Module:Bio::Align::DNAStatistics

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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. [jc69]
  2. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368-76. PubMed ID:7288891 | HubMed [f81]
  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. PubMed ID:7463489 | HubMed [k2p]
  4. Tamura K. The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA. Mol Biol Evol. 1992 Sep;9(5):814-25. PubMed ID:1528108 | HubMed [t92]
  5. Felsenstein, J. 1984. Distance methods for inferring phylogenies: A justification. Evolution 38, 16-24. [f84]
  6. Tajima F and Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol. 1984 Apr;1(3):269-85. PubMed ID:6599968 | HubMed [tn84]
  7. Jin L and Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol. 1990 Jan;7(1):82-102. PubMed ID:2299983 | HubMed [jn90]
  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. PubMed ID:3934395 | HubMed [hky]
All Medline abstracts: PubMed | HubMed
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