Literature

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