Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

Molecular Biology and Evolution

Volumn 22, Issue 6, 2005, Pages 1386-1392

  Sullivan, Jack ^a   Abdo, Zaid ^a   Joyce, Paul ^a   Swofford, David L ^b  

^a UNIVERSITY OF IDAHO   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Maximum likelihood; Models; Parameter estimation; Phylogeny; Successive approximations

Indexed keywords

MITOCHONDRIAL DNA;

ACCURACY; ARTICLE; CALCULATION; DNA SEQUENCE; EVALUATION; MAXIMUM LIKELIHOOD METHOD; MOLECULAR MODEL; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAMETER; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; PROCESS OPTIMIZATION; RELIABILITY; SUCCESSIVE APPROXIMATION; TECHNIQUE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, THEORETICAL; PHYLOGENY; SOFTWARE; TIME FACTORS;

EID: 19544387609     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi129     Document Type: Article

References (21)

1. Abdo, Z., V. Minin, P. Joyce, and J. Sullivan. 2005. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Mol. Biol. Evol. 22:691-703.
2. D'Erchia, A. M., C. Gissi, G. Pesole, C. Saccone, and U. Arnason. 1996. The guinea pig is not a rodent. Nature 381: 597-600.
3. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
4. -. 2004. Inferring phytogenies. Sinauer Associates, Sunderland, Mass.
5. Frati, F., C. Simon, J. Sullivan, and D. L. Swofford. 1997. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. J. Mol. Evol. 44:154-158.
6. Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phytogenies by maximum likelihood. Syst. Biol. 52:696-704.
7. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
8. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
9. Mallatt, J., and J. Sullivan. 1998. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Mol. Biol. Evol. 15:1706-1718.
10. Mason-Gamer, R. J., C. Weil, and E. A. Kellogg. 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15:1658-1673.
11. Minin, V., Z. Abdo, P. Joyce, and J. Sullivan. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52:1-10.
12. Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Biofinormatics 14:817-818.
13. Robinson, D. F., and L. R. Foulds. 1982. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
14. Sullivan, J., E. Arellano, and D. S. Rogers. 2000. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. Am. Nat. 155:754-768.
15. Sullivan, J., K. E. Holsinger, and C. Simon. 1996. The effect of topology on estimates of among-site rate variation. J. Mol. Evol. 42:308-312.
16. Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4:77-86.
17. Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10a. Sinauer Associates, Sunderland, Mass.
18. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. Mable, eds. Molecular systematics. 2nd edition. Sinauer Associates, Sunderland, Mass.
19. Vinh, L. S., and A. von Haeseler. 2004. IQPNNI: moving fast through tree space and stopping in time. Mol. Biol. Evol. 21: 1565-1571.
20. Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
21. Yang, Z., N. Goldman, and A. Friday. 1995. Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44:384-399.