FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood

Bioinformatics

Volumn 10, Issue 1, 1994, Pages 41-48

  Olsen, Gary J ^a   Matsuda, Hideo ^a,b   Hagstrom, Ray ^a,b   Overbeek, Ross ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER; COMPUTER MEMORY; DATA BASE; DNA SEQUENCE; PHYLOGENY; PRIORITY JOURNAL;

ALGORITHMS; BACTERIA; DATABASES, FACTUAL; DNA; DNA, BACTERIAL; EVALUATION STUDIES; LIKELIHOOD FUNCTIONS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SOFTWARE; SUPPORT, U.S. GOV'T, NON-P.H.S.;

EID: 0027957393     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/10.1.41     Document Type: Article

References (19)

1. Boyle, J., Butler, R., Disz, T., Glickfeld, B., Lusk, E.L., Overbeek, R.A., Patterson, J. and Stevens, R. (1987) Portable Programs for Parallel Processors. Holt, Rinehart, and Winston, New York.
2. Cavalli-Sforza, L.L. and Edwards, A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. Am. J. Hum. Genet., 19, 233-257.
3. Felsenstein, J. (1973a) Maximum likelihood estimation of evolutionary trees from continuous characters. Genetics. 52, 349-363.
4. Felsenstein, J. (1973b) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discreet characters. Syst. Zool., 22, 240-249.
5. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
6. Felsenstein, J. (1982) Numerical methods for inferring evolutionary trees. Q. Rev. Biol., 57, 379-404.
7. Felsenstein, J. (1988) Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet., 22, 521-565.
8. Felsenstein, J. (1989) PHYLJP—phylogcny inference package (version 3.2). Cladistics. 5, 164-166.
9. Felsenstein, J. (1990) PHYUP Manual Version 3.3. University Herbarium, University of California, Berkeley, CA.
10. Jin, L. and Nei, M. (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol., 7, 82-102.
11. Li, W.-H. and Grauer, D. (1991) Fundamentals of Molecular Evolution. Sinauer, Sunderiand, MA.
12. Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press. New York.
13. Olsen, G.J., Overbeek, R., Ursen, N., Marsh, T.L., McCaughey, M.J., Maciukenas, M.A., Kuan, W.-M., Macke, T.J, Xing, Y. and Woese, C.R. (1992) The ribosomal database project. Nucleic Adds Res., 20, 2199-2200.
14. Saitou, N. (1990) Maximum likelihood methods. Methods Enzymol., 183, 584-598.
15. Sogin, M.L., Edman, U. and Elwood, H.J. (1989) A single kingdom of eukaryotes. In Femholm, B., Breme, B. and Jomvall, H. (eds), The Hierarchy of life. Elsevier Science Publishers, Amsterdam, pp. 133-143.
16. Swofford, D.L. (1990) PAUP: Phylogenetic Analysis Using Parsimony, Version 3.0. Illinois Natural History Survey, Champaign, PL.
17. Swofford, D.L. and Olsen, G.J. (1991) Phylogeny reconstruction. In Hillis, D. and Moritz, C. (eds). Molecular Systematics. Sinauer, Sunderiand, MA, pp. 411-501.
18. Thompson, E.A. (1975) Human Evolutionary Trees. Cambridge University Press, Cambridge.
19. Woese, C.R. (1987) Bacterial evolution. Microbiol. Rev., 51, 221-271.