Fábio K Mendes1,2, Dan Vanderpool1, Ben Fulton1,3, Matthew W Hahn1,4. 1. Department of Biology, Indiana University, Bloomington, IN 47405, USA. 2. School of Biological Sciences, The University of Auckland, Auckland, New Zealand. 3. University Information Technology Services Indiana University, Bloomington, IN 47405, USA. 4. Department of Computer Science, Indiana University, Bloomington, IN 47405, USA.
Abstract
MOTIVATION: Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, CAFE (Computational Analysis of gene Family Evolution), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. RESULTS: Here we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modelling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. AVAILABILITY: CAFE 5 source code, documentation, test data, and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases.
MOTIVATION: Genome sequencing projects have revealed frequent gains and losses of genes between species. Previous versions of our software, CAFE (Computational Analysis of gene Family Evolution), have allowed researchers to estimate parameters of gene gain and loss across a phylogenetic tree. However, the underlying model assumed that all gene families had the same rate of evolution, despite evidence suggesting a large amount of variation in rates among families. RESULTS: Here we present CAFE 5, a completely re-written software package with numerous performance and user-interface enhancements over previous versions. These include improved support for multithreading, the explicit modelling of rate variation among families using gamma-distributed rate categories, and command-line arguments that preclude the use of accessory scripts. AVAILABILITY: CAFE 5 source code, documentation, test data, and a detailed manual with examples are freely available at https://github.com/hahnlab/CAFE5/releases.
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