Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol.25, issue.4, pp.224-232, 2010. ,
DOI : 10.1016/j.tree.2009.09.007
URL : https://hal.archives-ouvertes.fr/hal-00539397
Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2129, 1999. ,
DOI : 10.1126/science.284.5423.2124
Prokaryotic Evolution in Light of Gene Transfer, Molecular Biology and Evolution, vol.19, issue.12, pp.2226-2238, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004046
Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions, Proceedings of the Royal Society B: Biological Sciences, vol.267, issue.1449, pp.1213-1221, 2000. ,
DOI : 10.1098/rspb.2000.1130
An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics, Systematic Biology, vol.54, issue.5, pp.743-757, 2005. ,
DOI : 10.1080/10635150500234609
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies, Systematic Biology, vol.56, issue.3, pp.389-399, 2007. ,
DOI : 10.1080/10635150701397643
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions, Journal of Computational Biology, vol.14, issue.4, pp.517-535, 2007. ,
DOI : 10.1089/cmb.2007.A010
Some Approximation Results for the Maximum Agreement Forest Problem. RANDOM-APPROX, pp.18-20, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-00427146
The maximum agreement forest problem: Approximation algorithms and computational experiments, Theoretical Computer Science, vol.374, issue.1-3, pp.91-110, 2007. ,
DOI : 10.1016/j.tcs.2006.12.011
URL : https://hal.archives-ouvertes.fr/hal-00434715
RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer, 2005. ,
DOI : 10.1007/11533719_11
SPR-BASED TREE RECONCILIATION: NON-BINARY TREES AND MULTIPLE SOLUTIONS, Proceedings of the 6th Asia-Pacific Bioinformatics Conference, pp.14-17, 2008. ,
DOI : 10.1142/9781848161092_0027
Phylogenetic identification of lateral genetic transfer events, BMC Evolutionary Biology, vol.6, issue.1, p.15, 2006. ,
DOI : 10.1186/1471-2148-6-15
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer, 2008. ,
DOI : 10.1007/978-3-540-87989-3_9
Inferring confidence sets of possibly misspecified gene trees, Proceedings of the Royal Society B: Biological Sciences, vol.269, issue.1487, pp.137-142, 2002. ,
DOI : 10.1098/rspb.2001.1862
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.170-179, 1989. ,
DOI : 10.1007/BF02100115
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1116, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026201
An Approximately Unbiased Test of Phylogenetic Tree Selection, Systematic Biology, vol.51, issue.3, pp.492-508, 2002. ,
DOI : 10.1080/10635150290069913
TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics, BMC Evolutionary Biology, vol.4, issue.1, p.18, 2004. ,
DOI : 10.1186/1471-2148-4-18
A Model of Horizontal Gene Transfer and the Bacterial Phylogeny Problem, Systematic Biology, vol.56, issue.4, pp.633-642, 2007. ,
DOI : 10.1080/10635150701546231
URL : https://hal.archives-ouvertes.fr/halsde-00424419
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships, BMC Bioinformatics, vol.9, issue.1, p.322, 2008. ,
DOI : 10.1186/1471-2105-9-322
Universal trees based on large combined protein sequence data sets, Nature Genetics, vol.28, issue.3, pp.281-285, 2001. ,
DOI : 10.1038/90129
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the ??-Proteobacteria, PLoS Biology, vol.51, issue.1, p.19, 2003. ,
DOI : 10.1371/journal.pbio.0000019.st001
URL : https://hal.archives-ouvertes.fr/hal-00427440
Toward Automatic Reconstruction of a Highly Resolved Tree of Life, Science, vol.311, issue.5765, pp.1283-1287, 2006. ,
DOI : 10.1126/science.1123061
Genome Phylogenies Indicate a Meaningful ??-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales, Molecular Biology and Evolution, vol.23, issue.1, pp.74-85, 2006. ,
DOI : 10.1093/molbev/msj009
A Robust Species Tree for the Alphaproteobacteria, Journal of Bacteriology, vol.189, issue.13, pp.4578-4586, 2007. ,
DOI : 10.1128/JB.00269-07
Ancient horizontal gene transfer can benefit phylogenetic reconstruction, Trends in Genetics, vol.22, issue.7, pp.361-366, 2006. ,
DOI : 10.1016/j.tig.2006.05.004
Bio++: a set of C++ libraries for sequence analysis phylogenetics, molecular evolution and population genetics, BMC Bioinformatics, vol.7, issue.1, p.188, 2006. ,
DOI : 10.1186/1471-2105-7-188
URL : https://hal.archives-ouvertes.fr/halsde-00323971
The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, issue.3, pp.275-282, 1992. ,
DOI : 10.1093/bioinformatics/8.3.275
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach, 31. R Development Core Team: R: A Language and Environment for Statistical Computing, pp.691-699, 2001. ,
DOI : 10.1093/oxfordjournals.molbev.a003851