Journal Article

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

Ádám Novák, István Miklós, Rune Lyngsø and Jotun Hein

in Bioinformatics

Volume 24, issue 20, pages 2403-2404
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btn457
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

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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 user-friendly 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 summarization 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 summarized 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@ramet.elte.hu

Journal Article.  1171 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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