Properties of Subtree-Prune-and-Regraft Operations on Totally-Ordered Phylogenetic Trees
نویسندگان
چکیده
منابع مشابه
Properties of Subtree-Prune-and-Regraft Operations on Totally-Ordered Phylogenetic Trees
We study some properties of subtree-prune-and-regraft (SPR) operations on leaflabelled rooted binary trees in which internal vertices are totally ordered. Since biological events occur with certain time ordering, sometimes such totally-ordered trees must be used to avoid possible contradictions in representing evolutionary histories of biological sequences. Compared to the case of plain leaf-la...
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We develop a time-optimal O(mn)-time algorithm for the problem of constructing the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of O(mn). Such graphs are used to better understand the behaviour of phylogenetic methods and recommend parameter choices and diagnostic criteria. The limiting factor in these analyses has ...
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Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying pro...
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The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo phylogenetic inference. Although the rooted version of SPR distance can be computed relatively efficiently between rooted trees using fixed-parameter-tractable algo...
متن کاملCalculating the Unrooted Subtree Prune-and-Regraft Distance
The subtree prune-and-regraft (SPR) distance metric is a fundamen-tal way of comparing evolutionary trees. It has wide-ranging applications,such as to study lateral genetic transfer, viral recombination, and Markovchain Monte Carlo phylogenetic inference. Although the rooted versionof SPR distance can be computed relatively efficiently between rootedtrees using fixed-paramet...
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ژورنال
عنوان ژورنال: Annals of Combinatorics
سال: 2006
ISSN: 0218-0006,0219-3094
DOI: 10.1007/s00026-006-0279-5