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Record 14 of 465
Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search
External Online Source: doi:10.1111/j.1096-0031.2003.tb00369.x
Author and Affiliation:
Wheeler, Ward C.(American Museum of Natural History, Division of Invertebrate Zoology, New York, NY 10024-5192, United States)
Abstract: A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.
Publication Date: Jun 01, 2003
Document ID:
20040087569
(Acquired Sep 07, 2004)
Subject Category: LIFE SCIENCES (GENERAL)
Document Type: Journal Article
Publication Information: Cladistics : the international journal of the Willi Hennig Society (ISSN 0748-3007); Volume 19; 3; 261-8
Publisher Information: United States
Description: In English
Distribution Limits: Unclassified; Publicly available; Unlimited
Rights: Copyright
NASA Terms: ALIGNMENT; COMPUTER PROGRAMS; EVOLUTION; ARTHROPODS; CLASSIFICATIONS
Other Descriptors: EVOLUTION; SEQUENCE ALIGNMENT/METHODS; SEQUENCE ANALYSIS, PROTEIN/METHODS; SOFTWARE; ANIMALS; ARTHROPODS; CRUSTACEA; PHYLOGENY; SEQUENCE HOMOLOGY; SUPPORT, U.S. GOV'T, NON-P.H.S; NASA DISCIPLINE EVOLUTIONARY BIOLOGY; NON-NASA CENTER
Availability Source: Other Sources
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