Literature

AuthorsYearsort descendingTitle
J. S. Farris1989The retention index and the rescaled consistency index
K. Bremer1990Combinable component consensus
W. C. Wheeler1990Nucleic acid sequence phylogeny and random outgroups
M. Källersjö, Farris, J. S., Kluge, A. G., Bult, C.1992Skewness and permutation
A. G. Kluge, Wolf A. J.1993Cladistics: what's in a word?
K. C. Nixon, Carpenter J. M.1993On outgroups
R. D. M. Page1993On describing the shape of rooted and unrooted trees
Z. Skála, Zrzavπ J.1994Phylogenetic reticulations and cladistics: discussion of methodological concepts
J. S. Farris, Källersjö, M., Kluge, A. G., Bult, C.1995Testing significance of incongruence
J. S. Farris, Albert, V. A., Källersjö, M., Lipscomb, D., Kluge, A. G.1996Parsimony jackknifing outperforms neighbor-joining
K. C. Nixon, Carpenter J. M.1996On simultaneous analysis
W. C. Wheeler1996Optimization alignment: the end of multiple sequence alignment in phylogenetics?
J. De Laet, Smets E.1998On the three taxon approach to parsimony analysis
M. E. Siddall1998Stratigraphic fit to phylogenies: a proposed solution
M. W. Allard, Farris, J. S., Carpenter, J. M.1999Congruence among mammalian mitochondrial genes
M. Björklund1999Are third positions really that bad? A test using vertebrate cytochrome b
J. S. Farris1999Likelihood and inconsistency
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
P. A. Goloboff1999Analyzing large data sets in reasonable times: solutions for composite optima
M. Källersjö, Albert, V. A., Farris, J. S.1999Homoplasy increases phylogenetic structure
K. C. Nixon1999The parsimony ratchet, a new method for rapid parsimony analysis
E. E. Strong, Lipscomb D.1999Character coding and inapplicable data
J. W. Wenzel, Siddall M. E.1999Noise
W. Wheeler1999Fixed character states and the optimization of molecular sequence data
W. C. Wheeler1999Measuring topological congruence by extending character techniques
J. S. Farris2000Corroboration versus "strongest evidence"
G. Giribet2001Exploring the behavior of POY, a program for direct optimization of molecular data
P. A. Goloboff, Farris J. S.2001Methods for quick consensus estimation
D. A. Janies, Wheeler W. C.2001Efficiency of parallel direct optimization
W. Wheeler2001Homology and the optimization of DNA sequence data
D. Pol, Norell M. A.2001Comments on the manhattan stratigraphic measure
S. Schulmeister, Wheeler, W. C., Carpenter, J. M.2002Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
J. V. Freudenstein, Pickett, K. M., Simmons, M. P., Wenzel, J. W.2003From basepairs to birdsongs: phylogenetic data in the age of genomics
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
T. Grant, Kluge A. G.2003Data exploration in phylogenetic inference: scientific, heuristic, or neither
W. C. Wheeler2003Iterative pass optimization of sequence data
W. C. Wheeler2003Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search
J. S. Sparks, Smith W. L.2004Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae)
S. Bertelli, Giannini N. P.2005A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences
N. P. Giannini, Simmons N. B.2005Conflict and congruence in a combined DNA–morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)
G. Giribet2005Generating implied alignments under direct optimization using POY
T. Grant, Kluge A. G.2005Stability, sensitivity, science and heurism
W. C. Wheeler2006Dynamic homology and the likelihood criterion
W. C. Wheeler, Ramírez, M. J., Aagesen, L., Schulmeister, S.2006Partition-free congruence analysis: implications for sensitivity analysis
O. Rieppel2008Origins, taxa, names and meanings
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith