O. Åkerborg, B. Sennblad, L. Arvestad, and J. Lagergren, Simultaneous Bayesian gene tree reconstruction and reconciliation analysis, Proc Natl Acad Sci, vol.106, pp.5714-5719, 2009.

M. Anisimova, D. A. Liberles, H. Philippe, J. Provan, T. Pupko et al., State-of the art methodologies dictate new standards for phylogenetic analysis, BMC Evol Biol, vol.13, p.161, 2013.

M. Arenas, Simulation of molecular data under diverse evolutionary scenarios, PLoS Comput Biol, vol.8, issue.5, p.1002495, 2012.

S. A. Benner, M. D. Caraco, J. M. Thomson, and E. A. Gaucher, Planetary biology-paleontological, geological, and molecular histories of life, Science, vol.296, pp.864-868, 2002.

B. Boussau, G. J. Szöllo-00-si, L. Duret, M. Gouy, E. Tannier et al., Genome-scale coestimation of species and gene trees, Genome Res, vol.23, pp.323-330, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00750148

B. Chang and M. Donoghue, Recreating ancestral proteins, Trends Ecol Evol, vol.15, pp.109-114, 2000.

B. Chang, K. Jönsson, M. Kazmi, M. J. Donoghue, and T. P. Sakmar, Recreating a functional ancestral archosaur visual pigment, Mol Biol Evol, vol.19, issue.9, pp.1483-1489, 2002.

F. Chen, E. A. Gaucher, N. A. Leal, D. Hutter, S. A. Havemann et al., Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection, Proc Natl Acad Sci U S A, vol.107, pp.1948-1953, 2010.

M. F. Cole and E. A. Gaucher, Utilizing natural diversity to evolve protein function: applications towards thermostability, Curr Opin Chem Biol, vol.15, pp.399-406, 2011.

A. Criscuolo and S. Gribaldo, BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol Biol, vol.10, p.210, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02445904

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

J. P. Doyon, V. Ranwez, V. Daubin, and V. Berry, Models, algorithms and programs for phylogeny reconciliation, Brief Bioinform, vol.12, pp.392-400, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00825041

J. Dutheil and B. Boussau, Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evol Biol, vol.8, p.255, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00428202

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

G. C. Finnigan, V. Hanson-smith, T. H. Stevens, and J. W. Thornton, Evolution of increased complexity in a molecular machine, Nature, vol.481, pp.360-364, 2012.

E. A. Gaucher, S. Govindarajan, and O. K. Ganesh, Palaeotemperature trend for Precambrian life inferred from resurrected proteins, Nature, vol.451, pp.704-708, 2008.

E. A. Gaucher, J. M. Thomson, M. F. Burgan, and S. A. Benner, Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins, Nature, vol.425, pp.285-288, 2003.

R. Grantham, Amino acid difference formula to help explain protein evolution, Science, vol.185, issue.4154, pp.862-864, 1974.

M. Groussin, B. Boussau, and M. Gouy, A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences, Syst Biol, vol.62, pp.523-538, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02401848

L. Gu-eguen, S. Gaillard, B. Boussau, M. Gouy, M. Groussin et al., Bio++: efficient extensible libraries and tools for computational molecular evolution, 2013.

, Mol Biol Evol, vol.30, pp.1745-1750

S. Guindon, J. F. 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, Syst Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

V. Hanson-smith, B. Kolaczkowski, and J. W. Thornton, Robustness of ancestral sequence reconstruction to phylogenetic uncertainty, Mol Biol Evol, vol.27, pp.1988-1999, 2010.

M. J. Harms and J. W. Thornton, Analyzing protein structure and function using ancestral gene reconstruction, Curr Opin Struct Biol, vol.20, pp.360-366, 2010.

M. J. Harms and J. W. Thornton, Evolutionary biochemistry: revealing the historical and physical causes of protein properties, Nat Rev Genet, vol.14, issue.8, pp.559-571, 2013.

J. K. Hobbs, C. Shepherd, D. J. Saul, N. J. Demetras, S. Haaning et al., On the Origin and evolution of thermophily: reconstruction of functional precambrian enzymes from ancestors of Bacillus, Mol Biol Evol, vol.29, pp.825-835, 2012.

S. Höhna and A. J. Drummond, Guided tree topology proposals for Bayesian phylogenetic inference, Syst Biol, vol.61, pp.1-11, 2012.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-780, 2013.

J. T. Kodra, M. Skovgaard, D. Madsen, and D. A. Liberles, Linking sequence to function in drug design with ancestral sequence reconstruction, pp.34-39, 2007.

