title: BadiRate: estimating family turnover rates by likelihood-based methods.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain.
authors.forename: P
authors.initials: P
authors.lastname: Librado
authors.forename: F G
authors.initials: FG
authors.lastname: Vieira
authors.forename: J
authors.initials: J
authors.lastname: Rozas
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D004330:Drosophila / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D016678:Genome; D016013:Likelihood Functions; D035683:MicroRNAs / Q000378:metabolism; D010802:Phylogeny; D012044:Regression Analysis; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors