Fixed-Parameter Tractability and Completeness I: Basic Results
SIAM Journal on Computing
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Reconstructing phylogenetic networks with one recombination
WEA'08 Proceedings of the 7th international conference on Experimental algorithms
An evolutionary approach to the inference of phylogenetic networks
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Optimizing Phylogenetic Networks for Circular Split Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Phylogenies 驴 the evolutionary histories of groups of organisms 驴 are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.