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Maximum likelihood estimates of pairwise rearrangement distances

Citation

Serdoz, S and Egri-Nagy, A and Sumner, J and Holland, BR and Jarvis, PD and Tanaka, MM and Francis, AR, Maximum likelihood estimates of pairwise rearrangement distances, Journal of Theoretical Biology, 423 pp. 31-40. ISSN 0022-5193 (2017) [Refereed Article]


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DOI: doi:10.1016/j.jtbi.2017.04.015

Abstract

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. Corresponding corrections for genome rearrangement distances fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here, we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using a group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. The second aspect tackles the problem of accounting for the symmetries of circular arrangements. While, generally, a frame of reference is locked, and all computation made accordingly, this work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference. The philosophy of accounting for symmetries can be applied to any existing correction method, for which examples are offered.

Item Details

Item Type:Refereed Article
Keywords:genome rearrangement, inversion, maximum likelihood, phylogeny, algebraic biology, group theory, coset
Research Division:Mathematical Sciences
Research Group:Applied Mathematics
Research Field:Biological Mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Mathematical Sciences
Author:Sumner, J (Dr Jeremy Sumner)
Author:Holland, BR (Associate Professor Barbara Holland)
Author:Jarvis, PD (Dr Peter Jarvis)
ID Code:116013
Year Published:2017
Web of Science® Times Cited:1
Deposited By:Mathematics and Physics
Deposited On:2017-04-27
Last Modified:2017-11-21
Downloads:0

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