A parsimony-based metric for phylogenetic trees
نویسندگان
چکیده
منابع مشابه
Reduction rules for the maximum parsimony distance on phylogenetic trees
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in tree inference, we recently introduced the maximum parsimony (MP) distance, which enjoys various attractive properties due to its connection with several other...
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Swofford and Berlocher (1987) described a method for inferring trees from polymorphic character data that searches for trees that minimize the total amount of allelic frequency change as measured by the Manhattan metric. We provided three primary arguments for choosing our method over other parsimony methods proposed for polymorphic data: (1) it accommodates polymorphism without resorting to co...
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Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the chara...
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This paper investigates the computational geometry relevant to calculations of the Fréchet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability measures on spaces of nonpositive curvature developed by Sturm. We show that the combinatorics of geodesics with a specified fixed endpoint in tree space are dete...
متن کاملEfficient parsimony-based methods for phylogenetic network reconstruction
MOTIVATION Phylogenies--the evolutionary histories of groups of organisms-play a major role in representing relationships among biological entities. Although many biological processes can be effectively modeled as tree-like relationships, others, such as hybrid speciation and horizontal gene transfer (HGT), result in networks, rather than trees, of relationships. Hybrid speciation is a signific...
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ژورنال
عنوان ژورنال: Advances in Applied Mathematics
سال: 2015
ISSN: 0196-8858
DOI: 10.1016/j.aam.2015.02.002