Phylogenetic inference from conserved sites alignments

Journal of Experimental Zoology

Volumn 285, Issue 2, 1999, Pages 128-139

  Grundy, William Noble ^a   Naylor, Gavin J P ^b  

^a University of California Santa Cruz   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA; PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER PROGRAM; GENETICS; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; VERTEBRATES;

ANIMALIA; VERTEBRATA;

EID: 0033567124     PISSN: 0022104X     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-010X(19990815)285:2<128::AID-JEZ5>3.0.CO;2-C     Document Type: Article

References (47)

1. Aguinaldo AMA, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 387:489-493.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. A basic local alignment search tool. J Mol Biol 215:403-410.
3. Bailey TL. 1999. MEME - Multiple EM for Motif Elicitation. http://www.sdsc.edu/MEME.
4. Bailey TL, Elkan CP. 1994. Fitting a mixture model by expectation-maximization to discover motifs in biopolymers. In: Altman R, Brutlag D, Karp P, Lathrop R, Searls D, editors. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press.
5. Bailey TL, Elkan CP. 1995. The value of prior knowledge in discovering motifs with MEME. In: Rawlings C, Clark D, Altman R, Hunter LC, Rawlings LC, editors. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, p 28-36.
6. Bailey TL, Gribskov M. 1996. The megaprior heuristic for discovering protein sequence patterns. In: States DJ, Agarwal P, Gaasterland T, Hunter L, Smith R, editors. Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press. p 15-24.
7. Bailey TL, Gribskov M. 1998. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48-54.
8. Bailey TL, Grundy WN. 1999. Classifying proteins by family using the product of correlated p-values In: Istrail S, Puzner P, Waterman M, editors. Proceedings of the Third Annual International Conference on Computational Molecular Biology. New York: ACP. p 10-14.
9. Baldauf SL, Palmer JD, Doolittle WF. 1996. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc National Acad Sci USA 93:7749-7754.
10. Baldi P, Chauvin Y, Haunkapiller T, McClure MA. 1994. Hidden Markov models of biological primary sequence information. Proc National Acad USA 91:1059-1063.
11. Benton MJ. 1993. The fossil record 2. New York: Chapman and Hall. 845 p.
12. Bourque M. 1978. Arbres de Steiner et Reseaux dont Varie l'Emplagement de Certains Somments. PhD thesis, Montréal: Univ. Montréal.
13. Bremer K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
14. Brown M, Hughey R, Korgh A, Mian L, Sjolander K, Haussler D. 1995. Using Dirichlet mixture priors to derive hidden Markov models for protein families. In: Rawlings C, editor. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, p 47-55.
15. Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
16. Cloutier R, Ahlberg PE. 1996. Morphology characters and the inter-relationships of basal sarcopterigians. In: Stiassney MLJ, Parenti LR, Johnson GD, editors. Interrelationships of fishes. New York: Academic Press, p 445-479.
17. Donoghue MJ, Olmstead RG, Smith JF, Palmer JD. 1992. Phylogenetic relationships of dipscales based on rbcL sequences. Announce Missouri Botanical Gardens. 79:333-345.
18. Eddy SR. 1995. Multiple alignment using hidden Markov models. In: Rawlings C, editor. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, p 114-120.
19. Eddy SR. 1998. Profile hidden Markov models. Bioinformatics. 14:755-763.
20. Eernisse DJ. 1995. Stacks: HyperCard software utilities for molecular systematists, version 1.1. ftp://ftp.biology. indiana.edu.
21. Farrell B. 1998. "Inordinate fondness" explained: why are there so many beetles? Science 5376:555-559.
22. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
23. Felsenstein J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
24. Gauthier J. Kluge AG, Rowe T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105-209.
25. Golding GB, Dean AM. 1998. The structural basis of molecular adaptation. Mol Biol Evol 15:355-369.
26. Grundy WN, Bailey TL, Elkan CP. 1996. ParaMEME: a parallel implementation and a web interface for a DNA and protein motif disocivery tool. Comp Appl Biosci 12:303-310.
27. Grundy WN, TL Bailey, Elkan CP, Baker ME. 1997. Meta-MEME: motif-based hidden Markov models of protein families. Comp Appl Biosci 13:397-406.
28. Grundy WN, Elkan CP. 1999. Meta-MEME version 2.0.1. http://metameme.sdsc.edu/
29. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of the mitochondrial DNA. J Mol Evol 21:160-174.
30. Helfman GS, Collette BB, Facey DE. 1997. The diversity of fishes. Maiden, MA: Blackwell Science. 528 p.
31. Hudak J, McClure MA. 1999. A comparative analysis of computational motif-detection methods. In: Altman RB, Dunker AK, Hunter L, Klein TE, editors. Pacific Symp Biocomputing 48:138-149.
32. Juke TH, Cantor CR. 1969. Evolution of protein molecules. In: Muntu HN, editor. Mammalian protein metabolism, vol. 3. New York: Academic Press, p 21-132.
33. 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.
34. Krogh A, Brown M, Mian I, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology: applications to protein modeling. J Mol Biol 235:1501-1531.
35. Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evoluationary substitution rates. J Mol Evol 20:86-93.
36. Laudet V, Hanni C, Coll J, Catzelflis, Stehelin D. 1992. Evolution of the nuclear receptor gene superfamily. EMBO J 11:1003-1013.
37. Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262:208-214.
38. Maisey JG. 1986. Heads and tails: a chordate phylogeny. Cladistics 2:201-256.
39. Maisey JG. 1988. Phylogeny of early vertebrate skeletal induction and ossification patterns. Evol Biol 22:1-36.
40. Naylor GJP, Brown WM. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. System Biol 47:61-76.
41. Robinson DF, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci 53:131-147.
42. Rodríguez F, Oliver JL, Marín A, Medina JR. 1990. The general stochastic model of nucleotide substitions. J Theoret Biol 142:485-501.
43. Sjolander K, Karplus K, Brown M, Hughey R, Krogh A, Mian IS, Haussler D. 1996. Dirichlet mixtures: a method for improving detection of weak but significant protein sequence homology. Comp Appl Biosci 12:327-345.
44. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. Sunderland, MA: Sinauer Associates, p 407-514.
45. Tavaré S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures Math Life Sci 17:57-86.
46. Templeton AR. 1983. Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. In: Weir BS, editor. Statistical analysis of DNA sequence data. New York: Marcel Dekker. p 151-179.
47. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalities and weight matrix choice. Nucleic Acids Res 22:4673-4680.