Better methods for solving parsimony and compatibility
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogenetic Super-Networks from Partial Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computing recombination networks from binary sequences
Bioinformatics
The Fine Structure of Galls in Phylogenetic Networks
INFORMS Journal on Computing
Reconstruction of reticulate networks from gene trees
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Summarizing Multiple Gene Trees Using Cluster Networks
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
SuperQ: Computing Supernetworks from Quartets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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When multiple genes are used in a phylogenetic study, the result is often a collection of incompatible trees. Phylogenetic networks and super-networks can be employed to analyze and visualize the incompatible signals in such a data set. In many situations, it is important to have control over the amount of imcompatibility that is represented in a phylogenetic network, for example reducing noise by removing splits that do not recur among the source trees. Current algorithms for computing hybridization networks from trees are based on a combinatorial analysis of the arising set of splits, and are thus sensitive to false positive splits. Here, a filter is desirable that can identify and remove splits that are not compatible with a hybridization scenario. To address these issues, the concept of the distortion of a tree relative to a split is defined as a measure of how much the tree needs to be modified in order to accommodate the split, and some of its properties are investigated. We demonstrate the usefulness of the approach by recovering a plausible hybridization scenario for buttercups from a pair of gene trees that cannot be obtained by existing methods. In a second example, a set of seven gene trees from microgastrine braconid wasps is investigated using filtered networks. A user-friendly implementation of the method is provided as a plug-in for the program SplitsTree4.