Genomic duplication problems for unrooted gene trees
نویسندگان
چکیده
منابع مشابه
Anomalous unrooted gene trees.
The coalescent and multispecies coalescent model rooted genealogies backward through time. Often, the direction of time is unknown in trees estimated from molecular sequences due to reversible mutation models, absence of an appropriate outgroup, and the absence of the molecular clock. In this article, probabilities of unrooted gene-tree topologies under the multispecies coalescent are considere...
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Gene tree reconciliation is a method to reconcile gene trees that are confounded by complex histories of gene duplications with a provided species tree. The trees involved are required to be rooted and full binary. Reconciling gene trees allows not only to identify and study such histories for gene families, but is also the base for several higher level applications including the estimation of ...
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Gene tree reconciliation problems invoke the minimum number of evolutionary events that reconcile gene evolution within the context of a species tree. Here we focus on the deep coalescence (DC) problem, that is, given an unrooted gene tree and a rooted species tree, find a rooting of the gene tree that minimizes the number of DC events, or DC cost, when reconciling the gene tree with the specie...
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Gene duplication is widely believed to facilitate adaptation, but unambiguous evidence for this hypothesis has been found in only a small number of cases. Although gene duplication may increase the fitness of the involved organisms by doubling gene dosage or neofunctionalization, it may also result in a simple division of ancestral functions into daughter genes, which need not promote adaptatio...
متن کاملSPR Distance Computation for Unrooted Trees
The subtree prune and regraft distance (d(SPR)) between phylogenetic trees is important both as a general means of comparing phylogenetic tree topologies as well as a measure of lateral gene transfer (LGT). Although there has been extensive study on the computation of d(SPR) and similar metrics between rooted trees, much less is known about SPR distances for unrooted trees, which often arise in...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2016
ISSN: 1471-2164
DOI: 10.1186/s12864-015-2308-4