@article {7809,
	title = {Fixed character states and the optimization of molecular sequence data},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	pages = {379-385},
	keywords = {alignment, phylogenetics, poy},
	author = {Wheeler, Ward}
}
@article {7810,
	title = {Homology and the optimization of DNA sequence data},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {S3-S11},
	keywords = {direct optimization, dna, homology, molecules, phylogenetics, poy},
	author = {Wheeler, Ward}
}
@article {7812,
	title = {Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data},
	journal = {Systematic Biology},
	volume = {44},
	number = {3},
	year = {1995},
	note = {PDF},
	pages = {321-331},
	keywords = {alignment, congruence, phylogenetics, poy, sensitivity, support},
	author = {Wheeler, Ward C.}
}
@article {7813,
	title = {Optimization alignment: the end of multiple sequence alignment in phylogenetics?},
	journal = {Cladistics},
	number = {12},
	year = {1996},
	note = {PDF},
	pages = {1-9},
	keywords = {alignment, direct optimization, optimization, poy},
	author = {Wheeler, Ward C.}
}
@inbook {7816,
	title = {Homology and DNA sequence data},
	booktitle = {The character concept in evolutionary biology},
	year = {2001},
	note = {PDF},
	pages = {303-317},
	publisher = {Academic Press},
	organization = {Academic Press},
	address = {San Diego},
	keywords = {direct optimization, dynamic homology, homology, molecular characters, poy},
	author = {Wheeler, Ward C.},
	editor = {Wagner, G. P.}
}
@inbook {7817,
	title = {Optimization alignment: down, up, error, and improvements},
	booktitle = {Techniques in molecular systematicsand evolution},
	year = {2002},
	note = {DO NOT HAVE},
	pages = {55-69},
	publisher = {Birkh{\"a}user},
	organization = {Birkh{\"a}user},
	address = {Basel},
	keywords = {poy},
	author = {Wheeler, W. C.},
	editor = {DeSalle, Rob and Giribet, G. and Wheeler, W. C.}
}
@article {7818,
	title = {Iterative pass optimization of sequence data},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {254-260},
	keywords = {optimization, phylogenetics, poy},
	author = {Wheeler, Ward C.}
}
@article {7819,
	title = {Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {261-268},
	keywords = {alignment, direct optimization, implied alignment, phylogenetics, poy},
	author = {Wheeler, Ward C.}
}
@article {7820,
	title = {Dynamic homology and the likelihood criterion},
	journal = {Cladistics},
	volume = {22},
	year = {2006},
	note = {PDF},
	pages = {157-170},
	keywords = {homology, ML, phylogenetics, poy},
	author = {Wheeler, Ward C.}
}
@article {7516,
	title = {Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae)},
	journal = {Cladistics},
	volume = {20},
	number = {6},
	year = {2004},
	note = {PDFTimes Cited: 3ArticleEnglishCited References Count: 89896wq},
	month = {DEC},
	pages = {501-517},
	abstract = {Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family-level study. In a strict consensus of 81 equally most-parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only "labroid" lineages, have met with only limited success. (c) The Willi Hennig Society 2004.},
	keywords = {biogeography, direct optimization, dna, evolution, fishes, phylogeny, poy},
	url = {<u><Go to ISI>://000226965400001</u>},
	author = {Sparks, J. S. and Smith, W. L.}
}
@article {7499,
	title = {Mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and rearrangement data},
	journal = {American Museum Novitates},
	volume = {3652},
	year = {2009},
	note = {PDF},
	pages = {1-10},
	keywords = {dna rearrangement, molecular characters, mtDNA, poy},
	author = {Smith, W. L. and Smith, K. R. and Wheeler, W. C.}
}
@article {7500,
	title = {Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {32},
	number = {2},
	year = {2004},
	note = {PDFTimes Cited: 8ReviewEnglishCited References Count: 118838ry},
	month = {AUG},
	pages = {627-646},
	abstract = {Mitochondrial and nuclear DNA sequence data for 105 acanthomorph taxa are analyzed to address questions of scorpaeniform monophyly and relationships. The combination of 3425 aligned base pairs from the mitochondrial small subunit rDNA (12S), large subunit rDNA (16S), and tRNA-Val and the nuclear large subunit rDNA (28S), histone H3, and TMO-4c4 loci are analyzed. Representatives of all scorpaeniform suborders and 32 of 36 scorpaeniform families are included with most suborders represented by multiple species. In addition to 69 scorpaeniform taxa, 36 outgroup taxa, including representatives of most families previously conjectured to be related to the Scorpaeniformes, are analyzed due to serious concerns of scorpaeniform monophyly. The traditionally recognized scorpaeniform fishes are recovered as polyphyletic, The 13 representatives of the Atheriniformes, Blennioidei, Gasterosteoidei, Grammatidae, Notothenioidei, Percidae, Trichodontidae, and Zoarcoidei included in the analysis are all nested within the least inclusive clade that includes all traditionally recognized scorpaeniforms. The scorpaenoid lineage is widely polyphyletic, and its intrarelationships differed significantly from previous hypotheses. The cottoid lineage is paraphyletic with only the presence of the Trichodontidae, as the sister-taxon of the Cottoidei, disrupting the traditional subordinal hypothesis of relationships. (C) 2004 Elsevier Inc. All rights reserved.},
