Efficiently Calculating Evolutionary Tree Measures Using SAT
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast FPT algorithms for computing rooted agreement forests: theory and experiments
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Fast computation of the exact hybridization number of two phylogenetic trees
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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Motivation: Subtree prune and regraft (SPR) is one kind of tree rearrangements that has seen applications in solving several computational biology problems. The minimum number of rooted SPR (rSPR) operations needed to transform one rooted binary tree to another is called the rSPR distance between the two trees. Computing the rSPR distance has been actively studied in recent years. Currently, there is a lack of practical software tools for computing the rSPR distance for relatively large trees with large rSPR distance. Results: In this article, we present a simple and practical method that computes the exact rSPR distance with integer linear programming. By applying this new method on several simulated and real biological datasets, we show that our new method outperforms existing software tools in term of accuracy and ef.ciency. Our experimental results indicate that our method can compute the exact rSPR distance for many large trees with large rSPR distance. Availability: A software tool, SPRDist, is available for download from the web page: http://www.engr.uconn.edu/~ywu. Contact: ywu@engr.uconn.edu