Bayesian gene/species tree reconciliation and orthology analysis using MCMC, Bioinformatics, vol.19, issue.Suppl 1, pp.7-15, 2003. ,
DOI : 10.1093/bioinformatics/btg1000
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide, Nucleic Acids Research, vol.29, issue.1, pp.126-127, 2001. ,
DOI : 10.1093/nar/29.1.126
Jane: a new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.1, p.16, 2010. ,
DOI : 10.1186/1748-7188-5-16
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, pp.2087-2095, 2009. ,
DOI : 10.1093/molbev/msp123
Phylogenetics and the Cohesion of Bacterial Genomes, Science, vol.301, issue.5634, pp.829-832, 2003. ,
DOI : 10.1126/science.1086568
URL : https://hal.archives-ouvertes.fr/hal-00427390
Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2129, 1999. ,
DOI : 10.1126/science.284.5423.2124
Biology's next revolution, Nature, vol.445, issue.7126, p.369, 2007. ,
DOI : 10.1038/445369a
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
Reconstructing the evolution of genes along the species tree, Molecular Biology, vol.43, issue.5, pp.946-958, 2009. ,
DOI : 10.1134/S0026893309050197
Reconciliation problems for duplication, loss and horizontal gene transfer, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, 2004. ,
DOI : 10.1145/974614.974656
Reconstruction of Ancient Molecular Phylogeny, Molecular Phylogenetics and Evolution, vol.6, issue.2, pp.189-213, 1996. ,
DOI : 10.1006/mpev.1996.0071
Simultaneous identification of duplications and lateral transfers, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.347-356, 2004. ,
DOI : 10.1145/974614.974660
Horizontal gene transfer: A critical view, Proceedings of the National Academy of Sciences, vol.100, issue.17, pp.9658-9662, 2003. ,
DOI : 10.1073/pnas.1632870100
On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem, Journal of Computational Biology, vol.16, issue.1, pp.105-117, 2009. ,
DOI : 10.1089/cmb.2008.0084
The prokaryotic tree of life: past, present???and future?, Trends in Ecology & Evolution, vol.23, issue.5, pp.276-281, 2008. ,
DOI : 10.1016/j.tree.2008.01.008
Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information, Theory in Biosciences, vol.123, issue.4, pp.277-299, 2005. ,
DOI : 10.1016/j.thbio.2005.01.003
A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, issue.Suppl 1, p.60, 2010. ,
DOI : 10.1186/1471-2105-11-S1-S60
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
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.Suppl 6, p.3, 2009. ,
DOI : 10.1186/1471-2105-10-S6-S3
URL : https://hal.archives-ouvertes.fr/lirmm-00400099
Search for a 'Tree of Life' in the thicket of the phylogenetic forest, Journal of Biology, vol.8, issue.6, p.59, 2009. ,
DOI : 10.1186/jbiol159
Phylogen : phylogenetic tree simulator package, 2002. ,
Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, p.99, 2010. ,
DOI : 10.1109/TCBB.2010.14
Detecting LGTs using a novel probabilistic model integrating duplications, lgts, losses, rate variation, and sequence evolution, 2009. ,
Reconciliation with Non-Binary Species Trees, Journal of Computational Biology, vol.15, issue.8, pp.981-1006, 2008. ,
DOI : 10.1089/cmb.2008.0092
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205801