Module:Bio::Align::DNAStatistics
From BioPerl
| Pdoc documentation: Bio::Align::DNAStatistics | CPAN documentation: Bio::Align::DNAStatistics |
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Overview
This module implements the following simple sequence distance calculations.
- Jukes Cantor [1]
- Uncorrected
- Felsenstein 1981 (F81) [2]
- Kimura 2-parameter [3]
- Tamura [4]
- Felsenstein 1981 (F84) [5]
- Tajima Nei [6]
- Jin Nei not implemented yet [7]
- HKY not implmented [8]
Using the module
The module expects to be provided with an alignment of DNA sequences in the form of a Bio::Align::AlignI object, of which, Bio::SimpleAlign is the most commonly used one (you can get it by reading in an alignment from a file with Bio::AlignIO).
It will return a Bio::Matrix::PhylipDist object which can be written out to a PHYLIP matrix format with Bio::Matrix::IO or provided to a Bio::Tree::DistanceFactory to construct a distance-based tree either with the Neighbor-Joining or UPGMA method.
References
- Jukes TH, Cantor CR. Evolution of protein molecules in Mammalian protein metabolism, ed. H. N. Munro. 1969. New York: Academic Press. pp21-23.
- Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17(6) 368-76. pmid:7288891.
- Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980 Dec; 16(2) 111-20. pmid:7463489.
- Tamura K. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol Biol Evol 1992 Sep; 9(5) 814-25. pmid:1528108.
- Felsenstein, J. 1984. Distance methods for inferring phylogenies: A justification. Evolution 38, 16-24.
- Tajima F and Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1984 Apr; 1(3) 269-85. pmid:6599968.
- Jin L and Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 1990 Jan; 7(1) 82-102. pmid:2299983.
- Hasegawa M, Kishino H, and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985; 22(2) 160-74. pmid:3934395.
