The estimation of relative site variability among aligned homologous protein sequences

Bioinformatics

Volumn 19, Issue 5, 2003, Pages 600-606

  Horner, D S ^a   Pesole, Graziano ^a  

^a UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; GENE MUTATION; GENETIC VARIABILITY; MAXIMUM LIKELIHOOD METHOD; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STATISTICAL DISTRIBUTION; STATISTICAL MODEL;

EID: 0037460988     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg063     Document Type: Article

References (19)

1. Ayala,F.J. (1997) Vagaries of the molecular clock. Proc. Natl Acad. Sci. USA, 94, 7776-7783.
2. Felsenstein,J. (2001) Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol., 53, 447-423.
3. Grassly,N.C., Adachi,J. and Rambaut,A.E. (1997) PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Applic. Bios, 13, 559-560.
4. Gu,X. and Vander Velden,K. (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics, 18, 500-501.
5. Gu,X. and Zhang,J. (1997) A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol., 14, 1106-1113.
6. Horner,D.S., Foster,P.G. and Embley,T.M. (2000) Iron Hydrogenases and the Evolution of Anaerobic Eukaryotes. Mol. Biol. Evol., 17, 1695-1709.
7. Lockhart,P.J., Larkum,A.W.D., Steel,M.A., Waddel,P.J. and Penny,D. (1996) Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl Acad. Sci. USA, 93, 1930-1943.
8. Lopez,P., Casane,D. and Philippe,H. (2002) Heterotachy, an important process of protein evolution. Mol. Biol. Evol., 19, 1-7.
9. Otto,S.P. and Yong,P. (2002) The evolution of gene duplicates. Adv. Genet., 46, 451-483.
10. Pesole,G. and Saccone,C. (2001) A novel method for estimating substitution rate variation among sites in a large dataset of homologous DNA sequences. Genetics, 157, 859-865.
11. Philippe,H. and Adoutte,A. (1998) The molecular phylogeny of eukaryota: solid facts and uncertainties. In Coombes,G.H., Vickerman,K., Sleigh,M.A. and Warren,A. (eds), Evolutionary Relationships Among Protozoa. Kluwer Accademic, London, pp. 25-56.
12. Pupko,T. and Galtier,N. (2002) A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc. Roy. Soc. Lond., B 269, 1313-1316.
13. Strimmer,K. and Von Haeseler,A. (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol., 13, 964-969.
14. Sullivan,J., Holsinger,K.E. and Simon,C. (1996) The effect of topology on estimates of among-site rate variation. J. Mol. Evol., 42, 308-312.
15. Susko,E., Inagaki,Y., Field,C., Holder,M.E. and Roger,A.J. (2002) Testing for Differences in Rates-Across-Sites Distributions in Phylogenetic Subtrees. Mol. Biol. Evol., 19, 1514-1523.
16. Swofford,D.L. (1998) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland, Mass.
17. Tourasse,N.J. and Gouy,M. (1999) Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol. Phylogenet. Evol., 13, 159-168.
18. Uzzell,T. and Corbin,K.W. (1970) Fitting discrete probability distributions to evolutionary events. Science, 172, 1089-1096.
19. Yang,Z. (1996) Among site rate variation and its impact on phylogenetic analysis. Trends Ecol. Evol., 9, 367-372.