Modeling protein evolution with several amino acid replacement matrices depending on site rates

Molecular Biology and Evolution

Volumn 29, Issue 10, 2012, Pages 2921-2936

  Le, Si Quang ^a,b   Dang, Cuong Cao ^c   Gascuel, Olivier ^a  

^a CNRS   (France)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c VIETNAM NATIONAL UNIVERSITY   (Viet Nam)

Author keywords

amino acid substitutions; gamma and distribution free rate models; maximum likelihood estimations; phylogenetic inference; replacement matrices

Indexed keywords

PROTEIN;

ACID BASE BALANCE; AMINO ACID SUBSTITUTION; ARTICLE; EVOLUTION;

ALGORITHMS; AMINO ACID SUBSTITUTION; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION RATE; PROTEINS; TIME FACTORS;

EID: 84866924443     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss112     Document Type: Article

References (45)

1. Akaike H. 1974. A new look at statistical model identification. IEEE Trans Automatic Control. 19:716-722.
2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242. Available from: http://www.pdb. org (Pubitemid 30047768)
3. Berry V, Gascuel O. 1996. Interpretation of bootstrap trees: threshold of clade selection and induced gain. Mol Biol Evol. 13:999-1011. (Pubitemid 26284916)
4. Bryant D, Galtier N, Poursat MA. 2005. Likelihood calculations in phylogenetics. In: Gascuel O, editor. Mathematics of evolution and phylogeny. Oxford: Oxford University Press. p. 33-62.
5. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552. (Pubitemid 30210700)
6. Dayhoff MO, Eyck RV, Park CM. 1972. A model of evolutionary change in proteins. In: Dayhoff MO, editor. Atlas of protein sequence and structure. Vol. 5. Washington (DC): National Biomedical Research Foundation. p. 89-99.
7. Desper R, Gascuel O. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comp Biol. 19:687-705. (Pubitemid 36042994)
8. Durbin R, Eddy S, Krogh A, Mitchison G. 1998. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge: Cambridge University Press.
9. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376. (Pubitemid 11016207)
10. Felsenstein J. 2003. Inferring phylogenies. Sunderland (MA): Sinauer Associates, Inc.
11. Felsenstein J, Churchill GA. 1996. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 13: 93-104. (Pubitemid 26012458)
12. 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)
13. Gascuel O, Guindon S. 2007. Modelling the variability of evolutionary processes. In: Gascuel O, Steel M, editors. Reconstructing evolution: new mathematical and computational advances. Oxford: Oxford University Press. p. 65-99.
14. Goldman N, Thorne JL, Jones DT. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
15. 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.
16. Holder MT, Sukumaran J, Lewis PO. 2008. A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics. Syst Biol. 57:814-821.
17. Holmes I, Rubin GM. 2002. An expectation maximization algorithm for training hidden substitution models. J Mol Biol. 317:753-764. (Pubitemid 34722162)
18. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
19. Jones DT, Taylor WR, Thornton JM. 1994. A mutation data matrix for transmembrane proteins. FEBS Lett. 339:269-275. (Pubitemid 24063461)
20. Keane TMC, Creevey CJ, Pentony MM, Naughton TJ, McLnerney 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.
21. 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. (Pubitemid 19206089)
22. Klosterman PSA, Uzilov AV, Bendana 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.
23. Koshi JM, Goldstein RA. 1995. Context-dependent optimal substitution matrices. Protein Eng. 8:641-645.
24. Koshi JM, Goldstein RA. 1998. Models of natural mutations including site heterogeneity. Proteins 32:289-295. (Pubitemid 28360825)
25. Kyte J, Doolittle RF. 1982. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 157:105-132.
26. Lartillot N, Philippe H. 2004. A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
27. Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320. (Pubitemid 351882003)
28. Le SQ, Gascuel O. 2010. Accounting for accessibility to solvent and secondary structure in protein phylogenetics is clearly beneficial. Syst Biol. 59:277-287.
29. Le SQ, Gascuel O, Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24:2317-2323.
30. Le SQ, Lartillot N, Gascuel O. 2008. Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci. 363:3965-3976.
31. Lio P, Goldman N, Thorne JL, Jones DT. 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14:726-733. (Pubitemid 28504998)
32. Mayrose I, Friedman N, Pupko T. 2005. A Gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics 21:151-158.
33. Pagel M, Meade A. 2005. Mixture models in phylogenetic inference. In: Gascuel O, editor. Mathematics of evolution and phylogeny. Oxford: Oxford University Press. p. 121-142.
34. Raman P, Cherezov V, Caffrey M. 2006. The Membrane Protein Data Bank. Cell Mol Life Sci. 63:36-51. (Pubitemid 43100279)
35. Robinson D, Foulds L. 1979. Comparison of weighted labeled trees. Lect Notes Math. 748:119-126.
36. 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.
37. Schneider R, deDaruvarA, Sander C. 1997. TheHSSP database of protein structure-sequence alignments. Nucleic Acids Res. 25:226-230. (Pubitemid 27303184)
38. Shimodaira H. 1997. Assessing the error probability of the model selection test. Ann Inst Stat Math. 49:395-410. (Pubitemid 127485499)
39. Susko E, Field C, Blouin C, Roger AJ. 2003. Estimation of ratesacross-sites distributions in phylogenetic substitution models. Syst Biol. 52:594-603. (Pubitemid 37365042)
40. Thorne JL, Goldman N, Jones DT. 1996. Combining protein evolution and secondary structure. Mol Biol Evol. 13:666-673. (Pubitemid 26131888)
41. Wang HC, Li K, Susko E, Roger AJ. 2008. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol Biol. 8:331.
42. 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. (Pubitemid 32372940)
43. Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401. (Pubitemid 23352619)
44. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
45. Yang Z, Nielsen R, Hasegawa M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol. 15:1600-1611. (Pubitemid 28550985)