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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-specifi c evolutionary rates by using a maximum likelihood method or andoi:10.1177/117693430600200002 fatcat:w5qprxce6nculmiz7mfx4577mm