Authorssort descendingYearTitle
L. Aagesen2005Direct optimization, affine gap costs, and node stability
S. Bertelli, Giannini N. P.2005A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences
Wheeler, W. C.2002Optimization alignment: down, up, error, and improvements
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
D. R. Frost, Rodrigues, M. T., Grant, T., Titus, T. A.2001Phylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology
N. P. Giannini, Simmons N. B.2005Conflict and congruence in a combined DNA–morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)
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
G. Giribet2005Generating implied alignments under direct optimization using POY
G. Giribet2001Exploring the behavior of POY, a program for direct optimization of molecular data
G. Giribet, Wheeler W. C.2002On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data
G. Giribet, Wheeler W. C.2002On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data
G. Hormiga, Arnedo, M., Gillespie, R. G.2003Speciation on a conveyor belt: sequential colonization of the Hawaiian Islands by Orsonwelles spiders (Araneae, Linyphiidae)
D. Janies2001Phylogenetic relationships of extant echinoderm classes
D. Janies, Hill, A. W., Guralnick, R., Habib, F., Waltari, E., Wheeler, W. C.2007Genomic analysis and geographic visualization of the spread of avian influenza (H5N1)
D. A. Janies, Wheeler W. C.2001Efficiency of parallel direct optimization
J. De Laet2005Parsimony and the problem of inapplicables in sequence data
F. Legendre, Whiting, M. F., Bordereau, C., Cancello, Eliana, M., Evans, T. A., Grandcolas, P.2008The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors
A. J. Phillips2006Homology assessment and molecular sequence alignment
S. Schulmeister, Wheeler, W. C., Carpenter, J. M.2002Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
W. L. Smith, Smith, K. R., Wheeler, W. C.2009Mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and rearrangement data
W. L. Smith, Wheeler W. C.2004Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data
J. S. Sparks, Smith W. L.2004Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae)
W. C. Wheeler2006Dynamic homology and the likelihood criterion
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
W. Wheeler2001Homology and the optimization of DNA sequence data
W. Wheeler1999Fixed character states and the optimization of molecular sequence data
W. C. Wheeler1996Optimization alignment: the end of multiple sequence alignment in phylogenetics?
W. C. Wheeler1995Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data
W. C. Wheeler2001Homology and DNA sequence data
Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith