Lateral Gene Transfer as a Support for the Tree of Life, Proceedings of the National Academy of Sciences, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00752055
A Simulation Test Bed for Hypotheses of Genome Evolution, Bioinformatics, vol.23, issue.7, pp.825-856, 2007. ,
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation, Genome Biology and Evolution, vol.8, issue.5, pp.1427-1466, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01334923
Simulation of Genomes: A Review, Current Genomics, vol.9, issue.3, pp.155-59, 2008. ,
ALF-A Simulation Framework for Genome Evolution, Molecular Biology and Evolution, vol.29, issue.4, pp.1115-1138, 2011. ,
Gene Transfers Can Date the Tree of Life, Nature Ecology & Evolution, vol.2, issue.5, pp.904-913, 2018. ,
RecPhyloXML -a Format for Reconciled Gene Trees, Bioinformatics, 2018. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01800296
Horizontal Gene Transfer from Extinct and Extant Lineages: Biological Innovation and the Coral of Life, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol.364, pp.2229-2268, 1527. ,
Exact Stochastic Simulation of Coupled Chemical Reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-61, 1977. ,
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data, Molecular Biology and Evolution, vol.33, issue.6, pp.1635-1673, 2016. ,
On the Generalized 'Birth-and-Death' Process, Annals of Mathematical Statistics, vol.19, issue.1, pp.1-15, 1948. ,
SaGePhy: An Improved Phylogenetic Simulation Framework for Gene and Subgene Evolution, Bioinformatics, 2019. ,
Horizontal Transfer of Antibiotic Resistance Genes in Clinical Environments, Canadian Journal of Microbiology, vol.65, issue.1, pp.34-44, 2019. ,
SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees, Systematic Biology, vol.65, issue.2, pp.334-378, 2016. ,
GenPhyloData: Realistic Simulation of Gene Family Evolution, BMC Bioinformatics, vol.14, p.209, 2013. ,
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies, PloS One, vol.10, issue.9, p.139047, 2015. ,
Lateral Gene Transfer from the Dead, Systematic Biology, vol.62, issue.3, pp.386-97, 2013. ,
Horizontal Gene Transfer Constrains the Timing of Methanogen Evolution, Nature Ecology & Evolution, vol.2, issue.5, pp.897-903, 2018. ,
Cladogenesis, Coalescence and the Evolution of the Three Domains of Life, Trends in Genetics: TIG, vol.20, issue.4, pp.182-87, 2004. ,
A Simulation Test Bed for Hypotheses of Genome Evolution, Bioinformatics, vol.23, issue.7, pp.825-856, 2007. ,
ALF-A Simulation Framework for Genome Evolution, Molecular Biology and Evolution, vol.29, issue.4, pp.1115-1138, 2011. ,
SaGePhy: An Improved Phylogenetic Simulation Framework for Gene and Subgene Evolution, Bioinformatics, 2019. ,
,
SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees, Systematic Biology, vol.65, issue.2, pp.334-378, 2016. ,
GenPhyloData: Realistic Simulation of Gene Family Evolution, BMC Bioinformatics, vol.14, p.209, 2013. ,