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

Bioinformatics. 2006 May 15;22(10):1269-71. doi: 10.1093/bioinformatics/btl097. Epub 2006 Mar 16.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms*
  • Chromosome Mapping / methods*
  • DNA Mutational Analysis / methods*
  • Evolution, Molecular*
  • Genetic Variation / genetics
  • Multigene Family / genetics*
  • Phylogeny
  • Software*
  • User-Computer Interface