James J. Cai^1,2, David K. Smith³, Xuhua Xia⁴ and Kwok-yung Yuen²

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/.