On the Number of Ranked Species Trees Producing Anomalous Ranked Gene Trees
نویسندگان
چکیده
منابع مشابه
The probability distribution of ranked gene trees on a species tree.
The properties of random gene tree topologies have recently been studied under a coalescent model that treats a species tree as a fixed parameter. Here we develop the analogous theory for random ranked gene tree topologies, in which both the topology and the sequence of coalescences for a random gene tree are considered. We derive the probability distribution of ranked gene tree topologies cond...
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In the past, two basic approaches for sampling f5-om B+ trees have been suggested: sampling from the ranked trees and acceptance/rejection sampling i?om non-ranked trees. The first approach requires the entire root-to-leaf path to be updated with each insertion and deletion. The second has no update overhead, but incurs a high rejection rate for the compressed-key B+ trees commonly used in prac...
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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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—Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal tran...
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The availability of whole-genome sequence data has provided a rich resource of deep insights into many biological, medical and pharmaceutical problems and applications, and is promising even more. Yet, along with these insights and promises, genomic data have given rise to many challenging problems, mainly due to the quantity and heterogeneity of such data. One of these major challenges is the ...
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ژورنال
عنوان ژورنال: IEEE/ACM Transactions on Computational Biology and Bioinformatics
سال: 2014
ISSN: 1545-5963
DOI: 10.1109/tcbb.2014.2343977