CAFE v4.0 is now available on Github. This release includes an improved HTML report formatting option and fixes for various minor bugs. Please visit the CAFE website (https://hahnlab.github.io/CAFE/ ) where you will find the user manual and a tutorial on the usage of CAFE.
The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.
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