Chapter

Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment

Ward C. Wheeler and Gonzalo Giribet

in Sequence Alignment

Published by University of California Press

Published in print November 2009 | ISBN: 9780520256972
Published online March 2012 | e-ISBN: 9780520943742 | DOI: http://dx.doi.org/10.1525/california/9780520256972.003.0006
Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment

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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

Chapter.  3308 words.  Illustrated.

Subjects: Evolutionary Biology

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