Authorssort descendingYearTitle
L. Aagesen2005Direct optimization, affine gap costs, and node stability
M. W. Allard, Farris, J. S., Carpenter, J. M.1999Congruence among mammalian mitochondrial genes
F. E. Anderson, Swofford D. L.2004Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
L. C. Anderson, Roopnarine P. D.2005Role of constraint and selection in the morphologic evolution of Caryocorbula (Mollusca: Corbulidae) from the Caribbean Neogene
K. D. Angielczyk2002A character-based method for measuring the fit of a cladogram to the fossil record
K. D. Angielczyk, Fox D. L.2006Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record
Q. D. Atkinson, Gray R. D.2005Curious parallels and curious connections: phylogenetic thinking in biology and historical linguistics
Q. D. Atkinson, Meade, A., Venditti, C., Greenhill, S. J., Pagel, M.2007Languages evolve in punctuational bursts
R. H. Baker, DeSalle R.1997Multiple sources of character information and the phylogeny of Hawaiian drosophilids
R. H. Baker, Yu, X., DeSalle, R.1998Assessing the relative contribution of molecular and morphological characters in sumultaneous analysis trees
F. K. Barker, Lutzoni F. M.2002The utility of the incongruence length difference test
T. G. Barraclough, Nee S.2001Phylogenetics and speciation
T. G. Barraclough, Vogler A. P.2000Detecting the geographical pattern of speciation from species-level phylogenies
M. J. Benton, Hitchin, R., Wills, M. A.1999Assessing congruence between cladistic and stratigraphic data
M. Björklund1999Are third positions really that bad? A test using vertebrate cytochrome b
F. Bokma2008Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny
F. Bokma2008Bayesian estimation of speciation and extinction probabilities from (in)complete phylogenies
F. Bokma2003Testing for equal rates of cladogenesis in diverse taxa
F. Bokma2002Detection of punctuated equilibrium from molecular phylogenies
K. Bremer1988The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction
C. A. Brochu, Sumrall, C. D., Theodor, J. M.2004When clocks (and communities) collide: estimating divergence from molecules and the fossil record
L. Bromham, Woolfit, M., Lee, M. S. Y., Rambaut, A.2002Testing the relationship between morphological and molecular rates of change along phylogenies
J. J. Bull, Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L., Waddell, P. J.1993Partitioning and combining data in phylogenetic analysis
K. M. A. Chan, Moore B. R.2005SymmeTREE: whole-tree analysis of differential diversification rates
W. C. Clyde, Fisher D. C.1997Comparing the fit of stratigraphic and morphological data in phylogenetic analysis
D. J. Colgan, McLauchlan, A., Wilson, G. D. F., Livingston, S. P., Edgecomb, G. D., Macaranas, J., Cassis, G., Gray, M. R.1998Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution
G. C. Conant, Lewis P. O.2001Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference
J. Cracraft, Eldredge N.1979Phylogenetic analysis and paleontology. Proceedings of a symposium entitled "Phylogenetic Models," convened at the North American Paleontological Convention 2, Lawrence, Kansas, August 8, 1977
Eldredge, N.1979Cladism and common sense
M. P. Cummings, Neel, M. C., Shaw, K. L.2008A genealogical approach to quantifying lineage divergence
C. W. Cunningham1997Can three incongruence tests predict when data should be combined?
P. Darlu, Lecointre G.2002When does the incongruence length difference test fail?
B. Dayrat2005Ancestor-descendant relationships and the reconstruction of the Tree of Life
R. DeSalle, Freedman, T., Prager, E. M., Wilson, A. C.1987Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila
M. T. Dixon, Hillis D. M.1993Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis
K. Dolphin, Belshaw, R., Orme, C. D. L., Quicke, D. L. J.2000Noise and incongruence: interpreting results of the incongruence length difference test
M. Dowton, Austin A. D.2002Increased incongruence does not necessarily indicate increased phylogenetic accuracy—the behavior of the incongruence length difference test in mixed-model analysis
A. W. F. Edwards, Cavalli-Sforza L. L.1964Reconstruction of evolutionary trees
N. Eldredge, Cracraft J.1980Phylogenetic patterns and the evolutionary process: method and theory in comparative biology
O. R. P. Bininda-Emonds2004The evolution of supertrees
D. P. Faith, Trueman J. W. H.2001Towards an inclusive philosophy for phylogenetic inference
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. Farris1989The retention index and the rescaled consistency index
J. S. Farris, Albert, V. A., Källersjö, M., Lipscomb, D., Kluge, A. G.1996Parsimony jackknifing outperforms neighbor-joining
J. S. Farris1983The logical basis of phylogenetic analysis
J. S. Farris1973A probability model for inferring evolutionary trees
J. S. Farris1970Methods for computing Wagner trees
J. S. Farris1969A successive approximations approach to character weighting
J. S. Farris, Källersjö, M., Kluge, A. G., Bult, C.1995Constructing a significance test for congruence
J. S. Farris, Källersjö, M., Kluge, A. G., Bult, C.1995Testing significance of incongruence


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