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2016 Using ciliate operations to construct chromosome phylogenies
Jacob L. Herlin, Anna Nelson, Marion Scheepers
Involve 9(1): 1-26 (2016). DOI: 10.2140/involve.2016.9.1

Abstract

Whole genome sequencing has revealed several examples where genomes of different species are related by permutation. The number of certain types of rearrangements needed to transform one permuted list into another can measure the distance between such lists. Using an algorithm based on three basic DNA editing operations suggested by a model for ciliate micronuclear decryption, this study defines the distance between two permutations to be the number of ciliate operations the algorithm performs during such a transformation. Combining well-known clustering methods with this distance function enables one to construct corresponding phylogenies. These ideas are illustrated by exploring the phylogenetic relationships among the chromosomes of eight fruit fly (Drosophila) species, using the well-known UPGMA algorithm on the distance function provided by the ciliate operations.

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Jacob L. Herlin. Anna Nelson. Marion Scheepers. "Using ciliate operations to construct chromosome phylogenies." Involve 9 (1) 1 - 26, 2016. https://doi.org/10.2140/involve.2016.9.1

Information

Received: 23 January 2013; Revised: 11 December 2014; Accepted: 21 December 2014; Published: 2016
First available in Project Euclid: 22 November 2017

zbMATH: 1328.05004
MathSciNet: MR3438442
Digital Object Identifier: 10.2140/involve.2016.9.1

Subjects:
Primary: 05E15 , 20B99 , 92-08 , 92D15 , 92D99

Keywords: block interchanges , ciliate , fruit fly , permutations , phylogeny , reversals

Rights: Copyright © 2016 Mathematical Sciences Publishers

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