Format

Send to

Choose Destination
Bioinformatics. 2012 Jan 15;28(2):279-81. doi: 10.1093/bioinformatics/btr623. Epub 2011 Nov 10.

BadiRate: estimating family turnover rates by likelihood-based methods.

Author information

1
Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain.

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.

AVAILABILITY:

BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.

PMID:
22080468
DOI:
10.1093/bioinformatics/btr623
[Indexed for MEDLINE]
Free full text

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for Diposit Digital de la Universitat de Barcelona
Loading ...
Support Center