Effects of sequence alignment procedures on estimates of phylogeny

BioEssays

Volumn 20, Issue 4, 1998, Pages 287-290

  Goldman, Nick ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0031954745     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-1878(199804)20:4<287::AID-BIES4>3.0.CO;2-N     Document Type: Article

References (27)

1. Morrison DA, Ellis JT (1997) Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Mol Biol Evol 14:428-441.
2. Harvey PH, Brown AJL, Smith JM, Nee S (eds) (1996) New Uses for New Phylogenies. Oxford University Press, Oxford.
3. Taylor WR (1996) Evolution and relationships of protein families. In Bishop MJ, Rawlings CJ (eds): DNA and Protein Sequence Analysis. Oxford: IRL Press, pp 313-340.
4. Goldman N (1996) Phylogenetic estimation. In Bishop MJ, Rawlings CJ (eds): DNA and Protein Sequence Analysis. Oxford: IRL Press, pp 279-312.
5. Felsenstein J (1988) Phylogenies from molecular sequences: Inference and reliability. Annu Rev Genet 22:521-565.
6. Yang Z, Goldman N, Friday A (1995) Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem. Syst Biol 44:384-399.
7. Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 276:227-232.
8. Kuhner MK, Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11:459-468; see also Erratum: Mol Biol Evol 12:525 (1995).
9. Huelsenbeck JP (1995) Performance of phylogenetic methods in simulation. Syst Biol 44:17-48.
10. Feng D-F, Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25:351-360.
11. Thorne JL, Kishino H, Felsenstein J (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol 33:114-124; see also Erratum: J Mol Evol 34:91 (1992).
12. Thorne JL, Kishino H, Felsenstein J (1992) Inching toward reality: An improved likelihood model of sequence evolution. J Mol Evol 34:3-16.
13. Allison L, Wallace CS, Yee CN (1992) Finite-state models in the alignment of macromolecules. J Mol Evol 35:77-89.
14. Mitchison G, Durbin R (1995) Tree-based maximal likelihood substitution matrices and hidden Markov models. J Mol Evol 41:1139-1151.
15. Hein J (1990) Unified approach to alignment and phylogenies. Methods Enzymol 183:626-645.
16. Rubin DA, Dores RM (1995) Obtaining a more resolute teleost growth hormone phylogeny by the introduction of gaps in sequence alignment. Mol Phyl Evol 4:129-138.
17. Wagele JW, Stanjek G (1995) Arthropod phylogeny inferred from partial 12S rRNA revisited - monophyly of the Tracheata depends on sequence alignment J Zool Syst Evol Res 33:75-80.
18. Vingron M, Waterman MS (1994) Sequence alignment and penalty choice: Review of concepts, case studies and implications. J Mol Biol 235:1-12.
19. Goldman N (1990) Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst Zool 39:345-361.
20. Penny D (1982) Towards a basis for classification: The incompleteness of distance measures, incompatibility analysis and phenetic classification. J Theor Biol 96:129-142.
21. Lake J (1991) The order of sequence alignment can bias the selection of tree topology. Mol Biol Evol 8:378-385.
22. Thorne JL, Churchill GA (1995) Estimation and reliability of molecular sequence alignments. Biometrics 51:100-113.
23. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
24. Goldman N (1993) Statistical tests of models of DNA substitution. J Mol Evol 36:182-198.
25. Hasegawa M, Kishino H (1989) Confidence limits on the maximum-likelihood estimate of the hominoid tree from mitochondrial-DNA sequences. Evolution 43:672-677.
26. Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11:316-324.
27. Thorne JL, Kishino H (1992) Freeing phylogenies from artifacts of alignment. Mol Biol Evol 9:1148-1162.