BadiRate: Estimating family turnover rates by likelihood-based methods

P. Librado; F. G. Vieira; J. Rozas

doi:10.1093/bioinformatics/btr623

BadiRate: Estimating family turnover rates by likelihood-based methods

P. Librado, F. G. Vieira, J. Rozas^*

^*Corresponding author for this work

68 Citations (Scopus)

Abstract

Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites.Results: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset.

Original language	English
Article number	btr623
Journal	Bioinformatics
Volume	28
Issue number	2
Pages (from-to)	279-281
Number of pages	3
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btr623
Publication status	Published - Jan 2012
Externally published	Yes

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BadiRate: Estimating family turnover rates by likelihood-based methods

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