Literature

AuthorsYearTitlesort descending
M. Holder, Lewis P. O.2003[TITLE BLANK]
K. D. Angielczyk2002A character-based method for measuring the fit of a cladogram to the fossil record
H. Philippe, Lecointre, G., Lê, H. Lanh Vân, Le Guyader, H.1996A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting
M. D. Hendy, Penny D.1989A framework for the quantitative study of evolutionary trees
M. P. Cummings, Neel, M. C., Shaw, K. L.2008A genealogical approach to quantifying lineage divergence
P. J. Wagner1998A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
P. O. Lewis2001A likelihood approach to estimating phylogeny from discrete morphological character data
C. Lanave, Preparata, , G., Saccone, C., Serio, G.1984A new method for calculating evolutionary substitution rates
J. Hein1989A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given
N. P. Giannini, Simmons N. B.2003A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes
J. S. Farris1973A probability model for inferring evolutionary trees
A. Rzhetsky, Nei M.1992A simple method for estimating and testing minimum-evolution trees
M. Kimura1980A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
S. Guindon, Gascuel O.2003A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
M. K. Kuhner, Felsenstein J.1994A simulation comparison of phylogeny algorithms under equaland unequal evolutionary rates
J. S. Farris1969A successive approximations approach to character weighting
N. Saitou1989A theoretical study of the underestimation of brench length by the maximum parsimony principle
J. Hein1989A tree reconstruction method that is economical in the number of pairwise comparisons used
J. B. Losos, Ricklefs R. E.2009Adaptation and diversification on islands
T. Jiang, Lawler, E. L., Wang, A.1994Aligning sequences via an evolutionary tree: complexity and approximation
F. Krauss1988An empirical evaluation of the use of the ontogenetic polarization criterion in phylogenetic inference
O. Gotoh1982An improved algorithm for matching biological sequences
X. Xia, Xie, Z., Salemi, M., Chen, L., Wang, Y.2003An index of substitution saturation and its application
P. A. Goloboff1999Analyzing large data sets in reasonable times: solutions for composite optima
B. Dayrat2005Ancestor-descendant relationships and the reconstruction of the Tree of Life
D. M. Hillis, Huelsenbeck, J. P., Cunningham, C. W.1994Application and accuracy of molecular phylogenies
M. Björklund1999Are third positions really that bad? A test using vertebrate cytochrome b
M. J. Benton, Hitchin, R., Wills, M. A.1999Assessing congruence between cladistic and stratigraphic data
R. H. Baker, Yu, X., DeSalle, R.1998Assessing the relative contribution of molecular and morphological characters in sumultaneous analysis trees
F. Bokma2008Bayesian estimation of speciation and extinction probabilities from (in)complete phylogenies
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
A. Stamatakis, Ludwig, T., Meier, H.2005BRAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
C. W. Cunningham1997Can three incongruence tests predict when data should be combined?
J. Felsenstein1978Cases in which parsimony or compatibility methods will be positively misleading
E. E. Strong, Lipscomb D.1999Character coding and inapplicable data
Eldredge, N.1979Cladism and common sense
M. A. Larkin, Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G.2007Clustal W and Clustal X version 2.0
D. L. Sullivan1996Combining data with different distributions of among-site variation
D. Pol, Norell M. A.2001Comments on the manhattan stratigraphic measure
L. Ricardo L. Simone, Wilkinson S.2008Comparative morphological study of some Tellinidae from Thailand (Bivalvia: Tellinoidea)
W. C. Clyde, Fisher D. C.1997Comparing the fit of stratigraphic and morphological data in phylogenetic analysis
J. A. Finarelli, Clyde W. C.2002Comparing the gap excess ratio and the retention index of the stratigraphic character
H. Philippe, Sörhannus, U., Baroin, A., Perasso, R., Gasse, F., Adoutte, A.1995Comparison of molecular and paleontological data in doatoms suggests a major gap in the fossil record
Z. Yang2006Computational molecular evolution
M. W. Allard, Farris, J. S., Carpenter, J. M.1999Congruence among mammalian mitochondrial genes
M. A. Wills1999Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio
J. S. Farris, Källersjö, M., Kluge, A. G., Bult, C.1995Constructing a significance test for congruence
A. R. Templeton1983Convergent evolution and nonparametric inferences from restriction data and DNA sequences
J. Gatesy, O'Grady, P., Baker, R. H.1999Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa
Q. D. Atkinson, Gray R. D.2005Curious parallels and curious connections: phylogenetic thinking in biology and historical linguistics

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Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith