Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain.
Bioinformatics. 2012 Jan 15;28(2):279-81. doi: 10.1093/bioinformatics/btr623. Epub 2011 Nov 10.
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.
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.
BadiRate software and documentation is available from http://www.ub.edu/softevol/badirate.
基因增益和损失率的比较分析对于理解自然选择和适应在塑造基因家族大小方面的作用至关重要。研究来自密切相关物种的完整基因组数据可以准确估计基因家族周转率。然而，当前的方法和软件工具对于某些功能元件（如 microRNA 或转录因子结合位点）的处理效果并不理想。
在这里，我们描述了 BadiRate，这是一种新的软件工具，可通过基于似然和简约的方法来估计家族周转率以及内部系统发育节点中的元素数量。它实现了两个随机种群模型，为测试假设（例如谱系特异性基因家族扩张或收缩）提供了适当的统计框架。我们通过计算机模拟评估了 BadiRate 的准确性，并通过分析代表性的经验数据集说明了其功能。
BadiRate 软件和文档可从 http://www.ub.edu/softevol/badirate 获得。
