relation: https://eprints.uet.vnu.edu.vn/eprints/id/eprint/1858/
title: Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference
creator: Nguyen, Thi Hau
creator: Doyon, Jean-Philippe
creator: Pointet, Stéphanie
creator: Arigon Chifolleau, Anne-Muriel
creator: Ranwez, Vincent
creator: Berry, Vincent
subject: Information Technology (IT)
description: 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/
date: 2012
type: Article
type: PeerReviewed
identifier:   Nguyen, Thi Hau and Doyon, Jean-Philippe and Pointet, Stéphanie and Arigon Chifolleau, Anne-Muriel and Ranwez, Vincent and Berry, Vincent  (2012) Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference.  Lecture Notes in Computer Science, 7534 .   pp. 123-134.  ISSN 0302-9743     
relation: http://doi.org/10.1007/978-3-642-33122-0_10
relation: 10.1007/978-3-642-33122-0_10