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Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data

Citation

Tanabe, Akifumi S (2011), Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data, Dryad, Dataset, https://doi.org/10.5061/dryad.8646

Abstract

Proportional and separate models able to apply different combination of substitution rate matrix and among-site rate variation model to each locus are frequently used in phylogenetic studies of multilocus data. 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. The present study describes two programs, "Kakusan4" (for DNA sequences) and "Aminosan" (for amino-acid sequences), that 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 non-interactive command line interface. In the case of multilocus data, substitution rate matrices and among-site rate variation models 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. 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 GNU GPL Ver.2, and are able to run on Windows, MacOS X, and Linux.

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