	keywords = {direct optimization, evolution, mtDNA, nuDNA, phylogenetics, poy, taxonomy},
	url = {<u><Go to ISI>://000222732000016</u>},
	author = {Smith, W. L. and Wheeler, W. C.}
}
@article {7421,
	title = {Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis},
	journal = {Cladistics},
	volume = {18},
	number = {5},
	year = {2002},
	note = {PDFTimes Cited: 18ArticleEnglishCited References Count: 88612el},
	month = {OCT},
	pages = {455-484},
	abstract = {The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000-2700 by for each taxon) from the nuclear genes 18S and 285 and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA. sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae + Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))). (C) 2002 Elsevier Science (USA). All rights reserved.},
	keywords = {alignment, congruence, direct optimization, morphology, mtDNA, optimization, phylogenetics, poy, sensitivity},
	url = {<u><Go to ISI>://000179061500001</u>},
	author = {Schulmeister, S. and Wheeler, W. C. and Carpenter, J. M.}
}
@article {7188,
	title = {Homology assessment and molecular sequence alignment},
	journal = {Journal of Biomedical Informatics},
	volume = {39},
	year = {2006},
	note = {reprint},
	pages = {18-33},
	keywords = {alignment, homology, molecules, poy},
	author = {Phillips, Aloysius J.}
}
@article {6757,
	title = {The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {48},
	year = {2008},
	note = {PDF},
	pages = {615-627},
	keywords = {arthropoda, behavior, molecules, phylogenetics, phylogeny, poy, sensitivity, termites},
	author = {Legendre, Fr{\'e}d{\'e}ric and Whiting, Michael F. and Bordereau, Christian and Cancello, Eliana, M. and Evans, Theodore A. and Grandcolas, Philippe}
}
@article {6586,
	title = {Phylogenetic relationships of extant echinoderm classes},
	journal = {Canadian Journal of Zoology},
	volume = {79},
	year = {2001},
	pages = {1232-1250},
	keywords = {echinodermata, phylogenetics, poy, total evidence},
	author = {Janies, Daniel}
}
@article {6588,
	title = {Genomic analysis and geographic visualization of the spread of avian influenza (H5N1)},
	journal = {Systematic Biology},
	volume = {56},
	number = {2},
	year = {2007},
	note = {PDF},
	pages = {321-329},
	keywords = {biogeography, phylogenetics, poy, supermap},
	author = {Janies, Daniel and Hill, Andrew W. and Guralnick, Robert and Habib, Farhat and Waltari, Eric and Wheeler, W. C.}
}
@article {6589,
	title = {Efficiency of parallel direct optimization},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {S71-S82},
	keywords = {direct optimization, phylogenetics, poy},
	author = {Janies, Daniel A. and Wheeler, Ward C.}
}
@article {6529,
	title = {Speciation on a conveyor belt: sequential colonization of the Hawaiian Islands by <i>Orsonwelles</i> spiders (Araneae, Linyphiidae)},
	journal = {Systematic Biology},
	volume = {52},
	number = {1},
	year = {2003},
	note = {PDF},
	pages = {70-88},
	keywords = {arthropoda, biogeography, combined data analyses, molecular clock, partitioned bremer support, phylogeny, poy, sensitivity, speciation},
	author = {Hormiga, Gustavo and Arnedo, Miquel and Gillespie, Rosemary G.}
}
@article {6337,
	title = {Exploring the behavior of POY, a program for direct optimization of molecular data},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {S60-S70},
	keywords = {direct optimization, phylogenetics, poy},
	author = {Giribet, Gonzalo}
}
@article {6338,
	title = {Generating implied alignments under direct optimization using POY},
	journal = {Cladistics},
	volume = {21},
	year = {2005},
	note = {PDF},
	pages = {396-402},
	keywords = {direct optimization, implied alignment, phylogenetics, poy},
	author = {Giribet, Gonzalo}
}
@article {6344,
	title = {On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data},
	journal = {Invertebrate Biology},
	volume = {121},
	number = {4},
	year = {2002},
	note = {PDF},
	pages = {271-324},
	keywords = {18S, 28S, bivalvia, CO1, mollusca, morphology, phylogenetics, phylogeny, poy, systematics},
	author = {Giribet, Gonzalo and Wheeler, Ward C.}
}
@article {6331,
	title = {A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {496-511},
	keywords = {bats, chiroptera, mammalia, molecules, phylogenetics, phylogeny, poy},
