Estimation of reversible substitution matrices from multiple pairs of sequences

Journal of Molecular Evolution

Volumn 45, Issue 6, 1997, Pages 696-703

  Arvestad, Lars ^a   Bruno, William J ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Eigenvalues; Evolutionary distance; General reversible model; Rate matrix

Indexed keywords

DNA;

ARTICLE; CALCULATION; DNA SEQUENCE; GENETIC DISTANCE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIMATE; PSEUDOGENE; TAXONOMY;

ALGORITHMS; AMINO ACID SUBSTITUTION; ANIMALS; CEBIDAE; EVOLUTION, MOLECULAR; GLOBINS; GORILLA GORILLA; HUMANS; MACACA MULATTA; MARKOV CHAINS; MATHEMATICAL COMPUTING; MODELS, MOLECULAR; PAN TROGLODYTES; PONGO PYGMAEUS; PSEUDOGENES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

PRIMATES;

EID: 0031453046     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006274     Document Type: Article

References (20)

1. Bloom LB, Otto MR, Eritja R, Reha-Krantz LJ, Goodman MF, Beechem JM (1994) Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3′-exonuclease activity of bacteriophage T4 DNA polymerase. Biochemistry 33:7576-7586
2. Bruno WJ (1996) Modeling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evol 13:1368-1375
3. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
4. Felsenstein J (1989) PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166
5. Gojobori T (1983) Codon substitution in evolution and the "saturation" of synonymous changes. Genetics 105:1011-1027
6. Gojobori T, Li WH, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360-369
7. Goldstein DB, Pollock DD (1994) Least squares estimation of molecular distance - noise abatement in phylogenetic reconstruction. Theor Popul Biol 45:219-226
8. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
9. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York
10. Kelly FP (1979) Reversibility and stochastic networks. Wiley, Chichester
11. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Proc Natl Acad Sci USA 78:111-120
12. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculation evolutionary substitution rates. J Mol Evol 20:86-93
13. Miyamoto MM, Slightom JL, Goodman M (1987) Phylogenetic relations of humans and African apes from DNA sequences in the Ψη-globin region. Science 238:369-373
14. Rzhetsky A, Sitnikova T (1996) When is it safe to use an oversimplified substitution model in tree-making? Mol Biol Evol 13:1255-1265
15. Saccone C, Lanave C, Pesole G, Preparata G (1995) The reversible stationary Markov process for estimating the pattern of nucleotide substitution: a response to Ziheng Yang. J Mol Evol 41:253
16. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-426
17. Thorne JL, Goldman N, Jones DT (1996) Combining protein evolution and secondary structure. Mol Biol Evol 13:666-673
18. Yang Z (1994) Estimating the pattern of nucleotide substitution. J Mol Evol 39:105-111
19. Yang Z (1995) On the general reversible Markov process model of nucleotide substitution: a reply to Saccone et al. J Mol Evol 41: 254-255
20. Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogeny estimation. Mol Biol Evol 11:316-324