Liò P, Goldman N
Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Genome Res. 1998 Dec;8(12):1233-44. doi: 10.1101/gr.8.12.1233.
Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings and applications in a broad range of biological areas. Fundamental to these are the mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use of such models in phylogenetic reconstruction and statistical methods for the comparison of different models.
系统发育重建是一个快速发展的领域，不同的统计方法以及广泛生物学领域的研究成果和应用使其不断丰富。其中的基础是用于描述DNA碱基替换和氨基酸置换模式的数学模型。这些模型可能会成为比较基因组研究的一些基本模型。我们将讨论这些模型，包括对观察到的DNA碱基和氨基酸突变模式的分析、位点异质性的概念以及结构生物学数据的纳入，所有这些在近年来都变得尤为重要。我们还将描述此类模型在系统发育重建中的应用以及比较不同模型的统计方法。
