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Bioinformatics Advance Access published online on August 27, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn457
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

StatAlign: An Extendable Software Package for Joint Bayesian Estimation of Alignments and Evolutionary Trees

Ádám Novák 1, István Miklós 1,*, Rune Lyngsø 1 and Jotun Hein 1

1Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK

*To whom correspondence should be addressed. Dr. István Miklós, E-mail: miklosi{at}ramet.elte.hu


  Abstract

Motivation: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments and phylogenies should be inferred jointly as insertions and deletions also carry informative signals. Methods addressing these issues have been developed only recently and there has not been so far a userfriendly program with a graphical interface that implements these methods.

Results: We have developed an extendable software package in the Java programming language that samples from the joint posterior distribution of phylogenies, alignments and evolutionary parameters by applying the Markov chain Monte Carlo method. The package also offers tools for efficient on-the-fly summarisation of the results. It has a graphical interface to configure, start and supervise the analysis, to track the status of the Markov chain and to save the results. The background model for insertions and deletions can be combined with any substitution model. It is easy to add new substitution models to the software package as plugins. The samples from the Markov chain can be summarised in several ways, and new postprocessing plugins may also be installed.

Availability: The code is available from http://phylogeny-cafe.elte.hu/StatAlign/

Contact: miklosi{at}ramet.elte.hu

Associate Editor: Prof. Martin Bishop

Received on July 18, 2008; revised on August 21, 2008; accepted on August 21, 2008

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