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Bioinformatics Advance Access originally published online on March 16, 2006
Bioinformatics 2006 22(10):1269-1271; 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

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 Department of Statistics, U.C. Davis 360 Kerr Hall, One Shields Avenue, Davis CA 95616, USA
3 Department of Biology and School of Informatics, Indiana University 1001 E. Third Street Bloomington, IN 47405, USA

*To whom correspondence should be addressed.

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

Contact: mwh{at}indiana.edu

Received on January 20, 2006; revised on March 9, 2006; accepted on March 10, 2006

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