O. Akerborg, B. Sennblad, and J. Lagergren, Birth-death prior on phylogeny and speed dating, BMC Evol. Biol, vol.8, p.77, 2008.

O. Akerborg, B. Sennblad, L. Arvestad, and J. Lagergren, Simultaneous Bayesian gene tree reconstruction and reconciliation analysis, PNAS, vol.106, issue.14, pp.5714-5719, 2009.

D. L. Ayres, A. Darling, D. J. Zwickl, P. Beerli, M. T. Holder et al., BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics, Syst. Biol, vol.61, issue.1, pp.170-173, 2012.

F. U. Battistuzzi, .. A. Filipski, S. B. Hedges, and S. Kumar, Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals, Mol. Biol. Evol, vol.27, issue.6, pp.1289-1300, 2010.

G. Bello, C. P. Passaes, M. L. Guimarães, R. S. Lorete, S. E. Matos-almeida et al., Origin and evolutionary history of HIV-1 subtype C in Brazil, AIDS, vol.22, pp.1993-2000, 2008.

D. P. Bertsekas, S. Boyd, and L. Vandenberghe, Nonlinear programming, Convex optimization, p.244, 1999.

T. Britton, C. L. Anderson, D. Jacquet, S. Lundqvist, and K. Bremer, Estimating divergence times in large phylogenetic trees, Syst. Biol, vol.56, issue.5, pp.741-752, 2007.

M. C. Christman, A. Kedwaii, J. Xu, R. O. Donis, and G. Lu, Pandemic (H1N1) 2009 virus revisited: an evolutionary retrospective, Infect. Genet. Evol, vol.11, pp.803-811, 2011.

R. Desper and O. Gascuel, Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle, J. Comput. Biol, vol.19, issue.5, pp.687-705, 2002.
URL : https://hal.archives-ouvertes.fr/lirmm-00269513

E. J. Douzery, F. Delsuc, M. J. Stanhope, and D. Huchon, Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations, J. Mol. Evol, vol.57, issue.1, pp.201-213, 2003.
URL : https://hal.archives-ouvertes.fr/halsde-00193003

J. P. Doyon, V. Ranwez, V. Daubin, and V. Berry, Models, algorithms and programs for phylogeny reconciliation, Brief. Bioinform, vol.12, issue.5, pp.392-400, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00825041

A. Drummond and A. Rodrigo, Reconstruction genealogies of serial samples under the assumption of a molecular clock using serialsample UPGMA, Mol. Biol. Evol, vol.17, issue.12, pp.1807-1815, 2000.

A. J. Drummond, O. G. Pybus, A. Rambaut, R. Forsberg, and A. G. Rodrigo, Measurably evolving populations, Trends Ecol. Evol, vol.18, pp.481-488, 2003.

A. Drummond, O. G. Pybus, and A. Rambaut, Inference of viral evolutionary rates from molecular sequences, Adv. Parasitol, vol.54, pp.331-358, 2003.

A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, Relaxed phylogenetics and dating with confidence, PLoS Biol, vol.4, p.88, 2006.

A. J. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol, vol.7, p.214, 2007.

A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol, vol.29, issue.8, pp.1969-1973, 2012.

J. Felsenstein, PHYLIP -phylogeny inference package (Version 3.2), Cladistics, vol.5, pp.164-166, 1989.

W. M. Fitch and E. Margoliash, Construction of phylogenetic trees, Science, vol.155, pp.279-284, 1967.

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol. Biol. Evol, vol.14, issue.7, pp.685-695, 1997.
URL : https://hal.archives-ouvertes.fr/lirmm-00730410

B. T. Grenfell, O. G. Pybus, J. R. Gog, J. L. Wood, J. M. Daly et al., Unifying the epidemiological and evolutionary dynamics of pathogens, Science, vol.303, pp.327-332, 2004.

S. Guindon, Bayesian estimation of divergence times from large sequence alignments, Mol. Biol. Evol, vol.27, pp.1768-1781, 2010.
DOI : 10.1093/molbev/msq060

URL : https://hal.archives-ouvertes.fr/lirmm-00705189

S. Guindon and O. Gascuel, A simple, fast and accurate algorithm to infer large phylogenies by maximum-likelihood, Syst. Biol, vol.52, issue.5, pp.696-704, 2003.

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

J. Hedge, S. J. Lycett, and A. Rambaut, Real-time characterization of the molecular epidemiology of an influenza pandemic, Biol. Lett, vol.9, p.20130331, 2013.

S. B. Hedges and S. Kumar, The timetree of life, 2009.

W. Jetz, G. H. Thomas, J. B. Joy, D. W. Redding, K. Hartmann et al., Global distribution and conservation of evolutionary distinctness in birds, Curr. Biol, vol.24, issue.9, pp.919-930, 2014.

