An improved general amino acid replacement matrix

Molecular Biology and Evolution

Volumn 25, Issue 7, 2008, Pages 1307-1320

  Le, Si Quang ^a   Gascuel, Olivier ^a  

^a LIRMM   (France)

Author keywords

Amino acid substitutions; JTT; Maximum likelihood estimations; Phylogenetic inference; Replacement matrices; WAG

Indexed keywords

AMINO ACID;

ALGORITHM; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; GENETIC VARIABILITY; MOLECULAR EVOLUTION; PHYLOGENY;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 45849154166     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn067     Document Type: Article

References (49)

1. Abascal F, Posada D, Zardoya R. 2007. MtArt: a new model of amino acid replacement for arthropoda. Mol Biol Evol. 24:1-5.
2. Adachi J, Hasegawa M. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 42:459-468.
3. Adachi J, Waddell PJ, Martin W, Hasegawa M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol. 50:348-358.
4. Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. AU-19:716-722.
5. Arvestad L. 2006. Efficient methods for estimating amino acid replacement rates. J Mol Evol. 62:663-673.
6. Arvestad L, Bruno WJ. 1997. Estimation of reversible substitution matrices from multiple pairs of sequences. J Mol Evol. 45:696-703.
7. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280.
8. Benner S, Cohen M, Gonnet G. 1994. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 7:1323-1332.
9. Betts MJ, Russell RB. 2003. Amino acid properties and consequences of substitutions. In: Barnes MR, Gray IC, editors. Bioinformatics for geneticists. New York: Wiley.
10. Boeckmann B, Bairoch A, Apweiler R, et al. (12 co-authors). 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
11. Bryant D, Galtier N, Poursat MA. 2005. Likelihood calculations in phylogenetics. In: Gascuel O, editor. Mathematics of evolution and phylogeny. Oxford (UK): Oxford University Press. p. 33-62.
12. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
13. Dayhoff MO, Eyck RV, Park CM. 1972. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure. Volume 5. Washington, DC: National Biomedical Research Foundation. p. 89-99.
14. Dayhoff MO, Schwartz R, Orcutt B. 1978. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure. Volume 5, suppl. 3. Washington (DC): National Biomedical Research Foundation. p. 345-352.
15. Devauchelle C, Grossmann A, Hénaut A, Holschneider M, Monnerot M, Risler J, Torrésani B. 2001. Rate matrices for analyzing large families of protein sequences. J Comput Biol. 8:381-399.
16. Dimmic MW, Rest JS, Mindell DP, Goldstein RA. 2002. rtREV: a substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol. 55:65-73.
17. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
18. Felsenstein J. 2003. Inferring phylogenies. Sunderland (MA): Sinauer Associates, Inc.
19. Goldman N, Thorne JL, Jones DT. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics. 149:445-458.
20. Goldman N, Anderson JP, Rodrigo AG. 2000. Likelihood-based tests of topologies in phylogenetics. Syst Biol. 49:652-670.
21. Gu X, Fu YX, Li WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 12:546-557.
22. Guindon S, Gascuel O. 2003. A simple, fast and accurate algorithm to estimate larges phylogenies by maximum likelihood. Syst Biol. 52:696-704.
23. Holmes I, Rubin GM. 2002. An expectation maximization algorithm for training hidden substitution models. J Mol Biol. 317:753-764.
24. Hordijk W, Gascuel O. 2005. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics. 21:4338-4347.
25. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
26. Jones DT, Taylor WR, Thornton JM. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275.
27. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6:29.
28. Kishino H, Hasegawa M. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol. 29:170-179.
29. Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. 2006. XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics. 7:428.
30. Koshi JM, Goldstein RA. 1995. Context-dependent optimal substitution matrices. Protein Eng. 8:641-645.
31. Kosiol C, Goldman N. 2004. Different versions of the Dayhoff rate matrix. Mol Biol Evol. 22:193-199.
32. Kosiol C, Holmes I, Goldman N. 2007. An empirical codon model for protein sequence evolution. Mol Biol Evol. 24(7):1464-1479.
33. Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109.
34. MacStewart W. 1941. A note on the power of the sign test. Ann Math Stat. 12:236-239.
35. Müller T, Vingron M. 2000. Modeling amino acid replacement. J Comput Biol. 7:761-776.
36. Pagel M, Meade A. 2005. Mixture models in phylogenetic inference. In: Gascuel O, ed. Mathematics of evolution and phylogeny. Oxford (UK): Oxford University Press. p. 121-142
37. 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.
38. Rambaut A, Grassly N. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
39. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
40. Sanderson MJ, Donoghue MJ, Piel W, Eriksson T. 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am J Bot. 81:183.
41. Schwarz G. 1978. Estimating the dimension of a model. Ann Stat. 6:461-464.
42. Setubal J, Meidanis J. 1997. Introduction to computational molecular biology. Boston (MA): PWS Publishing Company.
43. Thorne J. 2000. Models of protein sequence evolution and their applications. Curr Opin Genet Dev. 10:602-605.
44. Thorne JL, Goldman N, Jones DT. 1996. Combining protein evolution and secondary structure. Mol Biol Evol. 13:666-673.
45. Veerassamy S, Smith A, Tillier ER. 2003. A transition probability model for amino acid substitutions from blocks. J Comput Biol. 10:997-1010.
46. Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
47. Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401.
48. Yang Z. 2006. Computational molecular evolution. Oxford (UK): Oxford University Press.
49. Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino-acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611.