Literature

Authors	Year	Title
W. C. Wheeler	1996	Optimization alignment: the end of multiple sequence alignment in phylogenetics?
W. Wheeler	1999	Fixed character states and the optimization of molecular sequence data
G. Giribet	2001	Exploring the behavior of POY, a program for direct optimization of molecular data
D. A. Janies, Wheeler W. C.	2001	Efficiency of parallel direct optimization
W. Wheeler	2001	Homology and the optimization of DNA sequence data
S. Schulmeister, Wheeler, W. C., Carpenter, J. M.	2002	Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis
N. P. Giannini, Simmons N. B.	2003	A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes
W. C. Wheeler	2003	Iterative pass optimization of sequence data
W. C. Wheeler	2003	Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search
J. S. Sparks, Smith W. L.	2004	Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae)
S. Bertelli, Giannini N. P.	2005	A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences
N. P. Giannini, Simmons N. B.	2005	Conflict and congruence in a combined DNA–morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)
G. Giribet	2005	Generating implied alignments under direct optimization using POY
W. C. Wheeler	2006	Dynamic homology and the likelihood criterion