Phylogenetic Super-Networks from Partial Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for combining rooted triplets into a galled phylogenetic network
SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
Reconstructing Phylogenetic Networks Using Maximum Parsimony
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Computing the maximum agreement of phylogenetic networks
Theoretical Computer Science - Pattern discovery in the post genome
Computing recombination networks from binary sequences
Bioinformatics
The Fine Structure of Galls in Phylogenetic Networks
INFORMS Journal on Computing
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
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
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The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proved NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes $O(dn2^{3h})$ time on an input recombination network over length-$d$ sequences in which there are $h$ recombination and $n - h$ tree nodes.