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


BACKGROUND
Software is available from http://www.bio.indiana.edu/~hahnlab/Software.html
De Bie
Tijl
T
K.U.Leuven, OKP Research Group Tiensestraat 102, 3000 Leuven, Belgium.
Cristianini
Nello
N
Demuth
Jeffery P
JP
Hahn
Matthew W
MW
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D010802:Phylogeny; D012984:Software; D014584:User-Computer Interface