Application of Ant Colony Optimization for Mapping the Combinatorial Phylogenetic Search Space

Alexander Safatli, Christian Blouin

Abstract

In bioinformatics, landscapes of phylogenetic trees for an alignment of sequence data are defined by a discrete state combinatorial space. The optimal solution in such a space is the best-fitting tree which provides insight on the evolutionary relationship between taxonomic groups. The underlying structure of this space is poorly understood. The Ant Colony Optimization (ACO) algorithm is applied in a novel manner to sample phylogenetic tree landscapes in order to understand more about this structure. The proposed implementation provides a probabilistic model for exploring this combinatorial space. This probabilistic model allows us to circumvent the complexity that arises due to increasing the number of sequences. In order to evaluate its performance, quantities of resultant solutions were judged in order to determine how much of the space can be sampled. The results show that the algorithm is robust to the starting location and consistently samples a majority of the search space.

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Paper Citation


in Harvard Style

Safatli A. and Blouin C. (2015). Application of Ant Colony Optimization for Mapping the Combinatorial Phylogenetic Search Space . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 195-200. DOI: 10.5220/0005255701950200


in Bibtex Style

@conference{bioinformatics15,
author={Alexander Safatli and Christian Blouin},
title={Application of Ant Colony Optimization for Mapping the Combinatorial Phylogenetic Search Space},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={195-200},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005255701950200},
isbn={978-989-758-070-3},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Application of Ant Colony Optimization for Mapping the Combinatorial Phylogenetic Search Space
SN - 978-989-758-070-3
AU - Safatli A.
AU - Blouin C.
PY - 2015
SP - 195
EP - 200
DO - 10.5220/0005255701950200