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• W2151384837 abstract "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. Contact: paquete@dei.uc.pt" @default.
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• W2151384837 date "2013-02-23" @default.
• W2151384837 modified "2023-10-16" @default.
• W2151384837 title "Improvements on bicriteria pairwise sequence alignment: algorithms and applications" @default.
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• W2151384837 doi "https://doi.org/10.1093/bioinformatics/btt098" @default.
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