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Bioinformatics Advance Access published online on March 16, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl097
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 20, 2006
Revised March 9, 2006
Accepted March 10, 2006

Applications note

CAFE: a computational tool for the study of gene family evolution

Tijl De Bie 1, Nello Cristianini 2, Jeffery P. Demuth 3, and Matthew W. Hahn 3 *

1 K.U.Leuven, OKP Research Group, Tiensestraat 102, 3000 Leuven, Belgium
2 U.C. Davis, Department of Statistics, 360 Kerr Hall, One Shields Ave., Davis CA-95616, USA
3 Indiana University, Department of Biology and School of Informatics, 1001 E. Third St. Bloomington, IN 47405, USA

* To whom correspondence should be addressed.
Matthew W. Hahn, E-mail: mwh{at}indiana.edu


  Abstract

Summary: We present CAFE (Computational Analysis of gene Family Evolution), a tool for the statistical analysis of the evolution of the size of gene families. It uses a stochastic birth and death process to model the evolution of gene family sizes over a phylogeny. For a specified phylogenetic tree, and given the gene family sizes in the extant species, CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss (quantified by a p-value), and identify which branches cause the p-value to be small for significant families.

Availability: Software is available from http://www.bio.indiana.edu/~hahnlab/Software.html.

Associate Editor: Chris Stoeckert
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