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

Authors:
Tijl De Bie;Nello Cristianini;Jeffery P. Demuth;Matthew W. Hahn
Affiliations:
K.U.Leuven, OKP Research Group Tiensestraat 102, 3000 Leuven, Belgium;Department of Statistics, U.C. Davis 360 Kerr Hall, One Shields Avenue, Davis CA 95616, USA;Department of Biology and School of Informatics, Indiana University 1001 E. Third Street Bloomington, IN 47405, USA;Department of Biology and School of Informatics, Indiana University 1001 E. Third Street Bloomington, IN 47405, USA
Venue:
Bioinformatics
Year:
2006

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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 Contact: mwh@indiana.edu