Chapter

Simulation Approaches to Evaluating Alignment Error and Methods for Comparing Alternate Alignments

Michael. S. Rosenberg and T. Heath Ogden

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/9780520256972.003.0009
Simulation Approaches to Evaluating Alignment Error and Methods for Comparing Alternate Alignments

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This chapter discusses the use of simulation approaches to test alignment accuracy, including the root causes for ambiguity, and explores a variety of approaches for directly comparing alternate alignments. It describes how recent advances in Bayesian statistical approaches identify the effects of alignment error on downstream bioinformatic analysis, particularly with respect to phylogeny reconstruction.

Keywords: alignment accuracy; alternate alignments; Bayesian statistical approaches; alignment error; bioinformatic analysis; phylogeny reconstruction

Chapter.  9190 words.  Illustrated.

Subjects: Evolutionary Biology

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