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 Švedas
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…
