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MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

James J Cai1*, David K Smith2, Xuhua Xia3 and Kwok-yung Yuen1

Author Affiliations

1 Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong, China

2 Department of Biochemistry, University of Hong Kong, Pokfulam, Hong Kong, China

3 Department of Biology, University of Ottawa, Canada

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BMC Bioinformatics 2005, 6:64  doi:10.1186/1471-2105-6-64

Published: 22 March 2005



MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution.


We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided.


MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at webcite and webcite.