Robinson-Foulds Supertrees
نویسندگان
چکیده
منابع مشابه
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
Motivation The estimation of phylogenetic trees is a major part of many biological dataset analyses, but maximum likelihood approaches are NP-hard and Bayesian MCMC methods do not scale well to even moderate-sized datasets. Supertree methods, which are used to construct trees from trees computed on subsets, are critically important tools for enabling the statistical estimation of phylogenies fo...
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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 (RF) metric is the measure most widely used in comparing phylogenetic trees; it can be computed in linear time using Day's algorithm. When faced with the need to compare large numbers of large trees, however, even linear time becomes prohibitive. We present a randomized approximation scheme that provides, in sublinear time and with high probability, a (1 + epsilon) approxima...
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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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In this paper, we introduce the HashRF(p, q) algorithm for computing RF matrices of large binary, evolutionary tree collections. The novelty of our algorithm is that it can be used to compute arbitrarilysized (p × q) RF matrices without running into physical memory limitations. In this paper, we explore the performance of our HashRF(p, q) approach on 20,000 and 33,306 biological trees of 150 ta...
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ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2010
ISSN: 1748-7188
DOI: 10.1186/1748-7188-5-18