A note on the height of binary search trees
Journal of the ACM (JACM)
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
Reconstructing reticulate evolution in species: theory and practice
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
The gene evolution model and computing its associated probabilities
Journal of the ACM (JACM)
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Simultaneous Identification of Duplications and Lateral Gene Transfers
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for rapid error correction for the gene duplication problem
ISBRA'11 Proceedings of the 7th 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
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We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the above-mentioned optimization in comparison to the naïve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at http://www.atgc-montpellier.fr/Mowgli/