MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods

Molecular Biology and Evolution

Volumn 28, Issue 10, 2011, Pages 2731-2739

  Tamura, Koichiro ^a   Peterson, Daniel ^b   Peterson, Nicholas ^b   Stecher, Glen ^b   Nei, Masatoshi ^c   Kumar, Sudhir ^b,d  

^a TOKYO METROPOLITAN UNIVERSITY   (Japan)

^b ARIZONA STATE UNIVERSITY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE;

ALGORITHM; ARTICLE; BIOINFORMATICS; BIOLOGY; BIOMEDICINE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTIONARY GENETICS ANALYSIS 5; PARSIMONY ANALYSIS; PLESIOMORPHY; SCIENTIST; SEQUENCE ALIGNMENT; SIMULATION;

ALGORITHMS; AMINO ACID SUBSTITUTION; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATA MINING; DATABASES, GENETIC; EVOLUTION, MOLECULAR; INTERNET; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR BIOLOGY; MUTATION; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 79957613599     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr121     Document Type: Article

References (41)

1. Alfaro ME, Huelsenbeck JP. 2006. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. Syst Biol. 55:89-96.
2. Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S. 2011. Fast and slow implementations of relaxed clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol. 28:2439-2442.
3. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113.
4. Edwards AWF. 1972. Likelihood; an account of the statistical concept of likelihood and its application to scientific inference. Cambridge (UK): Cambridge University Press.
5. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376. (Pubitemid 11016207)
6. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
7. Fitch WM. 1986. An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor. Prog Clin Biol Res. 218:149-159.
8. Fitch WM, Margoliash E. 1967. A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case. Biochem Genet. 1:65-71.
9. Gascuel O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 14:685-695. (Pubitemid 27287289)
10. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307-321.
11. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704. (Pubitemid 37365050)
12. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA . J Mol Evol. 22:160-174. (Pubitemid 16227864)
13. Hedges SB, Kumar S. 2009. Discovering the timetree of life. In: SB Hedges, S Kumar, editors. The timetree of life. New York: Oxford University Press. p. 3-18.
14. Hurvich CM, Tsai C-L. 1989. Regression and time series model selection in small samples. Biometrika 76:297-307.
15. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
16. Kumar S, Dudley J. 2007. Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. (Pubitemid 47250302)
17. Kumar S, Nei M, Dudley J, Tamura K. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 9:299-306. (Pubitemid 351890826)
18. Kumar S, Tamura K, Nei M. 1994. MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci. 10:189-191. (Pubitemid 24125441)
19. Mayrose I, Mitchell A, Pupko T. 2005. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol. 60:345-353. (Pubitemid 40685127)
20. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. Oxford: Oxford University Press.
21. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 53:793-808. (Pubitemid 39568279)
22. Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
23. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238. (Pubitemid 27249927)
24. Ripplinger J, Sullivan J. 2008. Does choice in model selection affect maximum likelihood analysis? Syst Biol. 57:76-85.
25. Ripplinger J, Sullivan J. 2010. Assessment of substitution model adequacy using frequentist and Bayesian methods. Mol Biol Evol. 27:2790-2803.
26. Rosenberg MS, Kumar S. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc Natl Acad Sci USA. 98:10751-10756. (Pubitemid 32878693)
27. Rosenberg MS, Kumar S. 2003. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol. 20:610-621. (Pubitemid 36437911)
28. Saitou N, Nei M. 1987. The Neighbor-Joining Method-a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
29. Schrago CG. 2006. An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping. Genet Mol Res. 5:233-241.
30. Schwarz G. 1978. Estimating the dimension of a model. Ann Stat. 6:461-464.
31. Shoemaker JS, Fitch WM. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol. 6:270-289.
32. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
33. Stamatakis A, Ludwig T, Meier H. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463. (Pubitemid 40310232)
34. Swofford DL. 1998. PAUP*: phylogenetic analysis using parsimony (and other methods). Sunderland, MA: Sinauer Associates.
35. Tajima F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607. (Pubitemid 23307610)
36. Takezaki N, Rzhetsky A, Nei M. 1995. Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol. 12:823-833.
37. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 10:512-526. (Pubitemid 23157236)
38. Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA. 101:11030-11035. (Pubitemid 38989579)
39. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314. (Pubitemid 24283346)
40. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
41. Yang Z, Kumar S, Nei M. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.