Modeling the distribution of distance data in Euclidean space

DOI10.1090/CONM/685/13750MaRDI QIDQ2979650zbMATH OpenOpenAlexWikidataFDO

Authors Ruth Davidson, Joseph Rusinko, Zoe Vernon, Jing Xi

Publication date 25 April 2017

Published in Algebraic and Geometric Methods in Discrete Mathematics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1606.06146

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Trees (05C05) Applications of functional analysis in probability theory and statistics (46N30) Taxonomy, cladistics, statistics in mathematical biology (92B10) Combinatorial aspects of finite geometries (05B25)

Abstract: Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the data contains a phylogenetic signal that will be recovered with varying accuracy due to the quality of the method used, and the quality of the data. The input for distance-based inference methods is an element of a Euclidean space with coordinates indexed by the pairs of organisms. For several algorithms there exists a subdivision of this space into polyhedral cones such that inputs in the same cone return the same tree topology. The geometry of these cones has been used to analyze the inference algorithms. In this chapter, we model how input data points drawn from DNA sequences are distributed throughout Euclidean space in relation to the space of tree metrics, which in turn can also be described as a collection of polyhedral cones.

Recommendations

• Geometry of the space of phylogenetic trees
• Phylogenetic trees and Euclidean embeddings
• Statistics for phylogenetic trees
• The space of ultrametric phylogenetic trees
• Phylogenetics

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Cited in

(4)

• Phylogenetic placement problem: a hyperbolic embedding approach
• Facility location in the phylogenetic tree space
• scientific article; zbMATH DE number 3951812 (Why is no real title available?)
• Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm

Describes a project that uses

Uses Software

• BIONJ
• MEGA
• ismev
• MUSCLE

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