z.yang{at}ucl.ac.uk
Received for publication March 20, 2007. Accepted for publication April 25, 2007.
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.
Key Words: codon models • likelihood • PAML • phylogenetic analysis • software
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Z. Yang Empirical evaluation of a prior for Bayesian phylogenetic inference Phil Trans R Soc B, December 27, 2008; 363(1512): 4031 - 4039. [Abstract] [Full Text] [PDF]
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M. Albu, X. J. Min, D. Hickey, and B. Golding Uncorrected Nucleotide Bias in mtDNA Can Mimic the Effects of Positive Darwinian Selection Mol. Biol. Evol., December 1, 2008; 25(12): 2521 - 2524. [Abstract] [Full Text] [PDF]
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M. M. Guisinger, J. V. Kuehl, J. L. Boore, and R. K. Jansen Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions PNAS, November 25, 2008; 105(47): 18424 - 18429. [Abstract] [Full Text] [PDF]
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H. Bourhy, J.-M. Reynes, E. J. Dunham, L. Dacheux, F. Larrous, V. T. Q. Huong, G. Xu, J. Yan, M. E. G. Miranda, and E. C. Holmes The origin and phylogeography of dog rabies virus J. Gen. Virol., November 1, 2008; 89(11): 2673 - 2681. [Abstract] [Full Text] [PDF]
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P.-A. Christin, N. Salamin, A. M. Muasya, E. H. Roalson, F. Russier, and G. Besnard Evolutionary Switch and Genetic Convergence on rbcL following the Evolution of C4 Photosynthesis Mol. Biol. Evol., November 1, 2008; 25(11): 2361 - 2368. [Abstract] [Full Text] [PDF]
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R. C. Karn, N. L. Clark, E. D. Nguyen, and W. J. Swanson Adaptive Evolution in Rodent Seminal Vesicle Secretion Proteins Mol. Biol. Evol., November 1, 2008; 25(11): 2301 - 2310. [Abstract] [Full Text] [PDF]
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G. Jayawardane, G. C. Russell, J. Thomson, D. Deane, H. Cox, D. Gatherer, M. Ackermann, D. M. Haig, and J. P. Stewart A captured viral interleukin 10 gene with cellular exon structure J. Gen. Virol., October 1, 2008; 89(10): 2447 - 2455. [Abstract] [Full Text] [PDF]
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D. C. S. G. Oliveira, R. Raychoudhury, D. V. Lavrov, and J. H. Werren Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae) Mol. Biol. Evol., October 1, 2008; 25(10): 2167 - 2180. [Abstract] [Full Text] [PDF]
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V. J. Lynch, A. Tanzer, Y. Wang, F. C. Leung, B. Gellersen, D. Emera, and G. P. Wagner Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals PNAS, September 30, 2008; 105(39): 14928 - 14933. [Abstract] [Full Text] [PDF]
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E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin Large-scale reconstruction and phylogenetic analysis of metabolic environments PNAS, September 23, 2008; 105(38): 14482 - 14487. [Abstract] [Full Text] [PDF]
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G. Li, J. Wang, S. J. Rossiter, G. Jones, J. A. Cotton, and S. Zhang The hearing gene Prestin reunites echolocating bats PNAS, September 16, 2008; 105(37): 13959 - 13964. [Abstract] [Full Text] [PDF]
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S. Yokoyama, T. Tada, H. Zhang, and L. Britt From the Cover: Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates PNAS, September 9, 2008; 105(36): 13480 - 13485. [Abstract] [Full Text] [PDF]
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 C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice Mol Plant, September 1, 2008; 1(5): 839 - 850. [Abstract] [Full Text] [PDF]
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