T. Treangen and E. Rocha, Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes, PLoS Genetics, vol.13, issue.1, p.1001284, 2011.
DOI : 10.1371/journal.pgen.1001284.s007

URL : https://hal.archives-ouvertes.fr/pasteur-00578535

B. Boussau and V. Daubin, Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol.25, issue.4, pp.1-9, 2009.
DOI : 10.1016/j.tree.2009.09.007

URL : https://hal.archives-ouvertes.fr/hal-00539397

M. Goodman, J. Czelusniak, and G. Moore, 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

R. Guigo, I. Muchnik, and T. Smith, Reconstruction of ancient molecular phylogeny. Molecular phylogenetics and evolution, pp.189-213, 1996.

R. Page, Maps Between Trees and Cladistic Analysis of Historical Associations among Genes,Organisms, and Areas, Systematic Biology, vol.43, issue.1, p.58, 1994.
DOI : 10.1093/sysbio/43.1.58

S. Abby, E. Tannier, and M. Gouy, Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol.11, issue.1, p.324, 2010.
DOI : 10.1186/1471-2105-11-324

URL : https://hal.archives-ouvertes.fr/inria-00527151

R. Beiko and N. Hamilton, Phylogenetic identification of lateral genetic transfer events, BMC Evolutionary Biology, vol.6, issue.1, p.15, 2006.
DOI : 10.1186/1471-2148-6-15

L. Nakhleh, F. Ruths, and W. L. Riata-hgt, A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer, Proceedings of the 11th International Computing and Combinatorics Conference 2005, pp.84-93

J. Dufayard, L. Duret, and S. Penel, Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-603, 2005.
DOI : 10.1093/bioinformatics/bti325

URL : https://hal.archives-ouvertes.fr/hal-00427861

C. Storm and E. Sonnhammer, Automated ortholog inference from phylogenetic trees and calculation of orthology reliability, Bioinformatics, vol.18, issue.1, p.92, 2002.
DOI : 10.1093/bioinformatics/18.1.92

R. Van-der-heijden, B. Snel, and V. Van-noort, Orthology prediction at scalable resolution by phylogenetic tree analysis, BMC Bioinformatics, vol.8, issue.1, p.83, 2007.
DOI : 10.1186/1471-2105-8-83

I. Wapinski, A. Pfeffer, and N. Friedman, Natural history and evolutionary principles of gene duplication in fungi, Nature, vol.32, issue.7158, pp.54-61, 2007.
DOI : 10.1038/nature06107

C. Zmasek and S. Eddy, RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC Bioinformatics, vol.3, issue.1, p.14, 2002.
DOI : 10.1186/1471-2105-3-14

F. Chen, A. Mackey, and J. Vermunt, Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, PLoS ONE, vol.17, issue.4, 2007.
DOI : 10.1371/journal.pone.0000383.s008

L. Koski and G. Golding, The Closest BLAST Hit Is Often Not the Nearest Neighbor, Journal of Molecular Evolution, vol.51, issue.6, pp.540-542, 2001.
DOI : 10.1007/s002390010184

A. Rivera, M. Pankey, and D. Plachetzki, Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach, BMC Evolutionary Biology, vol.10, issue.1, p.123, 2010.
DOI : 10.1186/1471-2148-10-123

L. David and E. Alm, Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.1-4
DOI : 10.1038/nature09649

O. Akerborg, B. Sennblad, and L. Arvestad, Simultaneous Bayesian gene tree reconstruction and reconciliation analysis, Proceedings of the National Academy of Sciences, vol.106, issue.14, pp.5714-5723, 2009.
DOI : 10.1073/pnas.0806251106

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

D. Durand, B. Halldórsson, and B. Vernot, A Hybrid Micro???Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, vol.13, issue.2, pp.320-335, 2006.
DOI : 10.1089/cmb.2006.13.320

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

M. Sanderson and M. Mcmahon, Inferring angiosperm phylogeny from EST data with widespread gene duplication, BMC Evolutionary Biology, vol.7, issue.Suppl 1, 2007.
DOI : 10.1186/1471-2148-7-S1-S3

URL : http://doi.org/10.1186/1471-2148-7-s1-s3

R. Page and M. Charleston, Trees within trees: phylogeny and historical associations. Trends in Ecology & Evolution, pp.356-359, 1998.
DOI : 10.1016/s0169-5347(98)01438-4

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

C. Nieberding, E. Jousselin, and Y. Desdevises, The use of co-phylogeographic patterns to predict the nature of interactions, and vice-versa, in The geography of host-parasite interactions by, 2010.

D. Brooks and A. Ferrao, The historical biogeography of co-evolution: emerging infectious diseases are evolutionary accidents waiting to happen, Journal of Biogeography, vol.3, issue.Suppl., pp.1291-1299, 2005.
DOI : 10.1111/j.1365-2699.2005.01315.x

P. Bonizzoni, G. Vedova, and R. Dondi, Reconciling a gene tree to a species tree under the duplication cost model. Theoretical computer science, pp.36-53, 2005.

