NDLI: Reconstructing phylogenetic networks using maximum parsimony

Content Provider	IEEE Xplore Digital Library
Author	Nakhleh, L. Jin, G. Zhao, F. Mellor-Crummey, J.
Copyright Year	2005
Description	Author affiliation: Dept. of Comput. Sci., Rice Univ., Houston, TX, USA (Nakhleh, L.; Jin, G.; Zhao, F.; Mellor-Crummey, J.)
Abstract	Phylogenies-the evolutionary histories of groups of organisms-are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organisms, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.
Sponsorship	IEEE Comput. Soc. Tech. Comm. on Bioinformatics
Starting Page	93
Ending Page	102
File Size	171020
Page Count	10
File Format	PDF
ISBN	0769523447
DOI	10.1109/CSB.2005.47
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-08-08
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Phylogeny History horizontal gene transfer Computer science Systematics Microorganisms Evolution (biology) Biological processes Binary trees maximum parsimony Biology computing Computer networks phylogenetic networks
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
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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