On reconstructing species trees from gene trees in term of duplications and losses
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
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
A Biologically Meaningful Model for Comparing Molecular Phylogenies
A Biologically Meaningful Model for Comparing Molecular Phylogenies
Traversing the tangle: algorithms and applications for cophylogenetic studies
Journal of Biomedical Informatics - Special issue: Phylogenetic inferencing: Beyond biology
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Natural Computing: an international journal
H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Simultaneous Identification of Duplications and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the structure of reconciliations
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Accounting for gene tree uncertainties improves gene trees and reconciliation inference
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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This paper presents a model of reconciling a species tree and a gene tree in an extended duplication-loss model. In the first part the definition of a model is introduced. In the second the horizontal transfer is defined and a new polynomial reconciliation algorithm is presented. We prove NP-completeness of the important problem related to the reconstruction of the species relationships with transfers from a given set of gene family trees. Some new problems are stated. We present a simple biological example.