Institute of Biological Sciences, Graduate School of Life and Environmental Sciences, University of Tsukuba, Ten-no-dai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan.
Mol Ecol Resour. 2011 Sep;11(5):914-21. doi: 10.1111/j.1755-0998.2011.03021.x. Epub 2011 May 19.
Proportional and separate models able to apply different combination of substitution rate matrix (SRM) and among-site rate variation model (ASRVM) to each locus are frequently used in phylogenetic studies of multilocus data. A proportional model assumes that branch lengths are proportional among partitions and a separate model assumes that each partition has an independent set of branch lengths. However, the selection from among nonpartitioned (i.e., a common combination of models is applied to all-loci concatenated sequences), proportional and separate models is usually based on the researcher's preference rather than on any information criteria. This study describes two programs, 'Kakusan4' (for DNA sequences) and 'Aminosan' (for amino-acid sequences), which allow the selection of evolutionary models based on several types of information criteria. The programs can handle both multilocus and single-locus data, in addition to providing an easy-to-use wizard interface and a noninteractive command line interface. In the case of multilocus data, SRMs and ASRVMs are compared at each locus and at all-loci concatenated sequences, after which nonpartitioned, proportional and separate models are compared based on information criteria. The programs also provide model configuration files for mrbayes, paup*, phyml, raxml and Treefinder to support further phylogenetic analysis using a selected model. When likelihoods are optimized by Treefinder, the best-fit models were found to differ depending on the data set. Furthermore, differences in the information criteria among nonpartitioned, proportional and separate models were much larger than those among the nonpartitioned models. These findings suggest that selecting from nonpartitioned, proportional and separate models results in a better phylogenetic tree. Kakusan4 and Aminosan are available at http://www.fifthdimension.jp/. They are licensed under gnugpl Ver.2, and are able to run on Windows, MacOS X and Linux.
能够为每个位点应用不同的替代率矩阵 (SRM) 和位点间速率变异模型 (ASRVM) 组合的比例和独立模型，常用于多基因座数据的系统发育研究。比例模型假设分支长度在分区之间成比例，而独立模型假设每个分区具有独立的分支长度集。然而，非分区模型（即，为所有位点串联序列应用共同的模型组合）、比例模型和独立模型的选择通常基于研究人员的偏好，而不是基于任何信息准则。本研究描述了两个程序，'Kakusan4'（用于 DNA 序列）和 'Aminosan'（用于氨基酸序列），它们允许根据几种类型的信息准则选择进化模型。该程序可以处理多基因座和单基因座数据，除了提供易于使用的向导界面和非交互命令行界面外。在多基因座数据的情况下，在每个位点和所有位点串联序列上比较 SRM 和 ASRVM，然后根据信息准则比较非分区、比例和独立模型。该程序还为 mrbayes、paup*、phyml、raxml 和 Treefinder 提供模型配置文件，以支持使用选定模型进行进一步的系统发育分析。当通过 Treefinder 优化似然时，发现最佳拟合模型因数据集而异。此外，非分区、比例和独立模型之间的信息准则差异比非分区模型之间的差异大得多。这些发现表明，从非分区、比例和独立模型中进行选择可以得到更好的系统发育树。Kakusan4 和 Aminosan 可在 http://www.fifthdimension.jp/ 获取。它们根据 gnugpl Ver.2 获得许可，能够在 Windows、MacOS X 和 Linux 上运行。
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