New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
From Gene Trees to Species Trees
SIAM Journal on Computing
Reconciliation problems for duplication, loss and horizontal gene transfer
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
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
Maximum likelihood of phylogenetic networks
Bioinformatics
The gene evolution model and computing its associated probabilities
Journal of the ACM (JACM)
Lowest common ancestors in trees and directed acyclic graphs
Journal of Algorithms
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
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Building species trees from larger parts of phylogenomic databases
Information and Computation
Removing noise from gene trees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
MURPAR: a fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An optimal reconciliation algorithm for gene trees with polytomies
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the differences between a gene tree and a corresponding species tree taking into account gene duplications, gene losses, and lateral gene transfers (also known as horizontal gene transfers). The reasonable biological constraint that a lateral gene transfer may only occur between contemporary species leads to the notion of acyclic DTL-scenarios. Parsimony methods are introduced by defining appropriate optimization problems. We show that finding most parsimonious acyclic DTL-scenarios is NP-hard. However, by dropping the condition of acyclicity, the problem becomes tractable, and we provide a dynamic programming algorithm as well as a fixed-parameter tractable algorithm for finding most parsimonious DTL-scenarios.