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Bioinformatics Advance Access originally published online on May 12, 2008
Bioinformatics 2008 24(13):1538-1539; doi:10.1093/bioinformatics/btn226
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Malin: maximum likelihood analysis of intron evolution in eukaryotes

Miklós Csurös 1,2

1Department of Computer Science and Operations Research, University of Montréal, Montréal, Québec, Canada and 2Collegium Budapest Institute for Advanced Study, Budapest, Hungary


  Abstract

Summary: Malin is a software package for the analysis of eukaryotic gene structure evolution. It provides a graphical user interface for various tasks commonly used to infer the evolution of exon–intron structure in protein-coding orthologs. Implemented tasks include the identification of conserved homologous intron sites in protein alignments, as well as the estimation of ancestral intron content, lineage-specific intron losses and gains. Estimates are computed either with parsimony, or with a probabilistic model that incorporates rate variation across lineages and intron sites.

Availability: Malin is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the website http://www.iro.umontreal.ca/~csuros/introns/malin/. The software is distributed under a BSD-style license.

Contact: csuros{at}iro.umontreal.ca

Associate Editor: Martin Bishop

Received on February 21, 2008; revised on April 14, 2008; accepted on May 6, 2008

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