M. Arenas, C. Weber, D. A. Liberles, and U. Bastolla, ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability, Syst Biol, vol.66, pp.1054-1064, 2017.

J. Beaulieu, B. O'meara, and M. Donoghue, Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms, Syst. Biol, vol.62, pp.725-737, 2013.

J. Brown, Probabilities of evolutionary trees, Syst. Biol, vol.43, pp.78-91, 1994.

M. Casanellas and M. Steel, Phylogenetic mixtures and linear invariants for equal input models, J. Math. Biol, vol.74, pp.1107-1138, 2017.

T. Cover and J. A. Thomas, Elements of information theory, 1991.

G. Dudas, L. M. Carvalho, T. Bedford, A. J. Tatem, G. Baele et al., Nature, vol.544, pp.309-315

C. J. Edwards, M. A. Suchard, P. Lemey, J. J. Welch, I. Barnes et al., Ancient hybridization and an Irish origin for the modern polar bear matriline, Curr. Biol, vol.21, pp.1251-1258, 2011.

W. Evans, C. Kenyon, Y. Peres, and L. Schulman, Broadcasting on trees and the Ising model, Ann. Appl. Probab, vol.10, pp.410-433, 2000.

J. Felsenstein, Inferring phylogenies, 2004.

O. Gascuel and M. Steel, Inferring ancestral sequences in taxon-rich phylogenies, Math. Biosci, vol.227, pp.125-135, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511772

O. Gascuel and M. Steel, Predicting the ancestral character changes in a tree is typically easier than predicting the root state, Syst. Biol, vol.63, pp.421-435, 2014.
URL : https://hal.archives-ouvertes.fr/lirmm-01397019

, New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins, New Phytol, vol.193, pp.304-312, 2012.

S. Guiasu, Information theory with applications, 1977.

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

E. Harding, The probabilities of rooted-tree shapes generated by random bifurcation, Adv. Appl. Probab, vol.3, pp.44-77, 1971.

M. Hasegawa, H. Kishino, and T. Yano, Dating of human-ape splitting by a molecular clock of mitochondrial DNA, J. Mol. Evol, vol.22, pp.160-174, 1985.

P. D. Heintzman, D. Froese, J. W. Ives, A. E. Soares, G. D. Zazula et al., Bison phylogeography constrains dispersal and viability of the Ice Free Corridor in western Canada, Proc. Natl. Acad. Sci. USA, vol.113, pp.8057-8063, 2016.

W. Heisenberg, Uber den anschaulichen inhalt der quantentheoretischen kinematik und mechanik, Z. Phys, vol.43, pp.172-198, 1927.

S. A. Ishikawa, A. Zhukova, W. Iwasaki, and O. Gascuel, A fast likelihood method to reconstruct and visualize ancestral scenarios, 2019.

, Mol. Biol. Evol

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

P. Lemey, V. N. Minin, F. Bielejec, S. Pond, and M. A. Suchard, A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection, Bioinformatics, vol.28, pp.3248-3256, 2012.

P. Lemey, A. Rambaut, T. Bedford, N. Faria, F. Bielejec et al., Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2, PLoS Pathog, vol.10, p.1003932, 2014.

P. Lemey, A. Rambaut, A. Drummond, and M. Suchard, Bayesian phylogeography finds its roots, PLoS Comput. Biol, vol.5, p.1000520, 2009.

D. Liberles, Ancestral sequence reconstruction, 2007.

D. R. Maddison, Phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters, Ann. Rev. Entomol, vol.39, pp.267-292, 1994.

B. Marazzi, C. Ané, M. F. Simon, A. Delgado-salinas, M. Luckow et al., Locating evolutionary precursors on a phylogenetic tree, Evolution, vol.66, pp.3918-3930, 2012.

T. Matsumoto, H. Akashi, and Z. Yang, Evaluation of ancestral sequence reconstruction methods to infer nonstationary patterns of nucleotide substitution, Genetics, vol.200, pp.873-890, 2015.

E. Mossel and Y. Peres, Information flow on trees, Ann. Appl. Probab, vol.13, pp.817-844, 2003.

E. Mossel and M. Steel, How much can evolved characters tell us about the tree that generated them?, Mathematics of evolution and phylogeny, pp.384-412, 2005.

N. A. Rosenberg, The mean and variance of the numbers of r-pronged nodes and r-caterpillars in Yule-generated genealogical trees, Ann. Combin, vol.10, pp.129-146, 2006.

C. Semple and M. Steel, Phylogenetics, 2003.

T. Stadler and A. Lambert, Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theor, Popul. Biol, vol.90, pp.113-128, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00936070

T. Stadler and M. Steel, Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models, J. Theor. Biol, vol.297, pp.33-40, 2012.

J. Wakeley, Coalescent theory: an introduction, 2009.

G. Werner, W. Cornwell, J. Sprent, J. Kattge, and E. Kiers, A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms, Nat. Commun, vol.5, p.4087, 2014.

Z. Yang, PAML 4: phylogenetic analysis by maximum likelihood, Mol. Biol. Evol, vol.24, pp.1586-1591, 2007.

Y. G. , A mathematical theory of evolution: Based on the conclusions of Dr, Trans. R. Soc. Lond. B, vol.213, pp.21-87, 1925.