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

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

Chapter:
(p.178) (p.179) Chapter 9 Simulation Approaches to Evaluating Alignment Error and Methods for Comparing Alternate Alignments
Source:
Sequence Alignment
Author(s):

Michael. S. Rosenberg

T. Heath Ogden

Publisher:
University of California Press
DOI:10.1525/california/9780520256972.003.0009

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

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