eprintid: 1858
rev_number: 7
eprint_status: archive
userid: 283
dir: disk0/00/00/18/58
datestamp: 2016-09-03 03:00:27
lastmod: 2016-09-03 03:00:27
status_changed: 2016-09-03 03:00:27
type: article
metadata_visibility: show
creators_name: Nguyen, Thi Hau
creators_name: Doyon, Jean-Philippe
creators_name: Pointet, Stéphanie
creators_name: Arigon Chifolleau, Anne-Muriel
creators_name: Ranwez, Vincent
creators_name: Berry, Vincent
title: Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference
ispublished: pub
subjects: IT
divisions: fac_fit
abstract: 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
date_type: published
official_url: http://doi.org/10.1007/978-3-642-33122-0_10
id_number: 10.1007/978-3-642-33122-0_10
full_text_status: none
publication: Lecture Notes in Computer Science
volume: 7534
pagerange: 123-134
refereed: TRUE
issn: 0302-9743
book_title: Algorithms in Bioinformatics
citation:   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