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2006 | OriginalPaper | Chapter

Constructing Camin-Sokal Phylogenies Via Answer Set Programming

Authors : Jonathan Kavanagh, David Mitchell, Eugenia Ternovska, Ján Maňuch, Xiaohong Zhao, Arvind Gupta

Published in: Logic for Programming, Artificial Intelligence, and Reasoning

Publisher: Springer Berlin Heidelberg

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Constructing parsimonious phylogenetic trees from species data is a central problem in phylogenetics, and has diverse applications, even outside biology. Many variations of the problem, including the cladistic Camin-Sokal (CCS) version, are NP-complete. We present Answer Set Programming (ASP) models for the binary CCS problem, as well as a simpler perfect phylogeny version, along with experimental results of applying the models to biological data. Our contribution is three-fold. First, we solve phylogeny problems which have not previously been tackled by ASP. Second, we report on variants of our CCS model which significantly affect run time, including the interesting case of making the program “slightly tighter”. This version exhibits some of the best performance, in contrast with a tight version of the model which exhibited poor performance. Third, we are able to find proven-optimal solutions for larger instances of the CCS problem than the widely used branch-and-bound-based PHYLIP package.

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Metadata
Title
Constructing Camin-Sokal Phylogenies Via Answer Set Programming
Authors
Jonathan Kavanagh
David Mitchell
Eugenia Ternovska
Ján Maňuch
Xiaohong Zhao
Arvind Gupta
Copyright Year
2006
Publisher
Springer Berlin Heidelberg
DOI
https://doi.org/10.1007/11916277_31

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