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BMC Bioinformatics. 2011 Apr 21;12:111. doi: 10.1186/1471-2105-12-111.

MixtureTree: a program for constructing phylogeny.

Author information

1
School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA. scchen@math.asu.edu

Abstract

BACKGROUND:

MixtureTree 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.

RESULTS:

The 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.html

CONCLUSIONS:

The 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.

PMID:
21615972
PMCID:
PMC3102041
DOI:
10.1186/1471-2105-12-111
[Indexed for MEDLINE]
Free PMC Article
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