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Bioinformatics Advance Access published online on May 12, 2008
Bioinformatics, 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 Csur ös a,b

aDepartment of Computer Science and Operations Research, University of Montréal, Montréal,Québec, Canada. b Collegium Budapest Institute for Advanced Study, Budapest, Hungary.

*To whom correspondence should be addressed. Prof. Miklós Csur ös, E-mail: csuros{at}iro.umontreal.ca


  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: 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: Prof. Martin Bishop

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

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[Abstract] [Full Text] [PDF]


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