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
The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogenetic Super-Networks from Partial Trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Unicyclic Networks: Compatibility and Enumeration
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)
Summarizing Multiple Gene Trees Using Cluster Networks
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Improved Layout of Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Drawing Rooted Phylogenetic Networks
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)
Beyond galled trees: decomposition and computation of galled networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Reducing distortion in phylogenetic networks
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Fast algorithms for computing the tripartition-based distance between phylogenetic networks
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
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One of the simplest evolutionary models has molecular sequences evolving from a common ancestor down a bifurcating phylogenetic tree, experiencing point-mutations along the way. However, empirical analyses of different genes indicate that the evolution of genomes is often more complex than can be represented by such a model. Thus, the following problem is of significant interest in molecular evolution: Given a set of molecular sequences, compute a reticulate network that explains the data using a minimal number of reticulations. This paper makes four contributions toward solving this problem. First, it shows that there exists a one-to-one correspondence between the tangles in a reticulate network, the connected components of the associated incompatibility graph and the netted components of the associated splits graph. Second, it provides an algorithm that computes a most parsimonious reticulate network in polynomial time, if the reticulations contained in any tangle have a certain overlapping property, and if the number of reticulations contained in any given tangle is bounded by a constant. Third, an algorithm for drawing reticulate networks is described and a robust and flexible implementation of the algorithms is provided. Fourth, the paper presents a statistical test for distinguishing between reticulations due to hybridization, and ones due to other events such as lineage sorting or tree-estimation error.