Different versions of the dayhoff rate matrix

Molecular Biology and Evolution

Volumn 22, Issue 2, 2005, Pages 193-199

  Kosiol, Carolin ^a   Goldman, Nick ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

Amino acid replacement; Dayhoff matrix; Markov models; Phylogenetic inference; Protein evolution

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DECOMPOSITION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR MODEL; MOLECULAR PHYLOGENY; PROBABILITY;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; MARKOV CHAINS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; SOFTWARE DESIGN;

EID: 12344269158     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi005     Document Type: Article

References (35)

1. Adachi, J., and M. Hasegawa. 1992. MOLPHY version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood. Computer Science Monographs 28, Institute of Statistical Mathematics, Tokyo. http://www.ism.ac.jp/software/ ismlib/softother.e.html#molphy
2. -. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468.
3. Adachi, J., P. J. Waddell, W. Martin, and M. Hasegawa. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50:348-358.
4. Cao, Y., J. Adachi, A. Janke, S. Pääbo, and M. Hasegawa. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene. J. Mol. Evol. 39: 519-527.
5. Dayhoff, M. O., R. V. Eck, and C. M. Park. 1972. A model of evolutionary change in proteins. Pp. 89-99 in M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure Vol. 5. National Biomedical Research Foundation, Washington, D.C.
6. Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pp. 345-352 in M. O. Dayhoff, ed., Atlas of Protein Sequence and Structure Vol. 5, suppl. 3. National Biomedical Research Foundation, Washington, D.C.
7. Devauchelle, C., A. Grossmann, A. Hénaut, M. Holschneider, M. Monnerot, J. L. Riesler, and B. Torrésani. 2001. Rate matrices for analyzing large families of protein sequences. J. Comp. Biol. 8:381-399.
8. Dimmic, M. W., J. S. Rest, D. P. Mindell, and R. A. Goldstein. 2002. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 55:65-73.
9. Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:418-427.
10. -. 2002. PHYLIP (Phylogeny Inference Package) Version 3.6a. Department of Genome Sciences, University of Washington, Seattle, Wash. http://evolution. genetics.washington. edu/phylip.html
11. -. 2003. Inferring phylogenies. Sinauer Associates, Sunderland, Mass.
12. Goldman, N., J. L. Thorne, and D. T. Jones. 1996. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analysis. J. Mol. Biol. 263:196-208.
13. -. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458.
14. Grassly, N. C., J. Adachi, and A. Rambaut. 1997. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. CABIOS 13:559-560. http://evolve.zoo.ox.ac.uk/software.html?id=pseqgen
15. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. http://atgc.lirmm.fr/phyml
16. International Chimpanzee Chromosome 22 Consortium. 2004. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429:382-388.
17. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
18. International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
19. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282.
20. Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J. Mol. Evol. 31:151-160.
21. Liò, P., and N. Goldman. 1998. Models of molecular evolution and phylogeny. Genome Res. 8:1233-1244.
22. Moler, C., and C. Van Loan. 2003. Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later. SIAM Rev. 45:3-49.
23. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
24. Müller, T., and M. Vingron. 2000. Modeling amino acid replacement. J. Comp. Biol. 7:761-776.
25. Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS 13:235-238. http://evolve. zoo.ox.ac.uk/software.html?id=seqgen
26. Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521.
27. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. http://morphbank.ebc.uu.se/mrbayes3
28. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. http://www.tree-puzzle.de
29. Swofford, D. L. 2002. PAUP*. *Phylogenetic analysis using parsimony (and other methods) version 4. Sinauer Associates, Sunderland, Mass, http://paup.csit.fsu.edu
30. Thorne, J. L., and N. Goldman. 2003. Probabilistic models for the study of protein evolution. Pp. 209-226 in D. J. Balding, M. Bishop, and C. Cannings, eds. Handbook of Statistical Genetics, 2nd Ed. Wiley, Chichester.
31. Veerassamy, S., A. Smith, and E. R. M. Tillier. 2003. A transition probability model for amino acid substitutions from Blocks. J. Comp. Biol. 10:997-1010.
32. Whelan, S., P. I. W. de Bakker, and N. Goldman. 2003. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19:1556-1563. http://www. ebi.ac.uk/goldman-srv/pandit
33. Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:691-699.
34. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556. http://abacus.gene.ucl.ac.uk/software/ paml.html
35. Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.