J. Koshi and R. Goldstein, Probabilistic reconstruction of ancestral protein sequences, J Mol Evol, vol.42, pp.313-320, 1996.

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

N. Lartillot and H. Philippe, A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process, Mol Biol Evol, vol.21, pp.1095-2004, 2004.
URL : https://hal.archives-ouvertes.fr/lirmm-00108585

S. Q. Le and O. Gascuel, An improved general amino acid replacement matrix, Mol Biol Evol, vol.25, pp.1307-1320, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

S. Q. Le and O. Gascuel, Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial, Syst Biol, vol.59, pp.277-287, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511776

S. Q. Le, O. Gascuel, and N. Lartillot, Empirical profile mixture models for phylogenetic reconstruction, Bioinformatics, vol.24, pp.2317-2323, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324090

S. Q. Le, N. Lartillot, and O. Gascuel, Phylogenetic mixture models for proteins, Philos Trans R Soc Lond B Biol Sci, vol.363, pp.3965-3976, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00365645

A. Löytynoja and N. Goldman, Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis, Science, vol.320, pp.1632-1635, 2008.

B. Malcolm, K. Wilson, B. Matthews, J. Kirsch, and A. Wilson, Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing, Nature, vol.345, pp.86-89, 1990.

S. Mirceta, A. Signore, J. Burns, A. Cossins, K. Campbell et al., Evolution of mammalian diving capacity traced by myoglobin net surface charge, Science, vol.340, p.1234192, 2013.

E. A. Ortlund, J. T. Bridgham, M. R. Redinbo, and J. W. Thornton, Crystal structure of an ancient protein: evolution by conformational epistasis, Science, vol.317, pp.1544-1548, 2007.

L. Pauling and E. Zuckerkandl, Chemical paleogenetics: molecular "restoration studies" of extinct forms of life, Acta Chem Scand, vol.17, pp.9-16, 1963.

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, p.3, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00400099

H. Philippe and B. Roure, Difficult phylogenetic questions: more data, maybe; better methods, certainly, BMC Biol, vol.9, p.91, 2011.

T. Pupko, A. Doron-faigenboim, D. A. Liberles, and G. M. Cannarozzi, Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences, Ancestral sequence reconstruction, pp.43-57, 2007.

T. Pupko, I. Pe'er, R. Shamir, and D. Graur, A fast algorithm for joint reconstruction of ancestral amino acid sequences, Mol Biol Evol, vol.17, pp.890-896, 2000.

M. D. Rasmussen and M. Kellis, Unified modeling of gene duplication, loss, and coalescence using a locus tree, Genome Res, vol.22, pp.755-765, 2012.

J. Stackhouse, S. Presnell, G. Mcgeehan, K. Nambiar, and S. Benner, The ribonuclease from an extinct bovid ruminant, FEBS Lett, vol.262, pp.104-106, 1990.

S. Szöllo-00, . Gj, B. Boussau, S. S. Abby, E. Tannier et al., Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proc Natl Acad Sci U S A, vol.109, pp.17513-17518, 2012.

, Use of Species Tree-Aware Gene Trees for ancestral sequence reconstruction, 2020.

S. Szöllo-00, . Gj, W. Rosikiewicz, B. Boussau, E. Tannier et al., Efficient exploration of the space of reconciled gene trees, Syst Biol, vol.62, pp.901-912, 2013.

S. Szöllo-00, . Gj, E. Tannier, N. Lartillot, and V. Daubin, Lateral gene transfer from the dead, Syst Biol, vol.62, pp.386-397, 2013.

J. L. Thorne, H. Kishino, and I. S. Painter, Estimating the rate of evolution of the rate of molecular evolution, Mol Biol Evol, vol.15, pp.1647-1657, 1998.

K. Voordeckers, C. A. Brown, K. Vanneste, E. Van-der-zande, A. Voet et al., Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication, PLoS Biol, vol.10, issue.12, p.1001446, 2012.

P. D. Williams, D. D. Pollock, B. P. Blackburne, and R. A. Goldstein, Assessing the accuracy of ancestral protein reconstruction methods, PLoS Comput Biol, vol.2, p.69, 2006.

Y. C. Wu, M. D. Rasmussen, M. S. Bansal, and M. Kellis, TreeFix: statistically informed gene tree error correction using species trees, Syst Biol, vol.62, pp.110-120, 2013.

Z. Yang, Computational molecular evolution, 2006.

Z. Yang, S. Kumar, and M. Nei, A new method of inference of ancestral nucleotide and amino acid sequences, Genetics, vol.141, pp.1641-1650, 1995.