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
From Gene Trees to Species Trees
SIAM Journal on Computing
On the Multiple Gene Duplication Problem
ISAAC '98 Proceedings of the 9th International Symposium on Algorithms and Computation
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
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
Inferring phylogeny from whole genomes
Bioinformatics
URec: a system for unrooted reconciliation
Bioinformatics
The multiple gene duplication problem revisited
Bioinformatics
The gene evolution model and computing its associated probabilities
Journal of the ACM (JACM)
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Heuristics for the gene-duplication problem: a Θ(n) speed-up for the local search
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
The gene-duplication problem: near-linear time algorithms for NNI based local searches
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Reconciling gene trees with apparent polytomies
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
Logic and Program Semantics
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In this paper, we present a model of evolution of genes in the context of evolution of species. The concept is based on reconciliation models. We assume that the gene evolution is modeled by macro-evolutionary events like gene duplications, losses and horizontal gene transfers (HGTs) while the evolution of species is shaped by speciation events. We define an evolutionary scenario (called an H-tree) which will represent the common evolution of genes and species. We propose a rewrite system for transforming the scenarios. We prove that the system is confluent, sound and strongly normalizing. We show that a scenario in a normal form (that is, non-reducible) is unique and minimal in the sense of the cost computed as the total number of gene duplications, losses and HGTs (mutation cost). We present a classification of the scenarios and analyze their hierarchies.