Altenhoff Adrian M, Dessimoz Christophe
Department of Computer Science, ETH Zurich, Zurich, Switzerland.
Methods Mol Biol. 2012;855:259-79. doi: 10.1007/978-1-61779-582-4_9.
The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases, and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.
直系同源基因和旁系同源基因之间的区别，即通过物种形成与基因复制开始分化的基因，在广泛的背景下都具有相关性，最显著的是在系统发育树推断和蛋白质功能注释方面。在本章中，我们概述了用于推断直系同源和旁系同源的方法。我们考察了基于图的方法（及其各种分组策略）和基于树的方法，后者解决了基因/物种树调和这一更普遍的问题。我们讨论了各种直系同源推断方法和数据库之间的概念差异，并研究了验证和基准测试直系同源预测这一难题。最后，我们回顾了直系同源基因、基因簇和调和树的典型应用，并对未来方法学的发展进行了思考。
