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
Algorithms for combining rooted triplets into a galled phylogenetic network
SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
Unicyclic Networks: Compatibility and Enumeration
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree
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)
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
On the Elusiveness of Clusters
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast algorithms for computing the tripartition-based distance between phylogenetic networks
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Reconstructing an ultrametric galled phylogenetic network from a distance matrix
MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
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Reticulation events occur frequently in many types of species. Therefore, to develop accurate methods for reconstructing phylogenetic networks in order to describe evolutionary history in the presence of reticulation events is important. Previous work has suggested that constructing phylogenetic networks by merging gene trees is a biologically meaningful approach. This paper presents two new efficient algorithms for inferring a phylogenetic network from a set $\mathcal{T}$ of gene trees of arbitrary degrees. The first algorithm solves the open problem of constructing a refining galled network for $\mathcal{T}$ (if one exists) with no restriction on the number of hybrid nodes; in fact, it outputs the smallest possible solution. In comparison, the previously best method (SpNet) can only construct networks having a single hybrid node. For cases where there exists no refining galled network for $\mathcal{T}$, our second algorithm identifies a minimum subset of the species set to be removed so that the resulting trees can be combined into a galled network. Based on our two algorithms, we propose two general methods named RGNet and RGNet+. Through simulations, we show that our methods outperform the other existing methods neighbor-joining, NeighborNet, and SpNet.