M. S. Bansal, E. J. Alm, and M. Kellis, Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, pp.283-291, 2012.

M. S. Bansal, Y. Wu, E. J. Alm, and M. Kellis, Improved gene tree reconstruction for deciphering microbial evolution, 2014.

W. Chang and O. Eulenstein, Reconciling gene trees with apparent polytomies, International Computing and Combinatorics Conference, vol.4112, pp.235-244, 2006.

L. A. David and E. J. Alm, Rapid evolutionary innovation during an archaean genetic expansion, Nature, vol.469, issue.7328, pp.93-96, 2011.

J. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöllosi, V. Ranwez et al., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, RECOMB International Workshop on Comparative Genomics, vol.6398, pp.93-108, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00818889

R. C. Edgar, Muscle: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, 2004.

M. Groussin, J. K. Hobbs, G. J. Szöll?si, S. Gribaldo, V. L. Arcus et al., Toward more accurate ancestral protein genotypephenotype reconstructions with the use of species tree-aware gene trees, Molecular Biology and Evolution, vol.32, issue.1, pp.13-22, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02044770

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

S. Höhna and A. J. Drummond, Guided tree topology proposals for Bayesian phylogenetic inference, Systematic Biology, issue.1, pp.1-11, 2012.

E. Jacox, C. Chauve, G. J. Szöll?si, Y. Ponty, and C. Scornavacca, ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony, Bioinformatics, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01276903

M. Kordi and M. S. Bansal, On the complexity of duplicationtransfer-loss reconciliation with non-binary gene trees, International Symposium on Bioinformatics Research and Applications, vol.9096, pp.187-198, 2015.

M. Kordi and M. S. Bansal, Exact algorithms for duplicationtransfer-loss reconciliation with non-binary gene trees, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp.285-294, 2016.

N. Lartillot, T. Lepage, and S. Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, Bioinformatics, vol.25, issue.17, pp.2286-2288, 2009.

E. Mossel and M. Steel, How much can evolved characters tell us about the tree that generated them, Mathematics of Evolution and Phylogeny, pp.384-412, 2005.

T. H. Nguyen, V. Ranwez, S. Pointet, A. 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.1, 2013.
URL : https://hal.archives-ouvertes.fr/lirmm-00812726

E. Noutahi, M. Semeria, M. Lafond, J. Seguin, B. Boussau et al., Efficient gene tree correction guided by genome evolution, PLoS ONE, vol.11, issue.8, p.159559, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01162963

S. Penel, A. Arigon, J. Dufayard, A. Sertier, V. Daubin et al., Seq-Gen: an application for the monte carlo simulation of dna sequence evolution along phylogenetic trees, Computer applications in the biosciences: CABIOS, vol.10, issue.6, pp.235-238, 1997.

C. Scornavacca, E. Jacox, and G. J. Szöllosi, Joint amalgamation of most parsimonious reconciled gene trees, Bioinformatics, issue.6, pp.841-848, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02154935

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

J. Sjöstrand, A. Tofigh, V. Daubin, L. Arvestad, B. Sennblad et al., A Bayesian method for analyzing lateral gene transfer, Systematic Biology, vol.63, issue.3, pp.409-429, 2014.

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.

G. J. Szöll?si, W. Rosikiewicz, B. Boussau, E. Tannier, and V. Daubin, Efficient exploration of the space of reconciled gene trees, Systematic Biology, vol.62, issue.6, pp.901-912, 2013.

G. J. Szöll?si, 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.

Y. Zheng and L. Zhang, Are the duplication cost and robinsonfoulds distance equivalent, Journal of Computational Biology, vol.21, issue.8, pp.578-590, 2014.

Y. Zheng and L. Zhang, Reconciliation with non-binary gene trees revisited, International Conference on Research in Computational Molecular Biology, vol.8394, pp.418-432, 2014.