Literature

AuthorsYearsort descendingTitle
A. W. F. Edwards, Cavalli-Sforza L. L.1964Reconstruction of evolutionary trees
J. S. Farris1973A probability model for inferring evolutionary trees
J. Felsenstein1978Cases in which parsimony or compatibility methods will be positively misleading
C. Lanave, Preparata, , G., Saccone, C., Serio, G.1984A new method for calculating evolutionary substitution rates
S. Tavaré1986Some probabilistic and statistical problems in the analysis of DNA sequences
M. D. Hendy, Penny D.1989A framework for the quantitative study of evolutionary trees
N. Goldman1990Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis
F. Rodriguez, Oliver, , J. F., Marin, A., Medina, J. R.1990The general stochastic model of nucleotide substitutions
K. Tamura, Nei M.1993Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
Z. Yang1993Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
P. J. Lockhart, Steel, M. A., Hendy, M. D., Penny, D.1994Recovering evolutionary trees under a more realistic model of sequence evolution
Z. Yang1994Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
X. Gu1995Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
Z. Yang1996Phylogenetic analysis using parsimony and likelihood methods
P. O. Lewis1998Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
P. J. Wagner1998A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
N. Takezaki, Gojobori T.1999Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
P. O. Lewis2001Phylogenetic systematics turns over a new leaf
P. O. Lewis2001A likelihood approach to estimating phylogeny from discrete morphological character data
D. L. Swofford, Waddell, P. J., Huelsenbeck, J. P., Foster, P. G., Lewis, P. O., Rogers, J. S.2001Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
L. Bromham, Woolfit, M., Lee, M. S. Y., Rambaut, A.2002Testing the relationship between morphological and molecular rates of change along phylogenies
H. Dreyer, Steiner, G., Harper, E. M.2003Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences
S. Guindon, Gascuel O.2003A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
F. E. Anderson, Swofford D. L.2004Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
D. Posada, Buckley T. R.2004Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests
J. Faivovich, Haddad, C. F. B., Garcia, P. C. A., Frost, D. R., Campbell, J. A.2005Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision
M. Spencer, Susko, E., Roger, A. J.2005Likelihood, parsimony, and heterogeneous evolution
J. Sullivan, Abdo, Z., Joyce, P., Swofford, D. L.2005Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation
A. Stamatakis2006RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
W. C. Wheeler2006Dynamic homology and the likelihood criterion
A. Stamatakis, Blagojevic, F., Nikolopoulos, D. S., Antonopoulos, C. D.2007Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM Cell
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith