Module:Bio::Align::DNAStatistics

Bio::Align::DNAStatistics
PDoc	Bio::Align::DNAStatistics
CPAN	Bio::Align::DNAStatistics
metaCPAN	Bio::Align::DNAStatistics

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

1. Jukes TH, Cantor CR. Evolution of protein molecules in Mammalian protein metabolism, ed. H. N. Munro. 1969. New York: Academic Press. pp21-23.
2. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368-76.
3. 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.
4. Tamura K. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol Biol Evol. 1992 Sep;9(5):814-25.
5. Felsenstein, J. 1984. Distance methods for inferring phylogenies: A justification. Evolution 38, 16-24.
6. Tajima F and Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol. 1984 Apr;1(3):269-85.
7. Jin L and Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol. 1990 Jan;7(1):82-102.
8. 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.