Are the Duplication Cost and Robinson-Foulds Distance Equivalent?
نویسندگان
چکیده
منابع مشابه
Are the Duplication Cost and Robinson-Foulds Distance Equivalent?
In the tree reconciliation approach for species tree inference, a tree that has the minimum reconciliation score for given gene trees is taken as an estimate of the species tree. The scoring models used in existing tree reconciliation methods include the duplication, mutation, and deep coalescence costs. Since existing inference methods all are heuristic, their performances are often evaluated ...
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The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not sim...
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The Robinson–Foulds distance, a widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two phylogenetic networks N1, N2 with n leaf labels and at most m nodes and e edges each, the Robinson–Foulds distance measures the number of clusters of descendant leaves not shared by N1 and N2. The fastest known algorithm for computing the Robinso...
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In this paper, we study two fast algorithms—HashRF and PGM-Hashed—for computing the Robinson-Foulds (RF) distance matrix between a collection of evolutionary trees. The RF distance matrix represents a tremendous data-mining opportunity for helping biologists understand the evolutionary relationships depicted among their trees. The novelty of our work results from using a variety of different ar...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2014
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2014.0021