title: MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution.
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/.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, CA, USA. jamescai@graduate.hku.hk
authors.forename: James J
authors.initials: JJ
authors.lastname: Cai
authors.forename: David K
authors.initials: DK
authors.lastname: Smith
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen