منابع مشابه
URec: a system for unrooted reconciliation
UNLABELLED URec is a software based on a concept of unrooted reconciliation. It can be used to reconcile a set of unrooted gene trees with a rooted species tree or a set of rooted species trees. Moreover, it computes detailed distribution of gene duplications and gene losses in a species tree. It can be used to infer optimal species phylogenies for a given set of gene trees. URec is implemented...
متن کاملDeep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms
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...
متن کاملThe Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase.
The function of UreC, the product of a 1,335-bp-long open reading frame upstream from the urease structural genes (ureAB) of Helicobacter pylori, was investigated. We present data showing that the ureC gene product is a phosphoglucosamine mutase. D. Mengin-Lecreulx and J. van Heijenoort (J. Biol. Chem. 271:32-39, 1996) observed that UreC is similar (43% identity) to the GlmM protein of Escheric...
متن کاملAnomalous 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...
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: Bioinformatics
سال: 2006
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btl634