Sequence Alignment: Methods, Models, Concepts, and Strategies

Front Cover
Michael S. Rosenberg
University of California Press, 2009 - Science - 337 pages
0 Reviews
"Sequence alignment represents the final frontier in the development of repeatable, comprehensive methods for phylogenetic analysis. This book will inform readers about the current status of alignment methods and will help stimulate additional work in the field."--David M. Hillis, University of Texas
""Sequence Alignment "provides an in-depth treatment of the prerequisite to many evolutionary analyses by presenting a diversity of opinions on the best way to align complex molecular sequence data. Topics covered include the basic algorithms used, global versus local procedures, the robustness alignment error detection, and a description of the programs now available. "Sequence Alignment "is a reassuring companion, guiding the reader through a large and complicated field."--John Huelsenbeck, Department of Integrative Biology, University of California, Berkeley
 

What people are saying - Write a review

We haven't found any reviews in the usual places.

Contents

1 Sequence Alignment
1
2 Insertion and Deletion Events Their Molecular Mechanisms and Their Impact on Sequence Alignments
23
3 Local versus Global Alignments
39
4 Computing Multiple Sequence Alignment with TemplateBased Methods
55
5 Sequence Evolution Models for Simultaneous Alignment and Phylogeny Reconstruction
71
6 Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment
95
7 Structural and Evolutionary Considerations for Multiple Sequence Alignment of RNA and the Challenges for Algorithms That Ignore Them
105
8 Constructing Alignment Benchmarks
151
9 Simulation Approaches to Evaluating Alignment Error and Methods for Comparing Alternate Alignments
179
10 Robust Inferences from Ambiguous Alignments
209
11 Strategies for Efficient Exploitation of the Informational Content of Protein Multiple Alignments
271
References
297
Index
333
Copyright

Other editions - View all

Common terms and phrases

About the author (2009)

Michael S. Rosenberg is Associate Professor of Computational Evolutionary Biology and Bioinformatics in the School of Life Sciences and the Center for Evolutionary Functional Genomics of the Biodesign Institute at Arizona State University.

Bibliographic information