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Displaying 1-15 out of 15 total
Constructing and Drawing Regular Planar Split Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Binh Nguyen, Andreas Spillner, Andreas Spillner, Andreas Spillner, Binh Nguyen, Vincent Moulton, Vincent Moulton, Vincent Moulton
Issue Date:March 2012
pp. 395-407
Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be ...
     
SuperQ: Computing Supernetworks from Quartets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Stefan Grunewald,Andreas Spillner,Sarah Bastkowski,Anja Bogershausen,Vincent Moulton
Issue Date:January 2013
pp. 151-160
Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is n...
 
Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Magnus Bordewich, Olivier Gascuel, Katharina T. Huber, Vincent Moulton
Issue Date:January 2009
pp. 110-117
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {\em balanced minimum evolution (BME)} principle, which computer studies have demonstra...
 
Constructing and Drawing Regular Planar Split Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Andreas Spillner,Binh T. Nguyen,Vincent Moulton
Issue Date:March 2012
pp. 395-407
Split networks are commonly used to visualize collections of bipartitions, also called splits, of a finite set. Such collections arise, for example, in evolutionary studies. Split networks can be viewed as a generalization of phylogenetic trees and may be ...
 
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Katharina T. Huber, Andreas Spillner, Radosław Suchecki, Vincent Moulton
Issue Date:July 2011
pp. 1029-1040
Multilabeled trees or MUL-trees, for short, are trees whose leaves are labeled by elements of some nonempty finite set X such that more than one leaf may be labeled by the same element of X. This class of trees includes phylogenetic trees and tree shapes. ...
 
Special Section: Phylogenetics
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Daniel H. Huson, Vincent Moulton, Mike Steel
Issue Date:January 2009
pp. 4-6
No summary available.
 
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Taoyang Wu, Vincent Moulton, Mike Steel
Issue Date:January 2009
pp. 118-125
Given a set X of taxa, a phylogenetic X-tree T that is only partially resolved, and a collection of characters on X, we consider the problem of finding a resolution (refinement) of T that minimizes the parsimony score of the given characters. Previous work...
 
Maximum Parsimony for Tree Mixtures
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Stefan Grünewald, Vincent Moulton
Issue Date:January 2009
pp. 97-102
With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to p...
 
Computing Phylogenetic Diversity for Split Systems
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Andreas Spillner, Binh T. Nguyen, Vincent Moulton
Issue Date:April 2008
pp. 235-244
In conservation biology it is a central problem to measure, predict, and preserve biodiversity as species face extinction. In 1992 Faith proposed measuring the diversity of a collection of species in terms of their relationships on a phylogenetic tree, and...
 
SuperQ: Computing Supernetworks from Quartets
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Andreas Spillner, Anja Bogershausen, Sarah Bastkowski, Stefan Grunewald, Vincent Moulton
Issue Date:January 2013
pp. 151-160
Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is n...
     
Metrics on Multilabeled Trees: Interrelationships and Diameter Bounds
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Andreas Spillner, Katharina T. Huber, Rados law Suchecki, Vincent Moulton
Issue Date:July 2011
pp. 1029-1040
Multilabeled trees or MUL-trees, for short, are trees whose leaves are labeled by elements of some nonempty finite set X such that more than one leaf may be labeled by the same element of X. This class of trees includes phylogenetic trees and tree shapes. ...
     
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Mike Steel, Taoyang Wu, Vincent Moulton
Issue Date:January 2009
pp. 118-125
Given a set X of taxa, a phylogenetic X-tree T that is only partially resolved, and a collection of characters on X, we consider the problem of finding a resolution (refinement) of T that minimizes the parsimony score of the given characters. Previous work...
     
Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Katharina T. Huber, Magnus Bordewich, Olivier Gascuel, Vincent Moulton
Issue Date:January 2009
pp. 110-117
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {\em balanced minimum evolution (BME)} principle, which computer studies have demonstra...
     
Maximum Parsimony for Tree Mixtures
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Stefan Grunewald, Vincent Moulton
Issue Date:January 2009
pp. 97-102
With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to p...
     
Special Section: Phylogenetics
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Daniel H. Huson, Mike Steel, Vincent Moulton
Issue Date:January 2009
pp. 4-6
The study of gene regulatory networks is a significant problem in systems biology. Of particular interest is the problem of determining the unknown or hidden higher level regulatory signals by using gene expression data from DNA microarray experiments. Sev...
     
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