NDLI: Optimization Over a Class of Tree Shape Statistics

Content Provider	ACM Digital Library
Author	Matsen, Frederick
Abstract	Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful tree shape statistic, formulas have been invented by hand and then evaluated for utility. This article presents the first method which is capable of optimizing over a class of tree shape statistics, called Binary Recursive Tree Shape Statistics (BRTSS). After defining the BRTSS class, a set of algebraic expressions is defined which can be used in the recursions. The tree shape statistics definable using these expressions in the BRTSS is very general, and includes many of the statistics with which phylogenetic researchers are already familiar. We then present a practical genetic algorithm which is capable of performing optimization over BRTSS given any objective function. The chapter concludes with a successful application of the methods to find a new statistic which indicates a significant difference between two distributions on trees which were previously postulated to have similar properties.
Starting Page	506
Ending Page	512
Page Count	7
File Format	PDF
ISSN	15455963
DOI	10.1109/tcbb.2007.1020
Volume Number	4
Issue Number	3
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2007-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biology and genetics, Evolutionary computing and genetic algorithms
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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