title: MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.
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.
  
  
  CONCLUSIONS
  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/ and http://bioinformatics.org/project/?group_id=454
authors.affiliation: Department of Microbiology, University of Hong Kong, Pokfulam, Hong Kong, China. jamescai@hkusua.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
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D016247:Information Storage and Retrieval; D020407:Internet; D008024:Ligands; D008957:Models, Genetic; D008967:Molecular Biology / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012815:Signal Processing, Computer-Assisted; D012984:Software; D012985:Software Design; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins