Skip Navigation


Bioinformatics Advance Access first published online on November 14, 2007
This version published online on November 20, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm532
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
24/1/56    most recent
btm532v3
btm532v2
btm532v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Rodrigue, N.
Right arrow Articles by Lartillot, N.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rodrigue, N.
Right arrow Articles by Lartillot, N.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Uniformization for sampling realizations of Markov processes: Applications to Bayesian implementations of codon substitution models

Nicolas Rodrigue a,*, Hervé Philippe a and Nicolas Lartillot b

aCanadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, C.P. 6821, Succ. Centre-ville, Montréal, Québec CANADA, H3C 3J7,bLaboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, URM 5506, CNRS-Université de Montpellier 2, Montpellier FRANCE

*To whom correspondence should be addressed. Nicolas Rodrigue, E-mail: nicolas.rodrigue{at}umontreal.ca


  Abstract

Motivation: Mapping character state changes over phylogenetic trees is central to the study of evolution. However, current probabilistic methods for generating such mappings are ill-suited to certain types of evolutionary models, in particular, the widely used models of codon substitution.

Results: We propose describe a general method, based on a uniformization technique, which can be utilized to generate realizations of a Markovian substitution process conditional on an alignment of character states and a given tree topology. The method is applicable under a wide range of evolutionary models, and to illustrate its usefulness in practice, we embed it within a data augmentation-based Markov chain Monte Carlo sampler, for approximating posterior distributions under previously proposed codon substitution models. The sampler is found to be more effcient than the conventional pruning-based sampler, with decorrelation times between draws from the posterior reduced by a factor of twenty or more.

Contact: nicolas.rodrigue{at}umontreal.ca

Associate Editor: Prof. Keith Crandall

Received on May 29, 2007; revised on September 9, 2007; accepted on October 16, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
N. Rodrigue, C. L. Kleinman, H. Philippe, and N. Lartillot
Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons
Mol. Biol. Evol., July 1, 2009; 26(7): 1663 - 1676.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Anisimova and C. Kosiol
Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models
Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
W. Delport, K. Scheffler, and C. Seoighe
Models of coding sequence evolution
Brief Bioinform, January 1, 2009; 10(1): 97 - 109.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
V. N Minin and M. A Suchard
Fast, accurate and simulation-free stochastic mapping
Phil Trans R Soc B, December 27, 2008; 363(1512): 3985 - 3995.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.