Approximation algorithms for NP-hard problems
Approximation algorithms for NP-hard problems
Some optimal inapproximability results
STOC '97 Proceedings of the twenty-ninth annual ACM symposium on Theory of computing
A 2-Approximation Algorithm for the Undirected Feedback Vertex Set Problem
SIAM Journal on Discrete Mathematics
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
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
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
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Constructing a smallest refining galled phylogenetic network
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Improved recombination lower bounds for haplotype data
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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Phylogenies play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks, rather than trees, of relationships. In a series of papers, we have extended the maximum parsimony (MP) criterion to phylogenetic networks, demonstrated its appropriateness, and established the intractability of the problem of scoring the parsimony of a phylogenetic network. In this work we show the hardness of approximation for the general case of the problem, devise a very fast (linear-time) heuristic algorithm for it, and implement it on simulated as well as biological data.