Subtree prune and regraft: A reversible real tree-valued Markov process
نویسندگان
چکیده
منابع مشابه
Subtree prune and regraft: a reversible real tree-valued Markov process
We use Dirichlet form methods to construct and analyze a reversible Markov process, the stationary distribution of which is the Brownian continuum random tree. This process is inspired by the subtree prune and re-graft (SPR)Markov chains that appear in phylogenetic analysis. A key technical ingredient in this work is the use of a novel Gromov– Hausdorff type distance to metrize the space whose ...
متن کاملChain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance
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...
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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...
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...
متن کاملA practical method for exact computation of subtree prune and regraft distance
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 ((r)SPR) operations needed to transform one rooted binary tree to another is called the (r)SPR distance between the two trees. Computing the (r)SPR distance has been actively studied in recent years. Currentl...
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ژورنال
عنوان ژورنال: The Annals of Probability
سال: 2006
ISSN: 0091-1798
DOI: 10.1214/009117906000000034