Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees

@inproceedings{Holland2003ConsensusNA,
  title={Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees},
  author={Barbara R. Holland and Vincent Moulton},
  booktitle={WABI},
  year={2003}
}
We present a method for summarising collections of phylogenetic trees that extends the notion of consensus trees. Each branch in a phylogenetic tree corresponds to a bipartition or split of the set of taxa labelling its leaves. Given a collection of phylogenetic trees, each labelled by the same set of taxa, all those splits that appear in more than a predefined threshold proportion of the trees are displayed using a median network. The complexity of this network is bounded as a function of the… Expand
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References

SHOWING 1-10 OF 30 REFERENCES
Pruned median networks: a technique for reducing the complexity of median networks.
Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcatingExpand
Visualizing Sets of Evolutionary Trees
One of the problems with current methods for phylogenetic reconstruction is the large number of equally parsimonious trees that are often found during a tree search; understanding these large sets ofExpand
Mitochondrial portraits of human populations using median networks.
TLDR
A novel network approach for portraying mtDNA relationships is proposed that reduces the complexity of the network by identifying parallelisms and is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. Expand
Phylogenetic networks
TLDR
In historical linguistics, the Ringe-Warnow model of language evolution is extended, to incorporate non-treelike evolutionary events; a new methodology is presented, called “perfect phylogenetic networks”, which shows a clear outperformance of existing methods. Expand
NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
TLDR
NeighborNet is introduced, a network construction and data representation method that combines aspects of the neighbor joining (NJ) and SplitsTree and can be used to represent multiple phylogenetic hypotheses simultaneously, or to detect complex evolutionary processes like recombination, lateral transfer and hybridization. Expand
A classification of consensus methods for phylogenetics
TLDR
This paper surveys the main consensus tree methods used in phylogenetics, and explores the links between the different methods, producing a classification of consensus Tree methods. Expand
Case study: visualizing sets of evolutionary trees
  • N. Amenta, J. Klingner
  • Computer Science
  • IEEE Symposium on Information Visualization, 2002. INFOVIS 2002.
  • 2002
TLDR
A visualization tool which allows a biologist to explore a large set of hypothetical evolutionary trees and identify distinct hypotheses about how different species or organisms evolved, which would not have been clear from traditional analyses. Expand
Quasi-median graphs from sets of partitions
TLDR
It is clarified when the generated quasi-median graph is the so-called relation graph associated with X, which immediately characterizes the instances where either a block graph or the total Hamming graph is generated. Expand
SplitsTree: analyzing and visualizing evolutionary data
  • D. Huson
  • Computer Science, Medicine
  • Bioinform.
  • 1998
TLDR
SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements the method of split decomposition, and supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping. Expand
SplitsTree-a program for analyzing and visualizing evolutionary data
TLDR
The concepts of splits, splits graphs, the method of split decomposition, and the SplitsTree program are reviewed, which is an interactive program for analyzing evolutionary data, that supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping. Expand
...
1
2
3
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