D. M. Lambert, P. A. Ritchie, C. D. Millar, B. Holland, A. J. Drummond et al., Rates of evolution in ancient DNA from Adelie penguins, Science, vol.295, pp.2270-2273, 2002.

C. H. Langley and W. Fitch, An examination of the constancy of the rate of molecular evolution, J. Mol. Evol, vol.3, pp.161-177, 1974.

V. Lefort, R. Desper, and O. Gascuel, FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program, Mol. Biol. Evol, vol.32, pp.2798-2800
URL : https://hal.archives-ouvertes.fr/lirmm-01283927

P. Lemey, M. Suchard, and A. Rambaut, Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatialtemporal model for the global spread of H1N1pdm, PLoS Curr, vol.1, p.1031, 2009.

T. Lepage, D. Bryant, H. Philippe, and N. Lartillot, A general comparison of relaxed molecular clock models, Mol. Biol. Evol, vol.24, pp.2669-2680, 2007.
URL : https://hal.archives-ouvertes.fr/lirmm-00193697

R. Mourad, F. Chevennet, D. T. Dunn, E. Fearnhill, V. Delpech et al., A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK, AIDS, vol.500, pp.15-00106, 2015.
URL : https://hal.archives-ouvertes.fr/lirmm-01348643

K. G. Murty, Linear complementarity, linear and nonlinear programming, Sigma Series in Applied Mathematics, vol.3, pp.447-448, 1988.

J. Nocedal and S. J. Wright, Numerical optimization, Chapter 16, pp.455-468, 2006.

O. T. O'meara, Introduction to quadratic forms, 2000.

D. Posada and K. A. Crandall, Evaluation of methods for detecting recombination from DNA sequences: Computer simulations, PNAS, vol.98, issue.24, pp.13757-13762, 2001.

A. Rambaut, Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies, Bioinformatics, vol.16, issue.4, pp.395-399, 2000.

A. Rambaut, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Appl. Biosci, vol.13, pp.235-238, 1997.

A. Rambaut and E. Holmes, The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic, PLoS Curr, vol.1, p.1003, 2009.

B. Rannala and Z. Yang, Inferring speciation times under an episodic molecular clock, Syst. Biol, vol.56, issue.3, pp.453-466, 2007.

M. D. Rasmussen and M. Kellis, Unified modeling of gene duplication, loss, and coalescence using a locus tree, Genome Res, vol.22, issue.4, pp.755-765, 2012.

F. Ronquist, S. Klopfstein, L. Vilhelmsen, S. Schulmeister, D. L. Murray et al., A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera, Syst. Biol, vol.61, issue.6, pp.973-999, 2012.

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, issue.4, pp.406-425, 1987.

M. J. Sanderson, A nonparametric approach to estimating divergence times in the absence of rate constancy, Mol. Biol. Evol, vol.14, pp.1218-1231, 1997.

M. J. Sanderson, Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach, Mol. Biol. Evol, vol.19, pp.101-109, 2002.

M. J. Sanderson, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, vol.19, issue.2, pp.301-302, 2003.

R. Shankarappa, J. B. Margolick, S. J. Gange, A. G. Rodrigo, D. Upchurch et al., Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection, J. Virol, vol.73, pp.10489-10502, 1999.

S. A. Smith and B. C. O'meara, treePL: divergence time estimation using penalized likelihood for large phylogenies, Bioinformatics, vol.28, pp.2689-2690, 2012.

R. Sokal and C. Michener, A statistical method for evaluating systematic relationships, Kans. Univ. Sci. Bull, vol.38, pp.1409-1438, 1958.

T. Stadler, Sampling-through-time in birth-death trees, J. Theor. Biol, vol.267, pp.396-404, 2010.

R. E. Tarjan, Data structures and network algorithms, 1983.

K. Tamura, F. U. Battistuzzi, P. Billing-ross, O. Murillo, A. Filipski et al., Estimating divergence times in large molecular phylogenies, PNAS, vol.109, pp.19333-19338, 2012.

J. L. Thorne, H. Kishino, and S. Painter, Estimating the rate of evolution of the rate of molecular evolution, Mol. Biol. Evol, vol.15, issue.12, pp.1647-1657, 1998.

J. L. Thorne and H. Kishino, Divergence time and evolutionary rate estimation with multilocus data, Syst. Biol, vol.51, issue.5, pp.689-702, 2002.

E. M. Volz, K. Koelle, and T. Bedford, Viral phylodynamics, PLoS Comput. Biol, vol.9, p.1002947, 2013.

X. Xia and Q. Yang, A distance-based least-square method for dating speciation events, Mol. Phylogenet. Evol, vol.59, pp.342-353, 2011.

Z. Yang, J. D. O'brien, X. Zheng, H. Q. Zhu, and Z. S. She, Tree and rate estimation by local evaluation of heterochronous nucleotide data, Bioinformatics, vol.23, issue.2, pp.169-176, 2007.