Multiple Sequence Alignment: Methods and Protocols

Preface... Table of Contents... Contributing Authors...
Part I Basic Tools for Computing MSAa
1. The Clustal Omega Multiple Alignment Package Fabian Sievers and Desmond G. Higgins
2. Phylogeny-Aware Alignment with PRANK and PAGAN Ari Löytynoja
3. Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI Jorge González-Domínguez
Part II Tools for Specific MSA Problems Handling DNA/Protein Sequences Simultaneously
4. Aligning Protein-Coding Nucleotide Sequences with MACSE Vincent Ranwez, Nathalie Chantret, and Frédéric Delsuc
5. Cooperation of Spalm and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment Osamu Gotoh
Large Number of Sequences
6. Multiple Sequence Alignment Computation using the T-Coffee Regressive Algorithm Implementation Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Evan Floden, and Cedric Notredame
7. Multiple Sequence Alignment for Large Heterogeneous Datasets using SATé, PASTA, and UPP Tandy Warnow and Siavash Mirarab
8. Sequence Comparison without Alignment: The SpaM Approaches Burkhard Morgenstern
Unreliable Data
9. Lamassemble: Multiple Alignment and Consensus Sequence of Long Reads Martin C. Frith, Satomi Mitsuhashi, and Kazutaka Katoh
10. Automated Removal of Non-Homologous Sequence Stretches with PREQUAL Iker Irisarri, Fabien Burki, and Simon Whelan
Protein Structures
11. Analysis of Protein Intermolecular Interaction with MAFFT-DASH John Rozewicki, Songling Li, Kazutaka Katoh, and Daron M. Standley
12. Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies Dmitry Suplatov, Yana Sharapova, and Vytas Svedas
Part III Visualization
13. Alignment of Biological Sequences with Jalview James B. Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton, Lauren Lui, Anne Menard, Natasha Sherstnev, David Roland-Martinez, Suzanne Duce, David M.A. Martin, and Geoffrey J. Marton
14. Evolutionary Sequence Analysis and Visualization with Wasabi Andres Veidenberg and Ari Löytynoja
15. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation Manolo Gouy, Eric Tannier, Nicolas Comte, and David Parsons
16. NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data Submission Anatoliy Kuznetsov and Colleen J. Bollin
Part IV Open Problems
17. Revisiting Evaluation of Multiple Sequence Alignment Methods Tandy Warnow
Subject Index List...