Chapter

Robust Inferences from Ambiguous Alignments

Benjamin D. Redeling and Marc A. Suchard

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/9780520256972.003.0010
Robust Inferences from Ambiguous Alignments

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This chapter discusses several traditional methods of handling ambiguity in multiple sequence alignments, as well as new statistical approaches to this problem, and describes how alignment uncertainty can affect phylogeny estimation by focusing on a small data example. This example demonstrates the negative effects of ignoring alignment uncertainty and illustrates the practical benefits of the new statistical methods.

Keywords: ambiguity; multiple sequence alignments; alignment uncertainty; phylogeny estimation

Chapter.  21210 words.  Illustrated.

Subjects: Evolutionary Biology

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