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Hadamard phylogenetic methods and the n-taxon process.

by: David Bryant

In: Bull Math Biol, Vol. 71, Nr. 2 Department of Mathematics, University of Auckland, Auckland, New Zealand. d.bryant@auckland.ac.nz: (February 2009) , p. 339-351.

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URL:	http://www.springerlink.com/content/f655597p10x68523/
DOI:	10.1007/s11538-008-9364-8

The Hadamard transform Hendy and Penny, Syst. Zool. 384:297-309, 1989; Hendy, Syst. Zool. 384:310-321, 1989 provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree space and the graphical structure of trees. Here we demonstrate that the transform can be expressed in terms of the familiar Ptau=e Qtau formula for Markov chains. The key idea is to study the evolution of vectors of states, one vector entry for each taxa; we call this the n-taxon process. We derive transition probabilities for the process. Significantly, the findings show that tree-based models are indeed in the family of multi-variate exponential distributions.

BibTeX record

@article{Bryant09,
  abstract = {The Hadamard transform (Hendy and Penny, Syst. Zool. 38(4):297-309, 1989; Hendy, Syst. Zool. 38(4):310-321, 1989) provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree space and the graphical structure of trees. Here we demonstrate that the transform can be expressed in terms of the familiar P[tau]=e ( Q[tau]) formula for Markov chains. The key idea is to study the evolution of vectors of states, one vector entry for each taxa; we call this the n-taxon process. We derive transition probabilities for the process. Significantly, the findings show that tree-based models are indeed in the family of (multi-variate) exponential distributions.},
  added-at = {2009-05-14T23:47:26.000+0200},
  address = {Department of Mathematics, University of Auckland, Auckland, New Zealand. d.bryant@auckland.ac.nz},
  au = {Bryant, D},
  author = {Bryant, David},
  biburl = {http://www.bibsonomy.org/bibtex/2fc25b4cacd00b5e065374fdc0a5114a4/compevol},
  crdt = {2008/10/11 09:00},
  da = {20090115},
  date-modified = {2009-01-28 13:04:38 +1300},
  dep = {20081010},
  doi = {10.1007/s11538-008-9364-8},
  edat = {2008/10/11 09:00},
  interhash = {bfc74cf2c3f2f14c3a542ebe98686563},
  intrahash = {fc25b4cacd00b5e065374fdc0a5114a4},
  issn = {1522-9602 (Electronic)},
  jid = {0401404},
  journal = {Bull Math Biol},
  jt = {Bulletin of mathematical biology},
  keywords = {from:davidjamesbryant},
  language = {eng},
  mhda = {2008/10/11 09:00},
  month = Feb,
  number = 2,
  own = {NLM},
  pages = {339-351},
  phst = {2007/12/11 {$[$}received{$]$}; 2008/09/18 {$[$}accepted{$]$}; 2008/10/10 {$[$}aheadofprint{$]$}},
  pl = {United States},
  pmid = {18846403},
  pst = {ppublish},
  pt = {Journal Article},
  sb = {IM},
  so = {Bull Math Biol. 2009 Feb;71(2):339-51. Epub 2008 Oct 10.},
  stat = {In-Process},
  timestamp = {2009-05-14T23:47:26.000+0200},
  title = {Hadamard phylogenetic methods and the n-taxon process.},
  url = {http://www.springerlink.com/content/f655597p10x68523/},
  volume = 71,
  year = 2009
}

Endnote record

%0 Journal Article
%1 Bryant09
%A Bryant, David
%C Department of Mathematics, University of Auckland, Auckland, New Zealand. d.bryant@auckland.ac.nz
%D 2009
%J Bull Math Biol
%K 
%N 2
%P 339-351
%T Hadamard phylogenetic methods and the n-taxon process.
%R 10.1007/s11538-008-9364-8
%U http://www.springerlink.com/content/f655597p10x68523/
%V 71
%X The Hadamard transform (Hendy and Penny, Syst. Zool. 38(4):297-309, 1989; Hendy, Syst. Zool. 38(4):310-321, 1989) provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree space and the graphical structure of trees. Here we demonstrate that the transform can be expressed in terms of the familiar P[tau]=e ( Q[tau]) formula for Markov chains. The key idea is to study the evolution of vectors of states, one vector entry for each taxa; we call this the n-taxon process. We derive transition probabilities for the process. Significantly, the findings show that tree-based models are indeed in the family of (multi-variate) exponential distributions.

BibSonomy :: publication ::

Hadamard phylogenetic methods and the n-taxon process.

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Abstract

BibTeX record

Endnote record