@article {7806,
	title = {Noise},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {51-54},
	author = {Wenzel, J. W. and Siddall, M. E.}
}
@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 {7811,
	title = {Nucleic acid sequence phylogeny and random outgroups},
	journal = {Cladistics},
	volume = {6},
	year = {1990},
	note = {DO NOT HAVE},
	pages = {363{\textendash}367},
	keywords = {outgroup, phylogenetics},
	author = {Wheeler, W. 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.}
}
@article {7814,
	title = {Measuring topological congruence by extending character techniques},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {DO NOT HAVE},
	pages = {131{\textendash}135},
	keywords = {congruence, phylogenetics},
	author = {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 {7823,
	title = {Partition-free congruence analysis: implications for sensitivity analysis},
	journal = {Cladistics},
	volume = {22},
	year = {2006},
	note = {PDF},
	pages = {256-263},
	keywords = {combined data analyses, molecular characters, phylogenetics, sensitivity, total evidence},
	author = {Wheeler, Ward C. and Ram{\'\i}rez, Mart{\'\i}n J. and Aagesen, Lone and Schulmeister, Susanne}
}
@article {7576,
	title = {Character coding and inapplicable data},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {363{\textendash}371},
	keywords = {character coding, missing data, phylogenetics},
	author = {Strong, Ellen E. and Lipscomb, Diana}
}
@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 {7476,
	title = {Phylogenetic reticulations and cladistics: discussion of methodological concepts},
	journal = {Cladistics},
	volume = {10},
	year = {1994},
	note = {PDF},
	pages = {305-313},
	keywords = {cladistics, network, phylogenetics, reticulation},
	author = {Sk{\'a}la, Zdenek and Zrzavπ, Jan}
}
@article {7460,
	title = {Stratigraphic fit to phylogenies: a proposed solution},
	journal = {Cladistics},
	volume = {14},
	year = {1998},
	note = {PDF},
	pages = {201{\textendash}208},
	keywords = {paleontology, phylogenetics, stratigraphy},
	author = {Siddall, Mark E.}
}
@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 {7303,
	title = {Origins, taxa, names and meanings},
	journal = {Cladistics},
	volume = {24},
	year = {2008},
	note = {DO NOT HAVE},
	pages = {598-610},
	keywords = {nomenclature, philosophy, phylocode, species concepts, taxonomy},
	author = {Rieppel, Olivier}
}
@article {7209,
	title = {Comments on the manhattan stratigraphic measure},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {285-289},
	keywords = {fossil record, phylogenetics, stratigraphy},
	author = {Pol, Diego and Norell, Mark A.}
}
@article {7132,
	title = {On describing the shape of rooted and unrooted trees},
	journal = {Cladistics},
	volume = {9},
	year = {1993},
	note = {do not have},
	pages = {93{\textendash}99},
	author = {Page, R. D. M.}
}
@article {7068,
	title = {The parsimony ratchet, a new method for rapid parsimony analysis},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {407-414},
	keywords = {parsimony, phylogenetics, ratchet},
	author = {Nixon, Kevin C.}
}
@article {7070,
	title = {On outgroups},
	journal = {Cladistics},
	volume = {9},
	year = {1993},
	note = {DO NOT HAVE},
	pages = {413-426},
	keywords = {cladistics, outgroup, phylogenetics},
	author = {Nixon, K. C. and Carpenter, J. M.}
}
@article {7071,
	title = {On simultaneous analysis},
	journal = {Cladistics},
	volume = {12},
	year = {1996},
	note = {PDF},
	pages = {221-241},
	author = {Nixon, K. C. and Carpenter, J. M.}
}
@article {6677,
	title = {Cladistics: what{\textquoteright}s in a word?},
	journal = {Cladistics},
	volume = {9},
	year = {1993},
	note = {DO NOT HAVE},
	pages = {183-199},
	author = {Kluge, A. G. and Wolf, A. J.}
}
@article {6618,
	title = {Homoplasy increases phylogenetic structure},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {91{\textendash}93},
	keywords = {homoplasy, molecular characters, phylogenetics, saturation},
	author = {K{\"a}llersj{\"o}, M. and Albert, V. A. and Farris, J. S}
}
@article {6619,
	title = {Skewness and permutation},
	journal = {Cladistics},
	volume = {8},
	year = {1992},
	note = {do not have},
	pages = {275-287},
	keywords = {g1, phylogenetics},
