MixtureTree

A program for constructing phylogeny

Shu Chuan Chen, Michael S. Rosenberg, Bruce G. Lindsay

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish (US)
Article number111
JournalBMC Bioinformatics
Volume12
DOIs
StatePublished - Apr 21 2011

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Phylogeny
Expectation-maximization Algorithm
Linux
C++
Maximum Parsimony
Majority Rule
Single nucleotide Polymorphism
Binary Sequences
Maximum Likelihood Method
Tree Algorithms
Mixture Model
Joining
Bootstrap
Timing
Binary sequences
Optimization
Nucleotides
Polymorphism
Maximum likelihood
Single Nucleotide Polymorphism

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

MixtureTree : A program for constructing phylogeny. / Chen, Shu Chuan; Rosenberg, Michael S.; Lindsay, Bruce G.

In: BMC Bioinformatics, Vol. 12, 111, 21.04.2011.

Research output: Contribution to journalArticle

Chen, Shu Chuan ; Rosenberg, Michael S. ; Lindsay, Bruce G. / MixtureTree : A program for constructing phylogeny. In: BMC Bioinformatics. 2011 ; Vol. 12.
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