Multiple Sequence Alignment (e-book) (used book) | bookbook.eu

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Preface...Table of Contents...Contributing Authors...
Part I Basic Tools for Computing MSAa
1. The Clustal Omega Multiple Alignment PackageFabian Sievers and Desmond G. Higgins
2. Phylogeny-Aware Alignment with PRANK and PAGANAri Löytynoja
3. Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPIJorge González-Domínguez
Part II Tools for Specific MSA ProblemsHandling DNA/Protein Sequences Simultaneously
4. Aligning Protein-Coding Nucleotide Sequences with MACSEVincent Ranwez, Nathalie Chantret, and Frédéric Delsuc
5. Cooperation of Spalm and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence AlignmentOsamu Gotoh
Large Number of Sequences
6. Multiple Sequence Alignment Computation using the T-Coffee Regressive Algorithm ImplementationEdgar 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 UPPTandy Warnow and Siavash Mirarab
8. Sequence Comparison without Alignment: The SpaM ApproachesBurkhard Morgenstern
Unreliable Data
9. Lamassemble: Multiple Alignment and Consensus Sequence of Long ReadsMartin C. Frith, Satomi Mitsuhashi, and Kazutaka Katoh
10. Automated Removal of Non-Homologous Sequence Stretches with PREQUALIker Irisarri, Fabien Burki, and Simon Whelan
Protein Structures
11. Analysis of Protein Intermolecular Interaction with MAFFT-DASHJohn Rozewicki, Songling Li, Kazutaka Katoh, and Daron M. Standley
12. Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein SuperfamiliesDmitry Suplatov, Yana Sharapova, and Vytas Svedas
Part III Visualization
13. Alignment of Biological Sequences with JalviewJames 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 WasabiAndres Veidenberg and Ari Löytynoja
15. Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree ReconciliationManolo Gouy, Eric Tannier, Nicolas Comte, and David Parsons
16. NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data SubmissionAnatoliy Kuznetsov and Colleen J. Bollin
Part IV Open Problems
17. Revisiting Evaluation of Multiple Sequence Alignment MethodsTandy Warnow
Subject Index List...