Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol.11, issue.1, p.324, 2010. ,
DOI : 10.1186/1471-2105-11-324
URL : https://hal.archives-ouvertes.fr/inria-00527151
Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences, vol.109, issue.13, pp.4962-4967, 2012. ,
DOI : 10.1073/pnas.1116871109
URL : https://hal.archives-ouvertes.fr/hal-00752055
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.5714-5719, 2009. ,
DOI : 10.1073/pnas.0806251106
Random paths and random surfaces on a digital computer, Physics Letters B, vol.106, issue.4, pp.323-326, 1981. ,
DOI : 10.1016/0370-2693(81)90545-1
Genome-scale coestimation of species and gene trees, Genome Research, vol.23, issue.2, pp.323-330, 2013. ,
DOI : 10.1101/gr.141978.112
URL : https://hal.archives-ouvertes.fr/hal-00750148
Polymers and g|??|4 theory in four dimensions, Nuclear Physics B, vol.215, issue.2, pp.209-248, 1983. ,
DOI : 10.1016/0550-3213(83)90213-4
DTLS-trees: proving the parsimony model for reconciling gene and species trees In preparation, 2013. ,
Space of Gene/Species Trees Reconciliations and Parsimonious Models, Journal of Computational Biology, vol.16, issue.10, pp.1399-1418, 2009. ,
DOI : 10.1089/cmb.2009.0095
An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Proceedings of the 2010 international conference on Comparative genomics, RECOMB-CG'10, pp.93-108, 2011. ,
DOI : 10.1007/978-3-642-16181-0_9
URL : https://hal.archives-ouvertes.fr/lirmm-00818889
Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, Systematic Zoology, vol.28, issue.2, pp.132-163, 1979. ,
DOI : 10.2307/2412519
Orthology prediction at scalable resolution by phylogenetic tree analysis, BMC Bioinformatics, vol.8, issue.1, p.83, 2007. ,
DOI : 10.1186/1471-2105-8-83
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process, Molecular Biology and Evolution, vol.21, issue.6, pp.1095-1109, 2004. ,
DOI : 10.1093/molbev/msh112
URL : https://hal.archives-ouvertes.fr/lirmm-00108585
Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods Accepted at PLOS ONE, 2013. ,
Maps Between Trees and Cladistic Analysis of Historical Associations among Genes,Organisms, and Areas, Systematic Biology, vol.43, issue.1, pp.58-77, 1994. ,
DOI : 10.1093/sysbio/43.1.58
A Bayesian Approach for Fast and Accurate Gene Tree Recon- struction URL papers://c574a988- 041f-48f0-a387-1407660e65a3/Paper, Molecular Biology and Evolution, vol.2810, issue.1, pp.273-290, 1093. ,
REPRESENTING A SET OF RECONCILIATIONS IN A COMPACT WAY, Journal of Bioinformatics and Computational Biology, vol.11, issue.02, 2013. ,
DOI : 10.1142/S0219720012500254
URL : https://hal.archives-ouvertes.fr/lirmm-00818801
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability, Bioinformatics, vol.18, issue.1, pp.92-99, 2002. ,
DOI : 10.1093/bioinformatics/18.1.92
Efficient Exploration of the Space of Reconciled Gene Trees, Systematic Biology, vol.62, issue.6, pp.901-912, 2013. ,
DOI : 10.1093/sysbio/syt054
Better event supports using all suboptimal reconciliations ,
Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, pp.517-535, 2011. ,
DOI : 10.1109/TCBB.2010.14