Logical description of context-free graph languages
Journal of Computer and System Sciences
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Perfect phylogenetic networks with recombination
Proceedings of the 2001 ACM symposium on Applied computing
Fixed Topology Alignment with Recombination
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
Graph isomorphism, general remarks
STOC '77 Proceedings of the ninth annual ACM symposium on Theory of computing
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Computing the maximum agreement of phylogenetic networks
Theoretical Computer Science - Pattern discovery in the post genome
Inferring a level-1 phylogenetic network from a dense set of rooted triplets
Theoretical Computer Science - Computing and combinatorics
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
Constructing the Simplest Possible Phylogenetic Network from Triplets
ISAAC '08 Proceedings of the 19th International Symposium on Algorithms and Computation
Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Journal of Discrete Algorithms
Comparison of Tree-Child Phylogenetic Networks
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
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
On the Elusiveness of Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion of level was recently introduced as a parameter on realistic kinds of phylogenetic networks to express their complexity and tree-likeness. We study the structure of level-k networks, and how they can be decomposed into level-k generators. We also provide a polynomial time algorithm which takes as input the set of level-k generators and builds the set of level-(k + 1) generators. Finally, with a simulation study, we evaluate the proportion of level-k phylogenetic networks among networks generated according to the coalescent model with recombination.