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

Alexander Safatli, Christian Blouin

2015

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.

References

  1. Albright, E., Hessel, J., Hiranuma, N., Wang, C., and Goings, S. (2014). A comparative analysis of popular phylogenetic reconstruction algorithms. Midwest Instruction and Computing Symposium (MICS) 2014 Proceedings.
  2. Bastert, O., Rockmore, D., Stadler, P. F., and Tinhofer, G. (2002). Landscapes on spaces of trees. Applied mathematics and computation, 131(2):439-459.
  3. Blum, C. and Roli, A. (2003). Metaheuristics in combinatorial optimization: Overview and conceptual comparison. ACM Comput. Surv., 35(3):268-308.
  4. Charleston, M. A. (1995). Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem. Journal of Computational Biology, 2(3):439-450.
  5. Dorigo, M., Di Caro, G., and Gambardella, L. M. (1999). Ant algorithms for discrete optimization. Artificial life, 5(2):137-172.
  6. Felsenstein, J. (2004). Inferring phylogenies, volume 2. Sinauer Associates Sunderland.
  7. Fitch, W. M. (1971). Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology, 20(4):406-416.
  8. Foulds, L. R. and Graham, R. L. (1982). The steiner problem in phylogeny is np-complete. Advances in Applied Mathematics, 3(1):43-49.
  9. Luke, S. (2013). Essentials of Metaheuristics. Lulu, second edition.
  10. Meehan, C. J. and Beiko, R. G. (2013). A phylogenomic view of ecological specialization in the lachnospiraceae, a family of digestive tract-associated bacteria. Technical report, PeerJ PrePrints.
  11. Price, M. N., Dehal, P. S., and Arkin, A. P. (2009). Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular biology and evolution, 26(7):1641-1650.
  12. Sanderson, M. J., McMahon, M. M., and Steel, M. (2011). Terraces in phylogenetic tree space. Science, 333(6041):448-450.
  13. Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51(3):492-508.
  14. Shimodaira, H. and Hasegawa, M. (2001). Consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics, 17(12):1246-1247.
  15. Stadler, P. F. (1996). Landscapes and their correlation functions. Journal of Mathematical chemistry, 20(1):1-45.
  16. Stamatakis, A. (2014). Raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics.
Download


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