Module:Bio::Align::DNAStatistics

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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 jc69
• Uncorrected
• Felsenstein 1981 (F81) f81
• Kimura 2-parameter k2p
• Tamura t92
• Felsenstein 1981 (F84) f84
• Tajima Nei tn84
• Jin Nei not implemented yet jn90
• HKY not implmented hky

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

<biblio>

1. f81 pmid=7288891
2. f84 Felsenstein, J. 1984. Distance methods for inferring phylogenies: A justification. Evolution 38, 16-24.
3. k2p pmid=7463489
4. t92 pmid=1528108
5. jc69 Jukes TH, Cantor CR. Evolution of protein molecules in Mammalian protein metabolism, ed. H. N. Munro. 1969. New York: Academic Press. pp21-23.
6. tn84 pmid=6599968
7. jn90 pmid=2299983
8. hky pmid=3934395

</biblio>