Estimating Species Trees 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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This paper studies various algorithmic issues in reconstructing a species tree from gene trees under the duplication and the mutation cost model. This is a fundamental problem in computational molecular biology. Our main results are as follows. 1. A linear time algorithm is presented for computing all the losses in duplications associated with the least common ancestor mapping from a gene tree ...
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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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—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: Systematic Biology
سال: 2011
ISSN: 1076-836X,1063-5157
DOI: 10.1093/sysbio/syr027