Fast algorithms for finding nearest common ancestors
SIAM Journal on Computing
Tree compatibility and inferring evolutionary history
Journal of Algorithms
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
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Journal of Computer and System Sciences - Special issue on bioinformatics II
Computing the maximum agreement of phylogenetic networks
Theoretical Computer Science - Pattern discovery in the post genome
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)
Inferring a level-1 phylogenetic network from a dense set of rooted triplets
Theoretical Computer Science - Computing and combinatorics
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
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
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
A Metric on the Space of Reduced Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Detecting highways of horizontal gene transfer
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
An evolutionary approach to the inference of phylogenetic networks
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Reducing distortion in phylogenetic networks
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
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
The maximum agreement of two nested phylogenetic networks
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
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
Phylogenetic networks, trees, and clusters
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Identifiability issues in phylogeny-based detection of horizontal gene transfer
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Phylogenetic networks: properties and relationship to trees and clusters
Transactions on Computational Systems Biology II
CSD Homomorphisms between Phylogenetic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
| Hi-index | 0.00 |
We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison's approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network. We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in network are node-disjoint ("galled"); we prove accuracy guarantees for our first method by presenting a formal characterization of the set of gene trees defined by a species network. Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method.