Les articles et les livres de cette liste ont tous été utiles à l'élaboration du logiciel PhyloGraphe. Les PDF de ces articles et de certains livres sont disponibles gratuitement à l'intention des enseignants et des étudiants qui voudraient approfondir ces sujets.
La non-polarisation à priori des caractères
Meacham C.A. (1984). The Role of Hypothesized Direction of Characters in the Estimation of Evolutionary History. Taxon, 33(1):26-38. Ouvrir
Meacham C.A. (1986). More about Directed Characters: A Reply to Donoghue and Maddison. Taxon, 35(3):538-40. Ouvrir
Nixon K.C., et Carpenter J.M. (1993). On outgroups. Cladistics, 9(4):413-426. Ouvrir
Sneath P.H.A. (1995). Thirty Years of Numerical Taxonomy. Syst Biol, 44(3):281-98. Ouvrir
Nixon K.C., et Carpenter J.M. (2012). On homology. Cladistics, 28(2):160-9. Ouvrir
Nixon K.C., et Carpenter J.M. (2012). More on homology. Cladistics, 28(3):225-6. Ouvrir
Nixon K.C., et Carpenter J.M. (2012). More on errors. Cladistics, 28(5):539-44. Ouvrir
Nixon K.C., et Carpenter J.M. (2013). More on absences. Cladistics, 29(1):1-6. Ouvrir
Le codage des caractères
Hawkins J.A., Hughes C.E., et Scotland R.W. (1997). Primary Homology Assessment, Characters and Character States. Cladistics, 13(3):275-83. Ouvrir
Strong E.E., et Lipscomb D. (1999). Character Coding and Inapplicable Data. Cladistics, 15(4):363-71. Ouvrir
Simmons M.P., et Ochoterena H. (2000). Gaps as Characters in Sequence-Based Phylogenetic Analyses. Syst Biol, 49(2):369-81. Ouvrir
Brazeau M.D. (2011). Problematic character coding methods in morphology and their effects. Biological Journal of the Linnean Society, 104(3):489-98. Ouvrir
Le mappage des caractères sur les cladogrammes
Farris J.S. (1970). Methods for Computing Wagner Trees. Syst Zool, 19(1):83-92. Ouvrir
Fitch W.M. (1971). Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology. Syst Zool, 20(4):406-16. Ouvrir
Sankoff D., et Rousseau P. (1975). Locating the vertices of a Steiner tree in an arbitrary metric space. Math Program, 9(1):240-6. Ouvrir
Swofford D.L., Maddison W.P. (1987). Reconstructing ancestral character states under Wagner parsimony. Math Biosci, 87(2):199-229. Ouvrir
Brazeau M.D., Guillerme T., et Smith M.R. (2019). An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data. Syst Biol, 68(4):619–31. Ouvrir
L'analyse de compatibilité et le critère de parcimonie
Meacham C.A. (1981). A Manual Method for Character Compatibility Analysis. Taxon, 30(3):591-600. Ouvrir
Meacham C.A., et Estabrook G.F. (1985). Compatibility Methods in Systematics. Ann Rev Ecol Syst, 6:431-46. Ouvrir
Prager E.M., et Wilson A.C. (1988). Ancient Origin of Lactalbumin from Lysozyme: Analysis of DNA and Amino Acid Sequences. J Mol Evol, 27(4):326-35. Ouvrir
Farris J.S. (1989). The retention index and the rescaled consistency index. Cladistics, 5(4):417-9. Ouvrir
Estabrook G.F. (2008). Fifty years of character compatibility concepts at work. J Syst Evol, 46(2):109-29. Ouvrir
Scotland R.W., et Steel M. (2015). Circumstances in Which Parsimony but not Compatibility will be Provably Misleading. Syst Biol 64(3):492–504. Ouvrir
Goloboff P.A., et Arias J.S. (2019). Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion. Cladistics 35(6):695-716. Ouvrir
Les distances phylogénétiques
La distance AAF (basée sur les k-mères)
Fan H., Ives A.R., Surget-Groba Y., et Cannon C.H. (2015). An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. BMC Genomics, 16:522. Ouvrir
La distance LogDet
Lockhart P.J., Steel M.A., Hendy M.D., et Penny D. (1994). Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol, 11(4):605-12. Ouvrir
Tamura K., et Kumar S. (2002). Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol, 19(10):1727-36. Ouvrir
Thollesson M. (2004). LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics, 20(3):416-18. Ouvrir
La distance JC69
Jukes T.H., et Cantor C.R. (1969). Evolution of Protein Molecules. In: Munro H.N. (Ed.), Mammalian Protein Metabolism, Academic Press, vol 3, 21-132. Ouvrir
La distance K2P
Kimura M. (1980). A Simple Method for Estimating Evolutionary Rates of Base Substitutions Through Comparative Studies of Nucleotide Sequences. J Mol Evol, 16(2):111-20. Ouvrir
La distance T92
Tamura K. (1992). Estimation of the Number of Nucleotide Substitutions When There Are Strong Transition-Transversion and G+C-Content Biases. Mol Biol Evol, 9(4):678-87. Ouvrir
La distance F84
Tateno Y., Takezaki N., et Nei M. (1994). Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol, 11(2):261-77. Ouvrir
La distance TN93
Tamura K., et Nei M. (1993). Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees. Mol Biol Evol, 10(3):512-26. Ouvrir
La distance empirique de Kimura
Kimura M. (1983). The Neutral Theory of Molecular Evolution, Cambridge University Press, 367 pages. Ouvrir
(la formule se trouve à la page 75)
La distance Scoredist
Henikoff S., et Henikoff J.G. (1992). Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA, 89(22):10915-19. Ouvrir
Jones D.T., Taylor W.R., et Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Bioinformatics, 8(3):275-82. Ouvrir
Sonnhammer E.L.L., et Hollich V. (2005). Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinformatics, 6:108. Ouvrir
La construction de dendrogrammes d'après des distances
Sneath P.H.A., et Sokal R.R. (1973). Numerical Taxonomy: The Principles and Practice of Numerical Classification, 2e éd., San Francisco : W.H. Freeman, 573 pages.
Saitou N., et Nei M. (1987). The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol Biol Evol, 4(4):406-25. Ouvrir
Gascuel O. (1994). A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances. Mol Biol Evol 11(6):961-3. Ouvrir
Gascuel O., et Steel M. (2006). Neighbor-Joining Revealed. Mol Biol Evol 23(11):1997–2000. Ouvrir
Tria F.D.K., Landan G., et Dagan T. (2017). Phylogenetic rooting using minimal ancestor deviation. Nat Ecol Evol 1:0193. Ouvrir
Les formats de données
Maddison D.R., Swofford D.L., et Maddison W.P. (1997). Nexus: An Extensible File Format for Systematic Information. Syst Biol, 46(4):590-621. Ouvrir
Ouvrages généralistes
Aubert D. (2017). Classer le vivant - Les perspectives de la systématique évolutionniste moderne, Éditions Ellipses, 498 pages. Voir les détails