Improvements on bicriteria pairwise sequence alignment: algorithms and applications

Abstract : Motivation: In this article, we consider the bicriteria pairwise sequence alignment problem and propose extensions of dynamic programming algorithms for several problem variants with a novel pruning technique that efficiently reduces the number of states to be processed. Moreover, we present a method for the construction of phylogenetic trees based on this bicriteria framework. Two exemplary cases are discussed. Results: Numerical results on a real dataset show that this approach is very fast in practice. The pruning technique saves up to 90% in memory usage and 80% in CPU time. Based on this method, phylogenetic trees are constructed from real-life data. In addition of providing complementary information, some of these trees match those obtained by the Maximum Likelihood method. Availability and implementation: Source code is freely available for download at URL http://eden.dei.uc.pt/paquete/MOSAL/, implemented in C and supported on Linux, MAC OS and MS Windows.
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Article dans une revue
Bioinformatics, Oxford University Press (OUP), 2013, 29 (8), pp.996-1003. 〈10.1093/bioinformatics/btt098〉
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https://hal.archives-ouvertes.fr/hal-00797793
Contributeur : Arnaud Liefooghe <>
Soumis le : jeudi 7 mars 2013 - 11:16:34
Dernière modification le : jeudi 21 février 2019 - 10:52:49

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Maryam Abbasi, Luis Paquete, Arnaud Liefooghe, Miguel Pinheiro, Pedro Matias. Improvements on bicriteria pairwise sequence alignment: algorithms and applications. Bioinformatics, Oxford University Press (OUP), 2013, 29 (8), pp.996-1003. 〈10.1093/bioinformatics/btt098〉. 〈hal-00797793〉

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