StatAlign

An extendable software package for joint Bayesian estimation of alignments and evolutionary trees

Ádám Novák, I. Miklós, Rune Lyngsø, Jotun Hein

Research output: Contribution to journalArticle

59 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)2403-2404
Number of pages2
JournalBioinformatics
Volume24
Issue number20
DOIs
Publication statusPublished - Oct 2008

Fingerprint

Evolutionary Tree
Bayesian Estimation
Software Package
Software packages
Markov Chains
Markov processes
Alignment
Substitution reactions
Software
Joints
Substitution
Phylogeny
Java programming language
Deletion
Insertion
Markov chain
Programming Languages
Monte Carlo Method
Bayes Theorem
Markov Chain Monte Carlo Methods

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

StatAlign : An extendable software package for joint Bayesian estimation of alignments and evolutionary trees. / Novák, Ádám; Miklós, I.; Lyngsø, Rune; Hein, Jotun.

In: Bioinformatics, Vol. 24, No. 20, 10.2008, p. 2403-2404.

Research output: Contribution to journalArticle

Novák, Ádám ; Miklós, I. ; Lyngsø, Rune ; Hein, Jotun. / StatAlign : An extendable software package for joint Bayesian estimation of alignments and evolutionary trees. In: Bioinformatics. 2008 ; Vol. 24, No. 20. pp. 2403-2404.
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