@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 {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}
}
