Using the tangle: A consistent construction of phylogenetic distance matrices for quartets

DOI10.1016/J.MBS.2006.05.008MaRDI QIDQ868196zbMATH OpenOpenAlexWikidataFDO

Authors Jeremy G. Sumner, Peter D Jarvis

Publication date 19 February 2007

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0510035

zbMATH Keywords

phylogeneticstangledistance methodslog det

Mathematics Subject Classification ID

Problems related to evolution (92D15) Continuous-time Markov processes on discrete state spaces (60J27) Computational methods for problems pertaining to biology (92-08)

Abstract: Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a measure of the evolutionary change between any pair of the extant taxa. A standard technique is to use the log det formula to construct pairwise distances from aligned sequence data. We review a distance measure valid for the most general models, and show how the log det formula can be used as an estimator thereof. We then show that the foundation upon which the log det formula is constructed can be generalized to produce a previously unknown estimator which improves the consistency of the distance matrices constructed from the log det formula. This distance estimator provides a consistent technique for constructing quartets from phylogenetic sequence data under the assumption of the most general Markov model of sequence evolution.

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Cited in

(6)

• Toward extracting all phylogenetic information from matrices of evolutionary distances
• Systematics and symmetry in molecular phylogenetic modelling: perspectives from physics
• Binary cumulant varieties
• Markov invariants, plethysms, and phylogenetics
• Adventures in invariant theory
• The hyperdeterminant and triangulations of the 4-cube

Describes a project that uses

Uses Software

• BIONJ
• fastDNAml

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