Literature

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