A Heuristic for the Live Parsimony Problem
Live Phylogeny generalizes the phylogeny theory by admitting living ancestors among the taxonomic objects. This theory suits cases of fast-evolving species like virus, and phylogenies of non-biological objects like documents, images and database records. In character-based live phylogeny, the input is a matrix with n objects and m characters, such each position i, j keeps the state of character j for the object i. The output is a tree where the input objects are represented as leaves or internal nodes labeled with a string of m symbols, representing the state of the characters. The goal is to obtain a tree with the minimal number of state changes along the edges, considering all characters, called the most parsimonious tree. In this paper we analyze problems related to most parsimonious tree using Live Phylogeny. We propose an improvement to a previously presented branch-and-bound algorithm and also a new heuristic for the problem. We present the results of experiments with a set of 20 Zika virus genome sequences, comparing the performance of our heuristic.
KeywordsPhylogeny Character state phylogeny Live phylogeny Parsimony Algorithms
RG and NFA thank Fundect grants TO141/2016 and TO 007/2015. NFA also thanks CNPq grants 305857/2013-4, 473221/2013-6 and CAPES grant 3377/2013. GPT acknowledges CNPq grant 310685/2015-0. MEMT thanks CNPq grant 308524/2015-2.
- 3.Cuadros, A.M., Paulovich, F.V., Minghim, R., Telles, G.P.: Point placement by phylogenetic trees and its application to visual analysis of document collections. In: Proceedings of the 2007 IEEE Symposium on Visual Analytics Science and Technology, pp. 99–106 (2007)Google Scholar
- 5.Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Sunderland (2004)Google Scholar
- 9.Güths, R., Telles, G.P., Walter, M.E.M.T., Almeida, N.F.: A branch and bound for the large live parsimony problem. In: Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), pp. 184–189. SCITEPRESS - Science and Technology Publications, Lda (2017)Google Scholar
- 11.Jones, N.C., Pevzner, P.A., Pevzner, P.: An Introduction to Bioinformatics Algorithms, vol. 2004. MIT Press, Cambridge (2004)Google Scholar
- 15.Setubal, J.C., Meidanis, J.: Introduction to Molecular Computational Biology, vol. 1997. PWS, Boston (1997)Google Scholar
- 17.Yan, M., Bader, D.A.: Fast character optimization in parsimony phylogeny reconstruction. Technical report TR-CS-2003-53. University of New Mexico (2003)Google Scholar