Optimization alignment: The end of multiple sequence alignment in phylogenetics?

Cladistics

Volumn 12, Issue 1, 1996, Pages 1-9

  Wheeler, Ward ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001857390     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1006/clad.1996.0001     Document Type: Article

References (14)

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2. FENG, D. AND R. F. DOOLITTLE. 1990. Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzomol. 183: 375-387.
3. FARRIS, J. S. 1970. A method for computing Wagner trees. Syst. Zool. 34: 21-34.
4. FITCH, W. M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20: 406-416.
5. GOLOBOFF, P. A. 1994. NONA/ Pee-Wee. Ver. 1.1. The American Museum of Natural History, New York.
6. HEIN, J. 1989. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when a phylogeny is given. Mol. Biol. Evol. 6: 649-668.
7. HEIN, J. 1990. Unified approach to alignment and phylogenies. Methods Enzomol. 183: 626-644.
8. HIGGINS, D. G. AND P. M. SHARP. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73: 237-244.
9. HIGGINS, D. G. AND P. M. SHARP. 1989. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. 5: 151-153.
10. MINDELL, D. 1991. Aligning DNA sequences: homology and phylogenetic weighting. In: M. J. Miyamoto and J. Cracraft (eds.). Phylogenetic Analysis of DNA Sequences. Oxford University Press, New York, pp. 73-89.
11. NEEDLEMAN, S. B. AND C. D. WUNSCH. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48: 443-453.
12. SANKOFF, D. D. AND R. J. CEDERGREN. 1983. Simultaneous comparison of three or more sequences related by a tree. In: D. Sankoff and J. B. Kruskal (eds). Time Warps, String Edits, and Macromolecules: the Theory and Practise of Sequence Comparison. Addison-Wesley, Reading, MA. pp. 253-264.
13. WHEELER, W. C. AND D. G. GLADSTEIN. 1992. MALIGN: A Multiple Sequence Alignment Program. Program and documentation. Vers. 2.0. The American Museum of Natural History, New York.
14. WHEELER, W. C. AND D. G. GLADSTEIN. 1994. MALIGN: a multiple nucleic and sequence alignment program. J. Hered. 85: 417.