Random Tree Optimization for the Construction of the Most Parsimonious Phylogenetic Trees
Name
Li-2009-Random Tree Optimization for the Construction of the Most Parsimonious Phylogenetic Trees.pdf
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90.98 KB
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Adobe PDF
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Author(s)
Li, Fulu
Lippman, Andrew B.
Date Issued
June 2009
Journal
43rd Annual Conference on Information Sciences and Systems, 2009. CISS 2009
Publisher
Institute of Electrical and Electronics Engineers
Citation
Fulu Li, and A. Lippman. “Random tree optimization for the construction of the most parsimonious phylogenetic trees.” Information Sciences and Systems, 2009. CISS 2009. 43rd Annual Conference on. 2009. 757-762.©2009 Institute of Electrical and Electronics Engineers.
Version
Final published version
Abstract
With the availability of ever-increasing gene sequence data across a large number of species, reconstruction of phylogenetic trees to reveal the evolution relationship among those species becomes more and more important. In this paper, we focus on the construction of the most parsimonious phylogenetic trees given sequence data of a group of species as parsimony is probably the most widely used among all tree building algorithms [4]. The major contribution of this paper is the presentation of a novel algorithm, the random tree optimization (RTO) algorithm based on cross-entropy method [16], for the construction of the most parsimonious phylogenetic trees. We analyze the RTO algorithm in the framework of expectation maximization (EM) and point out the similarities and differences between traditional EM algorithm and the RTO algorithm.
MIT Department
Massachusetts Institute of Technology. Media Laboratory
Program in Media Arts and Sciences (Massachusetts Institute of Technology)
Terms of Use
Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1109/CISS.2009.5054819
