@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 {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.}
}
@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 {7802,
	title = {Histone and histone gene compilation and alignment update},
	journal = {Nucleic Acids Research},
	volume = {19, suppl.},
	year = {1991},
	note = {PDF},
	pages = {2173-2188},
	keywords = {alignment, histone},
	author = {Wells, Dan and Brown, Doris}
}
@article {7653,
	title = {The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools},
	journal = {Nucleic Acids Research},
	volume = {24},
	year = {1997},
	pages = {4876-4882},
	keywords = {alignment, clustal, phylogenetics},
	author = {Thompson, J. D. and Gibson, T. J. and Plewniak, F. and Jeanmougin, F. and Higgins, D. G.}
}
@article {7426,
	title = {The deferred path heuristic for the generalized tree alignment problem},
	journal = {Journal of Comutational Biology},
	volume = {4},
	year = {1997},
	note = {DO NOT HAVE},
	pages = {415{\textendash}431},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Schwikowski, B. and Vingron, M.}
}
@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 {6985,
	title = {Multiple sequence alignment for phylogenetic purposes},
	journal = {Australian Systematic Botany},
	volume = {19},
	year = {2006},
	note = {PDF},
	pages = {479{\textendash}539},
	keywords = {alignment, homology, molecules, multiple sequence alignment, phylogenetics},
	author = {Morrison, David A.}
}
@article {6809,
	title = {Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis},
	journal = {Science},
	volume = {320},
	year = {2008},
	note = {PDF},
	pages = {1632-1635},
	keywords = {alignment, gap, homology, phylogenetics},
	author = {Löytynoja, Ari and Goldman, Nick}
}
@article {6744,
	title = {Clustal W and Clustal X version 2.0},
	journal = {Bioinformatics},
	volume = {23},
	year = {2007},
	note = {PDF},
	pages = {2947-2948},
	keywords = {alignment, multiple sequence alignment, phylogenetics},
	author = {Larkin, M. A. and Blackshields, G. and Brown, N. P. and Chenna, R. and McGettigan, P. A. and McWilliam, H. and Valentin, F. and Wallace, I. M. and Wilm, A. and Lopez, R. and Thompson, J. D. and Gibson, T. J. and Higgins, D. G.}
}
@proceedings {6593,
	title = {Aligning sequences via an evolutionary tree: complexity and approximation},
	year = {1994},
	note = {DO NOT HAVE},
	pages = {760{\textendash}769},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Jiang, T. and Lawler, E. L. and Wang, A.}
}
@article {6495,
	title = {A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given},
	journal = {Molecular Biology and Evolution},
	volume = {6},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {649{\textendash}668},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Hein, J.}
}
@article {6496,
	title = {A tree reconstruction method that is economical in the number of pairwise comparisons used},
	journal = {Molecular Biology and Evolution},
	volume = {6},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {669{\textendash}684},
	keywords = {alignment, molecular characters, phylogenetics},
	author = {Hein, J.}
}
@article {6424,
	title = {Lessons from an evolving rRNA: 16S and 23S r RNA structures from a comparative perspective},
	journal = {Microbiological Reviews},
	volume = {58},
	number = {1},
	year = {1994},
	note = {xerox},
	pages = {10-26},
	keywords = {16S, 23S, alignment, rDNA, secondary structure},
	author = {Gutell, Robin R. and Larsen, Niels and Woese, Carl R.}
}
@article {6364,
	title = {An improved algorithm for matching biological sequences},
	journal = {Journal of Molecular Biology},
	volume = {162},
	year = {1982},
	note = {DO NOT HAVE},
	pages = {705{\textendash}708},
	keywords = {alignment, gap, molecular characters, phylogenetics},
	author = {Gotoh, O.}
}
@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 {5738,
	title = {Basic local alignment search tool},
	journal = {Journal of Molecular Biology},
	volume = {215},
	year = {1990},
	note = {DO NOT HAVE},
	pages = {403-410},
	keywords = {alignment},
	author = {Altschul, S. F. and Gish, W. and Miller, W. and Myers, E. W. and Lipman, D. J.}
}
@article {5739,
	title = {Gapped BLAST and PSI-BLAST: a new generation of protein database search programs},
	journal = {Nucleic Acids Research},
	volume = {25},
	year = {1997},
	note = {DO NOT HAVE},
	pages = {3389-3402},
	keywords = {alignment},
	author = {Altschul, S. F. and Madden, T. L. and Sch{\"a}ffer, A. A. and Zhang, J. and Zhang, Z. and Miller, W. and Lipman, D. J.}
}
