M. S. Bansal, E. 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. A. Charleston, Jungles: a new solution to the host/parasite phylogeny reconciliation problem, Mathematical Biosciences, vol.149, issue.2, pp.191-223, 1998.

C. Conow, D. Fielder, Y. Ovadia, and R. Libeskind-hadas, Jane: A new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.16, 2010.

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

B. Donati, C. Baudet, B. Sinaimeri, P. Crescenzi, and M. Sagot, Eucalypt: efficient tree reconciliation enumerator, Algorithms for Molecular Biology, vol.10, issue.1, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01092977

J. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöll?si, V. Ranwez et al., An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers, Proceedings of the 8th annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2010), vol.6398, pp.93-108, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00818889

G. N. Frederickson and D. B. Johnson, Generalized selection and ranking: Sorted matrices, SIAM J. Comput, vol.13, issue.1, pp.14-30, 1984.

K. T. Huber, V. Moulton, M. Sagot, and B. Sinaimeri, Exploring and Visualizing Spaces of Tree Reconciliations, Systematic Biology, vol.68, issue.4, pp.607-618, 2018.

K. T. Huber, V. Moulton, M. Sagot, and B. Sinaimeri, Geometric medians in reconciliation spaces of phylogenetic trees, Information Processing Letters, vol.136, pp.96-101, 2018.

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

R. Libeskind-hadas, Y. Wu, M. S. Bansal, and M. Kellis, Pareto-optimal phylogenetic tree reconciliation, Bioinformatics, vol.30, issue.12, pp.87-95, 2014.

D. Merkle, M. Middendorf, and N. Wieseke, A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, 2010.

Y. Ovadia, D. Fielder, C. Conow, and R. Libeskind-hadas, The cophylogeny reconstruction problem is np-complete, Journal of Computational Biology, vol.18, issue.1, pp.59-65, 2011.

R. D. Page, Parallel phylogenies: reconstructing the history of hostparasite assemblages, Cladistics, vol.10, issue.2, pp.155-173, 1994.

P. M. Simões, Diversity and dynamics of Wolbachia-host associations in arthropods from the Society archipelago, French Polynesia, 2012.

P. M. Simões, G. Mialdea, D. Reiss, M. Sagot, and S. Charlat, Wolbachia detection: an assessment of standard PCR protocols, Mol. Ecol. Resour, vol.11, issue.3, pp.567-572, 2011.

M. L. 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.409-415, 2012.

A. Tofigh, M. Hallett, and J. Lagergren, Simultaneous identification of duplications and lateral gene transfers, Journal of IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, pp.517-535, 2011.

Y. Wang, A. Mary, M. Sagot, and B. Sinaimeri, Lazy listing of equivalence classes -a paper on dynamic programming and tropical circuits, 2020.