MixtureTree: a program for constructing phylogeny

BMC Bioinformatics

Software

Michael S Rosenberg¹  Bruce G Lindsay²  Shu-Chuan Chen³ 

[1] Center for Evolutionary Medicine and Informatics, Biodesign Institute, and School of Life Sciences, Arizona State University, 85287, Tempe, AZ, USA;Department of Statistics, Pennsylvania State University, 16802, University Park, PA, USA;School of Mathematical and Statistical Sciences, Arizona State University, 85287, Tempe, AZ, USA;

关键词: Maximum Parsimony;    Binary Sequence;    Mixture Tree;    Optimization Option;    Bootstrap Tree;   

DOI  :  10.1186/1471-2105-12-111

 received in 2010-09-01, accepted in 2011-04-21,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundMixtureTree v1.0 is a Linux based program (written in C++) which implements an algorithm based on mixture models for reconstructing phylogeny from binary sequence data, such as single-nucleotide polymorphisms (SNPs). In addition to the mixture algorithm with three different optimization options, the program also implements a bootstrap procedure with majority-rule consensus.ResultsThe MixtureTree program written in C++ is a Linux based package. The User's Guide and source codes will be available at http://math.asu.edu/~scchen/MixtureTree.htmlConclusionsThe efficiency of the mixture algorithm is relatively higher than some classical methods, such as Neighbor-Joining method, Maximum Parsimony method and Maximum Likelihood method. The shortcoming of the mixture tree algorithms, for example timing consuming, can be improved by implementing other revised Expectation-Maximization(EM) algorithms instead of the traditional EM algorithm.

【 授权许可】

CC BY   
© Chen et al; licensee BioMed Central Ltd. 2011