	author = {K{\"a}llersj{\"o}, M. and Farris, J. S and Kluge, A. G. and Bult, 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 {6389,
	title = {Data exploration in phylogenetic inference: scientific, heuristic, or neither},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {379{\textendash}418},
	keywords = {philosophy, phylogenetics, sensitivity, stability, support},
	author = {Grant, Taran and Kluge, Arnold G.}
}
@article {6390,
	title = {Stability, sensitivity, science and heurism},
	journal = {Cladistics},
	volume = {21},
	year = {2005},
	note = {PDF},
	pages = {597{\textendash}604},
	keywords = {philosophy, phylogenetics, sensitivity, stability, support},
	author = {Grant, Taran and Kluge, Arnold G.}
}
@article {6355,
	title = {Analyzing large data sets in reasonable times: solutions for composite optima},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {415-428},
	keywords = {phylogenetics, tree drifting, tree fusing},
	author = {Goloboff, Pablo A.}
}
@article {6357,
	title = {Methods for quick consensus estimation},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {S26{\textendash}S34},
	keywords = {consensus, phylogenetics},
	author = {Goloboff, Pablo A. and Farris, James S.}
}
@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 {6325,
	title = {Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {271-313},
	keywords = {combined data analyses, phylogenetics, support},
	author = {Gatesy, J. and O{\textquoteright}Grady, P. and Baker, Richard H.}
}
@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 {6302,
	title = {From basepairs to birdsongs: phylogenetic data in the age of genomics},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {333-347},
	keywords = {genomics, hierarchy, morphology, phylogenetics},
	author = {Freudenstein, John V. and Pickett, Kurt M. and Simmons, Mark P. and Wenzel, John W.}
}
@article {6248,
	title = {The retention index and the rescaled consistency index},
	journal = {Cladistics},
	volume = {5},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {417-419},
	keywords = {ci, homoplasy, phylogenetics, ri},
	author = {Farris, J. S}
}
@article {6249,
	title = {Likelihood and inconsistency},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {DO NOT HAVE},
	pages = {199-204},
	author = {Farris, J. S}
}
@article {6250,
	title = {Corroboration versus "strongest evidence"},
	journal = {Cladistics},
	volume = {16},
	year = {2000},
	note = {DO NOT HAVE},
	pages = {385-393},
	author = {Farris, J. S}
}
@article {6251,
	title = {Parsimony jackknifing outperforms neighbor-joining},
	journal = {Cladistics},
	volume = {12},
	year = {1996},
	note = {PDF},
	pages = {99-124},
	keywords = {jackknife, neighbor-joining, phylogenetics, support},
	author = {Farris, J. S and Albert, V. A. and K{\"a}llersj{\"o}, M. and Lipscomb, D. and Kluge, A. G.}
}
@article {6253,
	title = {Testing significance of incongruence},
	journal = {Cladistics},
	volume = {10},
	year = {1995},
	note = {PDF},
	pages = {315{\textendash}319},
	keywords = {ild, incongruence, phylogenetics},
	author = {Farris, James S. and K{\"a}llersj{\"o}, Mari and Kluge, Arnold G. and Bult, Carol}
}
@article {6134,
	title = {On the three taxon approach to parsimony analysis},
	journal = {Cladistics},
	volume = {14},
	year = {1998},
	note = {PDF},
	pages = {363{\textendash}381},
	keywords = {homology, phylogenetics},
	author = {De Laet, J. and Smets, E.}
}
@article {5926,
	title = {Combinable component consensus},
	journal = {Cladistics},
	volume = {6},
	year = {1990},
	pages = {369-372},
	author = {Bremer, K.}
}
@article {5870,
	title = {Are third positions really that bad? A test using vertebrate cytochrome b},
	journal = {Cladistics},
	volume = {15},
	number = {2},
	year = {1999},
	note = {PDF},
	pages = {191{\textendash}197},
	keywords = {molecular characters, phylogenetics, saturation},
	author = {Bj{\"o}rklund, M.}
}
@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 {5729,
	title = {Congruence among mammalian mitochondrial genes},
	journal = {Cladistics},
	volume = {15},
	year = {1999},
	note = {PDF},
	pages = {75-84},
	keywords = {homoplasy, molecular characters, phylogenetics, saturation},
	author = {Allard, M. W. and Farris, J. S and Carpenter, J. M.}
}
