Perfect phylogeny and haplotype assignment
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Unicyclic Networks: Compatibility and Enumeration
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Constructing Phylogenetic Supernetworks from Quartets
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Improved Layout of Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring Pedigree Graphs from Genetic Distances
IEICE - Transactions on Information and Systems
Reducing distortion in phylogenetic networks
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Imputing supertrees and supernetworks from quartets
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Reconstruction of reticulate networks from gene trees
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
SuperQ: Computing Supernetworks from Quartets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computational Biology and Chemistry
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In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Additionally, the questions of assigning lengths to the edges of the network and how to restrict the "dimensionality驴 of the network are addressed. Applications to a set of five published partial gene trees relating different fungal species and to six published partial gene trees relating different grasses illustrate the usefulness of the method and an experimental study confirms its potential. The method is implemented as a plug-in for the program SplitsTree4.