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Using ciliate
operations to construct chromosome phylogenies
Jacob L. Herlin, Anna Nelson and Marion Scheepers
Vol. 9 (2016), No. 1, 1–26
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Abstract |
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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. |
Keywords
permutations, reversals, block interchanges, fruit fly,
ciliate, phylogeny
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Mathematical Subject Classification 2010
Primary: 05E15, 20B99, 92-08, 92D15, 92D99
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Milestones
Received: 23 January 2013
Revised: 11 December 2014
Accepted: 21 December 2014
Published: 17 December 2015
Communicated by Joseph A. Gallian
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Authors |
| Jacob L. Herlin | |
| Department of Mathematics Indiana University Rawles Hall 831 East 3rd Street Bloomington, IN 47405 United States |
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| Anna Nelson | |
| Department of Mathematics University of Utah 155 S 1400 E Room 233 Salt Lake City, UT 84112-0090 United States |
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| Marion Scheepers | |
| Department of Mathematics Boise State University Boise, ID 83725 United States |
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