Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in 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
Phylogenetic networks
Reconstructing Phylogenetic Networks Using Maximum Parsimony
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Maximum likelihood of phylogenetic networks
Bioinformatics
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Reconstructing evolution of natural languages: complexity and parameterized algorithms
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
Phylogenetic networks, trees, and clusters
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Phylogenetic networks: properties and relationship to trees and clusters
Transactions on Computational Systems Biology II
Parameterized Complexity
The Structure of Level-k Phylogenetic Networks
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Locating a tree in a phylogenetic network
Information Processing Letters
A quadratic kernel for computing the hybridization number of multiple trees
Information Processing Letters
Fishing for minimum evolution trees with Neighbor-Nets
Information Processing Letters
| Hi-index | 5.24 |
Phylogenetic networks are a restricted class of directed acyclic graphs that model evolutionary histories in the presence of reticulate evolutionary events, such as horizontal gene transfer, hybrid speciation, and recombination. Characterizing a phylogenetic network as a collection of trees and their branches has long been the basis for several methods of reconstructing and evaluating phylogenetic networks. Further, these characterizations have been used to understand molecular sequence evolution on phylogenetic networks. In this paper, we address theoretical questions with regard to phylogenetic networks, their characterizations, and sequence evolution on them. In particular, we prove that the problem of deciding whether a given tree is contained inside a network is NP-complete. Further, we prove that the problem of deciding whether a branch of a given tree is also a branch of a given network is polynomially equivalent to that of deciding whether the evolution of a molecular character (site) on a network is governed by the infinite site model. Exploiting this equivalence, we establish the NP-completeness of both problems, and provide a parameterized algorithm that runs in time O(2^k^/^2n^2), where n is the total number of nodes and k is the number of recombination nodes in the network, which significantly improves upon the trivial brute-force O(2^kn) time algorithm for the problem. This reduction in time is significant, particularly when analyzing recombination hotspots.