D. Aldous, Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today, Stat. Sci, vol.16, issue.23, 2001.

D. Aldous and J. A. , Reversible Markov chains and random walks on graphs, 2010.

J. Chang, Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency, Mathematical Biosciences, vol.137, issue.1, p.51, 1996.
DOI : 10.1016/S0025-5564(96)00075-2

R. Desper and O. Gascuel, Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting, Molecular Biology and Evolution, vol.21, issue.3, 2004.
DOI : 10.1093/molbev/msh049

URL : https://hal.archives-ouvertes.fr/lirmm-00108569

W. Evans, C. Kenyon, Y. Peres, and L. J. Schulman, Broadcasting on trees and the Ising model, The Annals of Applied Probability, vol.10, issue.2, p.410, 2000.
DOI : 10.1214/aoap/1019487349

J. M. Koshi and R. A. Goldstein, Models of natural mutations including site heterogeneity, Proteins, vol.32, issue.289, 1998.

N. Lartillot and H. Philippe, A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process, Molecular Biology and Evolution, vol.21, issue.6, p.1095, 2004.
DOI : 10.1093/molbev/msh112

URL : https://hal.archives-ouvertes.fr/lirmm-00108585

G. Li, J. Ma, and L. Zhang, Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies: Elimination Is Better than Insertion, PLoS ONE, vol.5, issue.2, p.8985, 2010.
DOI : 10.1371/journal.pone.0008985.s002

D. A. Liberles, Ancestral Sequence Reconstruction, 2007.
DOI : 10.1093/acprof:oso/9780199299188.001.0001

A. Mckenzie and M. A. Steel, Properties of phylogenetic trees generated by Yuletype speciation models, Math. Biosci, vol.170, p.91, 2001.

W. P. Maddison, Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees, Syst. Biol, pp.44-474, 1995.

B. A. Salisbury and J. Kim, Ancestral State Estimation and Taxon Sampling Density, Systematic Biology, vol.50, issue.4, 2001.
DOI : 10.1080/106351501750435103

E. Sober, Temporally Asymmetric Inference in a Markov Process, Philosophy of Science, vol.58, issue.3, p.398, 1991.
DOI : 10.1086/289624

E. Sober, Evolution and Evidence: The Logic Behind the Science, 2008.
DOI : 10.1017/CBO9780511806285

M. A. Steel, Distributions on bicoloured evolutionary trees, Bulletin of the Australian Mathematical Society, vol.41, issue.01, 1989.
DOI : 10.1017/S0004972700017950

M. Steel and D. Penny, Maximum parsimony and the phylogenetic information in multi-state characters, Parsimony, Phylogeny and Genomics, p.163, 2005.

M. A. Steel and L. A. Székely, Teasing Apart Two Trees, Combinatorics, Probability and Computing, vol.6, issue.06, p.903, 2007.
DOI : 10.1016/S0166-218X(98)00080-8

D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, Phylogenetic inference, Molecular Systematics, 1996.

C. Tuffley and M. A. Steel, Links between maximum likelihood and maximum parsimony under a simple model of site substitution, Bulletin of Mathematical Biology, vol.39, issue.3, p.581, 1997.
DOI : 10.1007/BF02459467

J. Zhang and M. Nei, Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods, Journal of Molecular Evolution, vol.141, issue.S1, pp.44-139, 1997.
DOI : 10.1007/PL00000067

L. X. Zhang, J. Shen, J. L. Yang, and G. L. Li, Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees, Bulletin of Mathematical Biology, vol.44, issue.7
DOI : 10.1007/s11538-010-9505-8