Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Simultaneous identification of duplications and lateral transfers
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
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
Reducing distortion in phylogenetic networks
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Minimum recombination histories by branch and bound
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
A fundamental decomposition theory for phylogenetic networks and incompatible characters
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Reconstruction of reticulate networks from gene trees
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
Path lengths in tree-child time consistent hybridization networks
Information Sciences: an International Journal
Constructing Level-2 Phylogenetic Networks from Triplets
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Constructing level-2 phylogenetic networks from triplets
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the Elusiveness of Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Optimizing Phylogenetic Networks for Circular Split Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Blocks and Cut Vertices of the Buneman Graph
SIAM Journal on Discrete Mathematics
An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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Reticulate networks are a type of phylogenetic network that are used to represent reticulate evolution involving hybridization, horizontal gene transfer or recombination. The simplest form of these networks are galled trees, in which all reticulations are independent of each other. This paper introduces a more general class of reticulate networks, that we call galled networks, in which reticulations are not necessarily independent, but may overlap in a tree-like manner. We prove a Decomposition Theorem for these networks that has important consequences for their computation, and present a fixed-parameter-tractable algorithm for computing such networks from trees or binary sequences. We provide a robust implementation of the algorithm and illustrate its use on two biological datasets, one based on a set of three gene-trees and the other based on a set of binary characters obtained from a restriction site map.