Multi loci phylogenetic analysis with gene tree clustering
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Authors
Yoshida, Ruriko
Fukumizu, Kenji
Vogiatzis, Chrysafis
Subjects
Advisors
Date of Issue
2018-10-08
Date
2018-10
Publisher
ArXiv
Language
Abstract
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide “biologically meaningful” and “statistically well-distributed” distance between trees. Thus, in this paper, we study the distributions of the three tree distance metrics: the edge difference, the path difference, and the precise K interval cospeciation distance, between two trees: First, we focus on distributions of the three tree distances between two random unrooted trees with n leaves (n ≥ 4); and then we focus on the distributions the three tree distances between a fixed rooted species tree with n leaves and a random gene tree with n leaves generated under the coalescent process with the given species tree. We show some theoretical results as well as simulation study on these distributions. Key Words: Coalescent, Phylogenetics, Tree metrics, Tree topologies.
Type
Preprint
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Series/Report No
Department
Operations Research (OR)
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Format
22 p.
Citation
Yoshida, Ruriko, Kenji Fukumizu, and Chrysafis Vogiatzis. "Multilocus phylogenetic analysis with gene tree clustering." Annals of Operations Research 276.1-2 (2019): 293-313.
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This publication is a work of the U.S. Government as defined in Title 17, United States Code, Section 101. Copyright protection is not available for this work in the United States.