J. Doyon, C. Chauve, and S. Hamel, Space of Gene/Species Trees Reconciliations and Parsimonious Models, Journal of Computational Biology, vol.16, issue.10, pp.1399-1418, 2009.
DOI : 10.1089/cmb.2009.0095

P. Górecki and J. Tiuryn, DLS-trees: a model of evolutionary scenarios. Theoretical computer science, pp.378-399, 2006.

C. Zmasek and S. Eddy, A simple algorithm to infer gene duplication and speciation events on a gene tree, Bioinformatics, vol.17, issue.9, p.821, 2001.
DOI : 10.1093/bioinformatics/17.9.821

B. Mirkin, I. Muchnik, and T. Smith, A Biologically Consistent Model for Comparing Molecular Phylogenies, Journal of Computational Biology, vol.2, issue.4, pp.493-507, 1995.
DOI : 10.1089/cmb.1995.2.493

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

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

M. Hahn, Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution, Genome Biology, vol.8, issue.7, p.141, 2007.
DOI : 10.1186/gb-2007-8-7-r141

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

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205801

A. Berglund-sonnhammer, P. Steffansson, and M. Betts, 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

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

A. Novozhilov, G. Karev, and E. Koonin, Biological applications of the theory of birth-and-death processes, Briefings in Bioinformatics, vol.7, issue.1, p.70, 2006.
DOI : 10.1093/bib/bbk006

L. Arvestad, A. Berglund, and J. Lagergren, Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution, Proceedings of the eighth annual international conference on Computational molecular biology , RECOMB '04, pp.326-335, 2004.
DOI : 10.1145/974614.974657

L. Arvestad, J. Lagergren, and B. Sennblad, The gene evolution model and computing its associated probabilities, Journal of the ACM, vol.56, issue.2, pp.1-44
DOI : 10.1145/1502793.1502796

B. Sennblad and J. Lagergren, Probabilistic Orthology Analysis, Systematic Biology, vol.58, issue.4, p.411, 2009.
DOI : 10.1093/sysbio/syp046

URL : http://sysbio.oxfordjournals.org/cgi/content/short/58/4/411

J. Doyon, S. Hamel, and C. Chauve, An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, issue.1, 2010.
DOI : 10.1109/TCBB.2011.64

URL : https://hal.archives-ouvertes.fr/lirmm-00448486

P. Górecki, G. Burleigh, and O. Eulenstein, Maximum likelihood models and algorithms for gene tree evolution with duplications and losses, BMC Bioinformatics, vol.12, issue.Suppl 1, 2011.
DOI : 10.1186/1471-2105-12-S1-S15

M. Cs?rös and I. Miklós, Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, p.2087, 2009.
DOI : 10.1093/molbev/msp123

Y. Ovadia, D. Fielder, and C. Conow, The Cophylogeny Reconstruction Problem Is NP-Complete, Journal of Computational Biology, vol.18, issue.1, pp.191-223, 2011.
DOI : 10.1089/cmb.2009.0240

M. Charleston and S. Perkins, Traversing the tangle: Algorithms and applications for cophylogenetic studies, Journal of Biomedical Informatics, vol.39, issue.1, pp.62-71, 2006.
DOI : 10.1016/j.jbi.2005.08.006

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, pp.517-535, 2011.
DOI : 10.1109/TCBB.2010.14

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

R. Libeskind-hadas and M. 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

J. Doyon, C. Scornavacca, and G. Szöll?si, An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB) 2011, pp.93-108
DOI : 10.1007/978-3-642-16181-0_9

URL : https://hal.archives-ouvertes.fr/lirmm-00818889

M. Charleston, Jungles: a new solution to the host/parasite phylogeny reconciliation problem, Mathematical Biosciences, vol.149, issue.2, pp.191-223, 1998.
DOI : 10.1016/S0025-5564(97)10012-8

M. Charleston and R. Page, TreeMap 3 program, 2002.

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

URL : http://doi.org/10.1186/1471-2105-11-s1-s60

C. Conow, D. Fielder, and Y. Ovadia, 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

J. Doyon, C. Scornavacca, and G. Szöll?si, Mowgli program, 2011.

T. De-bie, N. Cristianini, and J. Demuth, CAFE: a computational tool for the study of gene family evolution, Bioinformatics, vol.22, issue.10, pp.1269-71, 2006.
DOI : 10.1093/bioinformatics/btl097

N. Lartillot and R. Poujol, A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters, Molecular Biology and Evolution, vol.28, issue.1, pp.729-744, 2011.
DOI : 10.1093/molbev/msq244

M. Sanderson, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, vol.19, issue.2, p.301, 2003.
DOI : 10.1093/bioinformatics/19.2.301