@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 {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 {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 {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 {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 {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 {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 {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}
}
