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Sequence AlignmentMethods, Models, Concepts, and Strategies$
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Michael Rosenberg

Print publication date: 2009

Print ISBN-13: 9780520256972

Published to California Scholarship Online: March 2012

DOI: 10.1525/california/9780520256972.001.0001

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Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment

Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment

(p.94) (p.95) Chapter 6 Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment
Sequence Alignment

Ward C. Wheeler

Gonzalo Giribet

University of California Press

Multiple sequence alignment (MSA) is a potentially useful technique in phylogenetic analysis. This chapter examines the relative effectiveness of MSA and constructs and evaluates phylogenetic hypotheses without the use of this technique, first defining phylogenetic hypothesis, the problem, and the criteria used to assay the relative merits of hypotheses. It also defines the meaning of the utility of a technique, compares the results of alternate techniques, and criticizes the traditional approach to alignment and phylogenetic analysis, with a specific implementation of simultaneous phylogeny and alignment construction. The final section compares the results of a “one-step” optimization heuristic embodied in POY4 with the MSA + Search approach embodied by Clustal, using a large number of small data set simulations run under a variety of conditions and a few larger real data sets.

Keywords:   multiple sequence alignment, MSA, phylogenetic hypotheses, phylogeny, alignment construction, Clustal

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