IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing Phylogenetic Networks Using Maximum Parsimony
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Computing the minimum number of hybridization events for a consistent evolutionary history
Discrete Applied Mathematics
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
Counting Faces in Split Networks
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
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
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We address the problem of realizing a given distance matrix by a planar phylogenetic network with a minimum number of faces. With the help of the popular software SplitsTree4, we start by approximating the distance matrix with a distance metric that is a linear combination of circular splits. The main results of this paper are the necessary and sufficient conditions for the existence of a network with a single face. We show how such a network can be constructed, and we present a heuristic for constructing a network with few faces using the first algorithm as the base case. Experimental results on biological data show that this heuristic algorithm can produce phylogenetic networks with far fewer faces than the ones computed by SplitsTree4, without affecting the approximation of the distance matrix.