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607438.pdf (77.8 KB)

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2012

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Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/53350

BadiRate: estimating family turnover rates by likelihood-based methods

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Recurs relacionat

http://dx.doi.org/10.1093/bioinformatics/btr623
 http://hdl.handle.net/2445/53403

Resum

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.

Descripció

Podeu consultar el programari a: http://hdl.handle.net/2445/53403

Matèries

Genètica, Bioinformàtica, Programari, Filogènia, Processament de dades

Matèries (anglès)

Genetics, Bioinformatics, Computer software, Phylogeny, Data processing

Citació

Col·leccions

Articles publicats en revistes (Genètica, Microbiologia i Estadística)

Citació

LIBRADO SANZ, Pablo, VIEIRA, Filipe G. and ROZAS LIRAS, Julio A. BadiRate: estimating family turnover rates by likelihood-based methods. Bioinformatics. 2012. Vol. 28, num. 2, pags. 279-281. ISSN 1367-4803. [consulted: 6 of August of 2026]. Available at: https://hdl.handle.net/2445/53350

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