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
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Non-shared edges and nearest neighbor interchanges revisited
Information Processing Letters
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
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
Computing the maximum agreement of phylogenetic networks
Theoretical Computer Science - Pattern discovery in the post genome
The maximum agreement of two nested phylogenetic networks
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
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
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Consider two phylogenetic networks N and N′ of size n. The tripartition-based distance finds the proportion of tripartitions which are not shared by N and N′. This distance is proposed by Moret et al (2004) and is a generalization of Robinson-Foulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min{kn log n, n log n+hn})-time algorithm to compute this distance, where h is the number of hybrid nodes in N and N′ while k is the maximum number of hybrid nodes among all biconnected components in N and N′. Note that k h n in a phylogenetic network. In addition, we propose algorithms for comparing galled-trees, which are an important, biological meaningful special case of phylogenetic network. We give an O(n)-time algorithm for comparing two galled-trees. We also give an O(n + kh)-time algorithm for comparing a galled-tree with another general network, where h and k are the number of hybrid nodes in the latter network and its biggest biconnected component respectively.