	author = {Giannini, Norberto P. and Simmons, Nancy B.}
}
@article {6332,
	title = {Conflict and congruence in a combined DNA{\textendash}morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)},
	journal = {Cladistics},
	volume = {21},
	year = {2005},
	note = {PDF},
	pages = {411-437},
	keywords = {bats, combined data analyses, mammalia, molecules, morphology, phylogeny, poy},
	author = {Giannini, Norberto P. and Simmons, Nancy B.}
}
@article {6307,
	title = {Phylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {21},
	number = {3},
	year = {2001},
	note = {PDF},
	month = {DEC},
	pages = {352-371},
	abstract = {By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus Tropidurus were examined on the basis of both molecular (ca. 1.04 kb of sequences from 12S rDNA, valine tDNA, and 16S rDNA) and morphological (93 characters) data. Although equal weighting of all parsimony cost functions logically must maximize descriptive efficiency and explanatory power of all evidence, a sensitivity analysis demonstrated that equal weighting of indels, transitions, transversions, and morphological change provided the most congruent solution between the molecular and the morphological data partitions. The position of Uranoscodon is resolved as the sister taxon of the remaining members of the Tropidurinae. Plica, Uracentron, and Strobilurus, previously considered synonyms of Tropidurus, are resurrected; the group of these three genera form the sister taxon of the former Tropidurus nanuzae group (herein named Eurolophosaurus) plus Tropidurus sensu stricto (composed of the T. bogerti, T. semitaeniatus, T. spinulosus, and T. torquatus groups, herein diagnosed). (C) 2001 Elsevier Science.},
	keywords = {alignment, phylogenetics, poy, sensitivity},
	url = {<u><Go to ISI>://000173251300003</u>},
	author = {Frost, Darrel R. and Rodrigues, Miguel T. and Grant, Taran and Titus, Tom A.}
}
@article {6243,
	title = {Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision},
	journal = {Bulletin of the American Museum of Natural History},
	volume = {294},
	year = {2005},
	note = {PDF},
	pages = {1-240},
	keywords = {affine gap costs, ML, parsimony, phylogenetics, poy},
	author = {Faivovich, Juli{\'a}n and Haddad, C{\'e}lio F. B. and Garcia, Paulo C. A. and Frost, Darrel R. and Campbell, Jonathan A.}
}
@inbook {6133,
	title = {Parsimony and the problem of inapplicables in sequence data},
	booktitle = {Parsimony, phylogeny, and genomics},
	year = {2005},
	note = {PDF},
	pages = {81{\textendash}116},
	publisher = {Oxford University Press},
	organization = {Oxford University Press},
	keywords = {parsimony, phylogenetics, phylogeny, poy},
	author = {De Laet, J.},
	editor = {Albert, V. A.}
}
@article {5851,
	title = {A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences},
	journal = {Cladistics},
	volume = {21},
	year = {2005},
	note = {PDF},
	pages = {209-239},
	keywords = {aves, biogeography, character evolution, combined data analyses, molecules, morphology, mtDNA, phylogeny, poy},
	author = {Bertelli, Sara and Giannini, Norberto P.}
}
@article {5697,
	title = {Direct optimization, affine gap costs, and node stability},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {36},
	number = {3},
	year = {2005},
	note = {PDFTimes Cited: 0ArticleEnglishCited References Count: 57960lh},
	month = {SEP},
	pages = {641-653},
	abstract = {The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions. Robustness to changes in cost sets is measured as number of successive changes that can be made in a given cost set before a specific clade is lost. The changes are in all cases base change cost, gap penalties, and adding/removing/changing affine gap costs. When combining data partitions, the number of clades that appear in the entire parameter space is not remarkably increased, in some cases this number even decreased. However, when combining data partitions the trees from cost sets including affine gap costs were always more similar than the trees were from cost sets without affine gap costs. This was not the case when the data partitions were analyzed independently. When data sets were combined similar to 80\% of the clades found under cost sets including affine gap costs resisted at least one change to the cost set. (c) 2005 Elsevier Inc. All rights reserved.},
	keywords = {direct optimization, dna, evolution, gap, morphology, phylogenetics, poy, sensitivity, stability},
	url = {<u><Go to ISI>://000231591500017</u>},
	author = {Aagesen, Lone}
}
@article {1183,
	title = {On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data},
	journal = {Invertebrate Biology},
	volume = {121},
	number = {4},
	year = {2002},
	pages = {271-324},
	keywords = {18S, 28S, bivalvia, CO1, mollusca, phylogenetics, phylogeny, poy, systematics},
	author = {Giribet, Gonzalo and Wheeler, Ward C.}
}
