NDLI: An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace

Content Provider	IEEE Xplore Digital Library
Author	Nye, T.M.W.
Copyright Year	2004
Abstract	Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks, clustering and multidimensional scaling have been developed and applied to tree samples. This paper describes a stochastic algorithm for constructing a principal geodesic or line through treespace which is analogous to the first principal component in standard principal components analysis. A principal geodesic summarizes the most variable features of a sample of trees, in terms of both tree topology and branch lengths, and it can be visualized as an animation of smoothly changing trees. The algorithm performs a stochastic search through parameter space for a geodesic which minimizes the sum of squared projected distances of the data points. This procedure aims to identify the globally optimal principal geodesic, though convergence to locally optimal geodesics is possible. The methodology is illustrated by constructing principal geodesics for experimental and simulated data sets, demonstrating the insight into samples of trees that can be gained and how the method improves on a previously published approach. A java package called GeoPhytter for constructing and visualizing principal geodesics is freely available from www.ncl.ac.uk/ ntmwn/geophytter.
Sponsorship	IEEE Computer Society
Starting Page	304
Ending Page	315
Page Count	12
File Size	938757
File Format	PDF
ISSN	15455963
Volume Number	11
Issue Number	2
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Phylogeny Principal component analysis Topology Computational biology Bioinformatics Measurement Vegetation treespace principal components analysis
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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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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