Abstract
We introduce ACOPHY, a novel framework to apply Ant Colony Optimization (ACO) for phylogenetic reconstruction. ACOPHY overcomes a main drawback of other attempts to reconstruct phylogenies by defining a compact ACO graph that is nicely coupled with the tree space. The proposed graph allows the ants to walk globally through the tree space. Thus, ACOPHY can be generally applied to all well-known optimality criteria in phylogenetics. We compared ACOPHY with the traditional phylogenetic method PHYLIP and obtained slightly better results. This is promising since our current implementation of ACOPHY is still at the proof of concept stage. We list a number of points where ACOPHY can be improved. Once the improvements are integrated, we hope for competitive performance against other recent phylogenetic inference methods.
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References
Ando, S., Iba, H.: Ant algorithm for construction of evolutionary tree. In: Evolutionary Computation, vol. 2, pp. 1552–1557. IEEE Press, Los Alamitos (2002)
Bandelt, H.J., Dress, A.: Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7, 309–343 (1986)
Catanzaro, D., Pesenti, R., Milinkovitch, M.: An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle. BMC Evol. Biol. 7 (2007)
Cavalli-Sforza, L.L., Edwards, A.W.F.: Phylogenetic analysis: Models and estimation procedures. Amer. J. Human. Genet. 19, 233–257 (1967)
Dorigo, M., Stuetzle, T.: Ant Colony Optimization. The MIT Press, Cambridge (2004)
Felsenstein, J.: Infering Phylogenies. Sinauer Associates, Sunderland (2004)
Felsenstein, J.: PHYLIP – Phylogeny Inference Package (version 3.2). Cladistics 5, 164–166 (1989)
Fitch, W.M.: Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20, 406–416 (1971)
Foulds, L.R., Graham, R.L.: The Steiner problem in phylogeny is NP-complete. Adv. Appl. Math. 3, 43–49 (1982)
Guindon, S., Gascuel, O.: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003)
Harding, E.F.: The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Prob. 3, 44–77 (1971)
Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, vol. 3, pp. 21–123. Academic Press, New York (1969)
Lemmon, A.R., Milinkovitch, M.C.: The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proc. Natl. Acad. Sci. USA 99, 10516–10521 (2002)
Minh, B.Q., Vinh, L.S., von Haeseler, A., Schmidt, H.A.: pIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics 21, 3794–3796 (2005)
Perretto, M., Lopes, H.S.: Reconstruction of phylogenetic trees using the ant colony optimization paradigm. Genet. Mol. Res. 4, 581–589 (2005)
Rambaut, A., Grassly, N.C.: Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235–238 (1997)
Robinson, D.F., Foulds, L.R.: Comparison of phylogenetic trees. Math. Biosci. 53, 131–147 (1981)
Stamatakis, A.P.: An efficient program for phylogenetic inference using simulated annealing. In: Online Proceedings of the 4th IEEE International Workshop on High Performance Computational Biology, Denver (2005)
Stuetzle, T., Hoos, H.: Max-min ant system. Future Gener. Comp. Sy. 16, 889–914 (2000)
Vinh, L.S., von Haeseler, A.: IQPNNI: Moving fast through tree space and stopping in time. Mol. Biol. Evol. 21, 1565–1571 (2004)
Whelan, S.: New approaches to phylogenetic tree search and their application to large numbers of protein alignments. Syst. Biol. 56, 727–740 (2007)
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Dinh, H.Q., Minh, B.Q., Huan, H.X., von Haeseler, A. (2010). ACOPHY: A Simple and General Ant Colony Optimization Approach for Phylogenetic Tree Reconstruction. In: Dorigo, M., et al. Swarm Intelligence. ANTS 2010. Lecture Notes in Computer Science, vol 6234. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-15461-4_32
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DOI: https://doi.org/10.1007/978-3-642-15461-4_32
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