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.1, p.16, 2010.
DOI : 10.1186/1748-7188-5-16

M. Csuros and I. Miklos, Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, pp.2087-2095, 2009.
DOI : 10.1093/molbev/msp123

T. Gabaldon, Computational approaches for the prediction of protein function in the mitochondrion, AJP: Cell Physiology, vol.291, issue.6, pp.1121-1128, 2006.
DOI : 10.1152/ajpcell.00225.2006

M. Goodman, J. Czelusniak, G. W. Moore, R. A. Herrera, and G. Matsuda, Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, Systematic Zoology, vol.28, issue.2, pp.132-163, 1979.
DOI : 10.2307/2412519

K. Yu, V. A. Gorbunov, and . Lyubetsky, Reconstructing genes evolution along a species tree, Mol. Biol. (Mosk.), vol.43, pp.946-958, 2009.

K. Yu, V. A. Gorbunov, and . Lyubetsky, An algorithm of reconciliation of gene and species trees and inferring gene duplications, losses and horizontal transfers. Information processes, pp.140-144, 2010.

R. Libeskind-hadas and M. A. Charleston, On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem, Journal of Computational Biology, vol.16, issue.1, pp.105-117, 2009.
DOI : 10.1089/cmb.2008.0084

S. P. Loader, D. Pisani, J. A. Cotton, D. J. Gower, J. J. Day et al., Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians, Biology Letters, vol.3, issue.5, pp.505-508, 2007.
DOI : 10.1098/rsbl.2007.0266

D. Merkle and M. Middendorf, Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information, Theory in Biosciences, vol.123, issue.4, pp.277-299, 2005.
DOI : 10.1016/j.thbio.2005.01.003

D. Merkle, M. Middendorf, and N. Wieseke, A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, issue.Suppl 1, p.60, 2010.
DOI : 10.1186/1471-2105-11-S1-S60

S. Penel, A. M. Arigon, J. F. Dufayard, A. S. Sertier, V. Daubin et al., Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol.10, issue.Suppl 6, p.3, 2009.
DOI : 10.1186/1471-2105-10-S6-S3
URL : https://hal.archives-ouvertes.fr/lirmm-00400099

A. Rambaut, Phylogen: phylogenetic tree simulator package, 2002.

A. Tofigh, Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression, KTH Royal Institute of Technology, 2009.

A. Tofigh, M. Hallett, and J. Lagergren, Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, p.99, 2010.
DOI : 10.1109/TCBB.2010.14

A. Tofigh, J. Sjöstrand, B. Sennblad, L. Arvestad, and J. Lagergren, Detecting LGTs using a novel probabilistic model integrating duplications, lgts, losses, rate variation, and sequence evolution

B. Vernot, M. Stolzer, A. Goldman, and D. Durand, Reconciliation with Non-Binary Species Trees, Journal of Computational Biology, vol.15, issue.8, pp.981-1006, 2008.
DOI : 10.1089/cmb.2008.0092

L. Zhang, On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies, Journal of Computational Biology, vol.4, issue.2, pp.177-187, 1997.
DOI : 10.1089/cmb.1997.4.177