A few logs suffice to build (almost) all trees: part II
Theoretical Computer Science
Constructing optimal trees from quartets
Journal of Algorithms
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Rooted Maximum Agreement Supertrees
Algorithmica
Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network
SIAM Journal on Computing
Inferring a level-1 phylogenetic network from a dense set of rooted triplets
Theoretical Computer Science - Computing and combinatorics
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Constructing level-2 phylogenetic networks from triplets
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
New results on optimizing rooted triplets consistency
Discrete Applied Mathematics
Faster computation of the Robinson-Foulds distance between phylogenetic networks
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the Elusiveness of Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Faster computation of the Robinson-Foulds distance between phylogenetic networks
Information Sciences: an International Journal
CSD Homomorphisms between Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Complexity of Inferring A Minimally Resolved Phylogenetic Supertree
SIAM Journal on Computing
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Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network [24]. Here, we extend this work by showing that this problem is even polynomial time solvable for the construction of level-2 networks. This shows that, assuming density, it is tractable to construct plausible evolutionary histories from input triplets even when such histories are heavily nontree-like. This further strengthens the case for the use of triplet-based methods in the construction of phylogenetic networks. We also implemented the algorithm and applied it to yeast data.