Inferring duplication episodes from 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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Species tree estimation from multiple markers is complicated by the fact that gene trees can differ from each other (and from the true species tree) due to several biological processes, one of which is gene duplication and loss. Local search heuristics for two NP-hard optimization problems - minimize gene duplications (MGD) and minimize gene duplications and losses (MGDL) - are popular techniqu...
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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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Motivation: A major unresolved problem in phylogeny is to reconstruct the evolutionary history of a set of species when it cannot be modeled by a simple tree. When a reticulation event, such as hybrid speciation or horizontal transfer, occurs, separate regions of a species’ genetic data may evolve along different trees. Our approach uses the gene trees for each region to solve the inverse probl...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2018
ISSN: 1471-2164
DOI: 10.1186/s12864-018-4623-z