Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
From Gene Trees to Species Trees
SIAM Journal on Computing
The Haplotyping problem: an overview of computational models and solutions
Journal of Computer Science and Technology
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Simultaneous identification of duplications and lateral transfers
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reconciling a gene tree to a species tree under the duplication cost model
Theoretical Computer Science
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Complexity and approximation of the minimum recombinant haplotype configuration problem
Theoretical Computer Science
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Locating multiple gene duplications through reconciled trees
RECOMB'08 Proceedings of the 12th 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
Linear-Time haplotype inference on pedigrees without recombinations
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
Reconciling gene trees with apparent polytomies
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
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In Computational Biology, the notion of phylogeny has become synonymous with tree-like evolution. Recent advances in the Life Sciences have suggested that evolution has a much more diverse course. In this paper we will survey some of the models that have been proposed to overcome the limitations of using phylogenies to represent evolutionary histories.