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
On the equivalence of two tree mapping measures
Discrete Applied Mathematics - Special volume on computational molecular biology DAM-CMB series volume 2
New algorithms for the duplication-loss model
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
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
Reconciling gene trees to a species tree
CIAC'03 Proceedings of the 5th Italian conference on Algorithms and complexity
On the structure of reconciliations
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
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
Inferring a duplication, speciation and loss history from a gene tree
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
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
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Removing noise from gene trees
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
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
A robinson-foulds measure to compare unrooted trees with rooted trees
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Minimum leaf removal for reconciliation: complexity and algorithms
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
An optimal reconciliation algorithm for gene trees with polytomies
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
Unrooted Tree Reconciliation: A Unified Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Gene tree correction for reconciliation and species tree inference: Complexity and algorithms
Journal of Discrete Algorithms
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We present a model of evolution of gene trees in the context of species evolution. Its concept is similar to reconciliation models. We assume that the gene evolution is modelled by duplications and losses. Evolution of species is modelled by speciation events. We define an evolutionary scenario (called a DLS-tree) which can represent an evolution of genes in species. We are interested in all scenarios for a given species tree and a given gene tree--not only parsimonious ones. 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 normal form (i.e., non-reducible) is unique and minimal in the sense of the cost computed as the total number of gene duplications and losses (mutation cost). We present a classification of the scenarios and analyze their hierarchy. Finally, we prove that the reconciled tree can be easily transformed into DLS-tree in normal form. This solves some open problems for reconciled trees.