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Title: BadiRate: estimating family turnover rates by likelihood-based methods
Author: Librado Sanz, Pablo
Vieira, Filipe G.
Rozas Liras, Julio A.
Keywords: Genètica
Processament de dades
Computer software
Data processing
Issue Date: 2012
Publisher: Oxford University Press
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.
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It is part of: Bioinformatics, 2012, vol. 28, num. 2, p. 279-281
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ISSN: 1367-4803
Appears in Collections:Articles publicats en revistes (Genètica, Microbiologia i Estadística)

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