MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution

James J. Cai, David K. Smith, Xuhua Xia, Kwok-yung Yuen
2006 Evolutionary Bioinformatics  
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 an
more » ... d 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/.
doi:10.1177/117693430600200002 fatcat:w5qprxce6nculmiz7mfx4577mm