TY  - JOUR
ID  - SisLab1858
UR  - http://doi.org/10.1007/978-3-642-33122-0_10
A1  - Nguyen, Thi Hau
A1  - Doyon, Jean-Philippe
A1  - Pointet, Stéphanie
A1  - Arigon Chifolleau, Anne-Muriel
A1  - Ranwez, Vincent
A1  - Berry, Vincent
Y1  - 2012///
N2  - 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/
JF  - Lecture Notes in Computer Science
VL  - 7534
SN  - 0302-9743
TI  - Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference
SP  - 123
AV  - none
EP  - 134
ER  -