PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

CAFE: a computational tool for the study of gene family evolution
Tijl De Bie, Nello Cristianini, Jeffery Demuth and Matthew Hahn
Bioinformatics Volume 22, Number 10, pp. 1269-1271, 2006.


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.

EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Learning/Statistics & Optimisation
ID Code:3819
Deposited By:Tijl De Bie
Deposited On:25 February 2008