1Department of Biological Sciences, Stanford University, Stanford, CA, USA. 2Department of Microbiology, University of Hong Kong, Hong Kong SAR, China. 3Department of Biochemistry, University of Hong Kong, Hong Kong SAR, China. 4Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
Abstract: MBEToolbox is an extensible MATLAB-based software package for analysis of DNA and protein sequences. MBEToolbox version 2.0 includes enhanced functions for phylogenetic analyses by the maximum likelihood method. For example, it is capable of estimating the synonymous and nonsynonymous substitution rates using a novel or several known codon substitution models. MBEToolbox 2.0 introduces new functions for estimating site-specific evolutionary rates by using a maximum likelihood method or an empirical Bayesian method. It also incorporates several different methods for recombination detection. Multi-platform versions of the software are freely available at http://www.bioinformatics.org/mbetoolbox/.
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