J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

O. Akerborg, B. Sennblad, L. Arvestad, and J. Lagergren, 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

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667006

A. Berglund-sonnhammer, P. Steffansson, M. Betts, and D. Liberles, Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony, Journal of Molecular Evolution, vol.3, issue.2, pp.240-250, 2006.
DOI : 10.1007/s00239-005-0096-1

B. Boussau, G. Szöllosi, L. Duret, M. Gouy, E. Tannier et al., 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

P. Gorecki and O. Eulenstein, A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees, ISBRA, vol.24, issue.13, pp.148-159
DOI : 10.1093/bioinformatics/btn230

M. Rasmussen and M. Kellis, A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction, Molecular Biology and Evolution, vol.28, issue.1, pp.273-290, 2011.
DOI : 10.1093/molbev/msq189

G. Szöllosi, W. Rosikiewicz, B. Bousseau, E. Tannier, and V. Daubin, Efficient Exploration of the Space of Reconciled Gene Trees, Systematic Biology, vol.62, issue.6, 2013.
DOI : 10.1093/sysbio/syt054

P. Thomas, GIGA: a simple, efficient algorithm for gene tree inference in the genomic age, BMC Bioinformatics, vol.11, issue.1, p.312, 2010.
DOI : 10.1186/1471-2105-11-312

J. Jun, I. Mandoiu, and C. Nelson, Identification of mammalian orthologs using local synteny, BMC Genomics, vol.10, issue.1, p.630, 2009.
DOI : 10.1186/1471-2164-10-630

C. Chauve, N. El-mabrouk, L. Gueguen, M. Semeria, and E. Tannier, Models and algorithms for genome evolution Springer; 2013, chap. Duplication, rearrangement and reconciliation: a follow-up 13 years later

M. Lafond and K. Swenson, El-Mabrouk N: Models and algorithms for genome evolution Springer; 2013, chap. Error detection and correction of gene trees

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, Automatic genome-wide reconstruction of phylogenetic gene trees, Bioinformatics, vol.23, issue.13, pp.549-558, 2007.
DOI : 10.1093/bioinformatics/btm193

S. Bérard, C. Gallien, B. Boussau, G. Szöllosi, V. Daubin et al., Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol.28, issue.18, pp.382-388
DOI : 10.1093/bioinformatics/bts374

R. Chaudhary, J. Burleigh, and O. Eulenstein, Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence, BMC Bioinformatics, vol.13, issue.Suppl 10, pp.13-24, 2011.
DOI : 10.1186/1471-2105-12-S1-S14

P. Górecki and O. Eulenstein, Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem, BMC Bioinformatics, vol.13, issue.Suppl 10, p.14
DOI : 10.1006/jmbi.2000.4042

M. Muffato, A. Louis, C. Poisnel, and H. Crollius, Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes, Bioinformatics, vol.26, issue.8, pp.1119-1121, 2010.
DOI : 10.1093/bioinformatics/btq079

T. Nguyen, V. Ranwez, S. Pointet, A. Chifolleau, J. Doyon et al., Reconciliation and local gene tree rearrangement can be of mutual profit, Algorithms for Molecular Biology, vol.8, issue.1, p.12, 2013.
DOI : 10.1073/pnas.1202997109

URL : https://hal.archives-ouvertes.fr/lirmm-00812726

A. Vilella, J. Severin, A. Ureta-vidal, L. Heng, and E. Birney, EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates, Genome Research, vol.19, issue.2, pp.327-335, 2009.
DOI : 10.1101/gr.073585.107

C. Chauve and N. El-mabrouk, New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees, LNCS, vol.5541, pp.46-58, 2009.
DOI : 10.1007/978-3-642-02008-7_4

A. Doroftei and N. El-mabrouk, Removing Noise from Gene Trees, Algorithms in Bioinformatics LNCS, vol.4, issue.5, pp.76-91, 2011.
DOI : 10.1089/cmb.1997.4.177

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.225.2428

M. Lafond, K. Swenson, and N. El-mabrouk, An Optimal Reconciliation Algorithm for Gene Trees with Polytomies, Algorithms in Bioinformatics LNCS, vol.12, issue.2012, pp.106-122
DOI : 10.1007/978-3-642-33122-0_9

S. Guidon and O. Gascuel, A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood, Systematic Biology, vol.52, p.696704, 2003.

H. Shimodaira and M. Hasegawa, CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, vol.17, issue.12, pp.1246-1247, 2001.
DOI : 10.1093/bioinformatics/17.12.1246