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

doi:10.1186/1471-2105-6-64

BMC Bioinformatics
Volume 6

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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

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

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

³Department of Biology, University of Ottawa, Canada

author email corresponding author email

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


Published:	22 March 2005

Abstract

Background

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.

Results

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.

Conclusion

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 http://web.hku.hk/~jamescai/mbetoolbox/ webcite and http://bioinformatics.org/project/?group_id=454 webcite.