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Mathematical Properties of the Deep Coalescence Cost
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Cuong V. Than,Noah A. Rosenberg
Issue Date:January 2013
pp. 61-72
In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the d...
 
Coalescent Histories for Caterpillar-Like Families
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Noah A. Rosenberg
Issue Date:September 2013
pp. 1253-1262
A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree...
 
On the number of ranked species trees producing anomalous ranked gene trees
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Filippo Disanto,Noah Rosenberg
Issue Date:August 2014
pp. 1
Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked species tree. Here, to...
   
Coalescent Histories for Caterpillar-Like Families
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Noah A. Rosenberg
Issue Date:September 2013
pp. 1253-1262
A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree...
     
Mathematical Properties of the Deep Coalescence Cost
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Cuong V. Than, Noah A. Rosenberg
Issue Date:January 2013
pp. 61-72
In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the d...
     
A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By James H. Degnan, Noah A. Rosenberg, Tanja Stadler
Issue Date:November 2012
pp. 1558-1568
Ranked gene trees, which consider both the gene tree topology and the sequence in which gene lineages separate, can potentially provide a new source of information for use in modeling genealogies and performing inference of species trees. Recently, we have...
     
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