CAFE: a computational tool for the study of gene family evolution
Tijl De Bie1, Nello Cristianini, Jeffery P Demuth
1K.U.Leuven, OKP Research Group Tiensestraat 102, 3000 Leuven, Belgium.
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
Related Concept Videos
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Evolutionary Relationships through Genome Comparisons
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Families
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Gene Evolution - Fast or Slow?
In contrast, regions which code...


