S. Bérard, C. Gallien, B. Boussau, G. J. Szöll?-osi, V. Daubin et al., Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.28-382, 2012.
DOI : 10.1093/bioinformatics/bts374

C. Chauve, Y. Ponty, and J. P. Zanetti, Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach, Lecture Notes in Computer Science (Advances in Bioinformatics and Computational Biology, pp.8826-8875, 2015.
DOI : 10.1101/026310

URL : https://hal.archives-ouvertes.fr/hal-01216782

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

URL : http://doi.org/10.1093/nar/gkh340

L. Haggerty, P. Jachiet, W. Hanage, D. Fitzpatrick, P. Lopez et al., A Pluralistic Account of Homology: Adapting the Models to the Data, Molecular Biology and Evolution, vol.31, issue.3, pp.501-517, 2014.
DOI : 10.1093/molbev/mst228

E. Jacox, C. Chauve, G. J. Szöll?-osi, Y. Ponty, and C. Scornavacca, ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1., Bioinformatics, vol.32, issue.13, pp.1-3, 2016.
DOI : 10.1093/bioinformatics/btw105

S. Kummerfeld and S. Teichmann, Relative rates of gene fusion and fission in multi-domain proteins, Trends in Genetics, vol.21, issue.1, pp.35-65, 2005.
DOI : 10.1016/j.tig.2004.11.007

J. Ma, L. Zhang, B. Suh, B. Raney, R. Burhans et al., Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-65, 2006.
DOI : 10.1101/gr.5383506

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665639

J. Manuch, M. Patterson, R. Wittler, C. Chauve, and E. Tannier, Linearization of ancestral multichromosomal genomes, BMC Bioinformatics, vol.13, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00773071

D. E. Neafsey, R. M. Waterhouse, M. R. Abai, S. S. Aganezov, M. A. Alekseyev et al., Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes, Science, vol.10, issue.2, pp.347-1258522, 2015.
DOI : 10.1186/1471-2148-10-9

E. Nouhati, M. Semeria, M. Lafond, J. Seguin, B. Boussau et al., Efficient gene tree correction guided by species and synteny evolution, PLoS ONE, 2016.

S. Pasek, J. Risler, and P. Brézellec, Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins, Bioinformatics, vol.22, issue.12, pp.22-1418, 2006.
DOI : 10.1093/bioinformatics/btl135

M. Patterson, G. Szöll?-osi, V. Daubin, and E. Tannier, Lateral gene transfer, rearrangement, reconciliation, BMC Bioinformatics, vol.14, issue.Suppl 15, pp.14-18, 2013.
DOI : 10.1137/0128004

URL : https://hal.archives-ouvertes.fr/hal-00873233

S. Penel, A. Arigon, J. Dufayard, A. Sertier, V. Daubin et al., Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.Suppl 6, 2009.
DOI : 10.1186/1471-2105-10-S6-S3

URL : https://hal.archives-ouvertes.fr/lirmm-00400099

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

M. Stolzer, H. Lai, M. Xu, D. Sathaye, B. Vernot et al., Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees, Bioinformatics, vol.28, issue.18, pp.28-409, 2012.
DOI : 10.1093/bioinformatics/bts386

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436813

M. Stolzer, K. Siewert, H. Lai, M. Xu, D. et al., Event inference in multidomain families with phylogenetic reconciliation, BMC Bioinformatics, vol.16, issue.Suppl 14, pp.1-13, 2015.
DOI : 10.1186/1471-2105-16-S14-S8

URL : http://doi.org/10.1186/1471-2105-16-s14-s8

G. Szöll?-osi, E. Tannier, V. Daubin, and B. Boussau, The Inference of Gene Trees with Species Trees, Systematic Biology, vol.64, issue.1, pp.42-62, 2015.
DOI : 10.1093/sysbio/syu048

G. J. Szöll?-osi, E. Tannier, N. Lartillot, and V. Daubin, Lateral Gene Transfer from the Dead, Systematic Biology, vol.62, issue.3, pp.386-397, 2013.
DOI : 10.1093/sysbio/syt003

Y. Wu, M. D. Rasmussen, and M. Kellis, Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny, Molecular Biology and Evolution, vol.29, issue.2, pp.689-705, 2012.
DOI : 10.1093/molbev/msr222

Y. Wu, M. D. Rasmussen, M. S. Bansal, and M. Kellis, TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees, Systematic Biology, vol.62, issue.1, pp.110-120, 2013.
DOI : 10.1093/sysbio/sys076

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526801