生物
变化(天文学)
遗传学
进化生物学
计算生物学
基因组
计算机科学
遗传变异
作者
Fábio K. Mendes,Dan Vanderpool,Ben Fulton,Matthew W. Hahn
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2021-04-01
卷期号:36: 5516-5518
被引量:17
标识
DOI:10.1093/bioinformatics/btaa1022
摘要
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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