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
DLS-trees: a model of evolutionary scenarios
Theoretical Computer Science
An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
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
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In this paper we present an extended model related to reconciliation concepts. It is based on gene duplications, gene losses and speciation events. We define an evolutionary scenario (called a DLS-tree) which informally can represent an evolution of genes in species. We are interested in all scenarios – not only parsimonious ones. We propose a system of rules 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. Moreover, we present a classification of the scenarios and analyze their hierarchy. Finally, we prove that the tree in normal form could be easily transformed into the reconciled tree [12] in duplication-loss model. This solves some open problems stated in [13].