Part I: Theory
1. Dynamic Programming
Ö. Ufuk Nalbantoğlu
2. Heuristic Alignment Methods
Osamu Gotoh
3. Objective Functions
Haluk Doğan and Hasan H. Otu
4. An Appraisal of Benchmarks for Multiple Sequence Alignment
Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, and Christophe Dessimoz
5. BLAST and FASTA Similarity Searching for Multiple Sequence Alignment
William R. Pearson
Part II: Alignment Techniques
6. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences
Fabian Sievers and Desmond G. Higgins
7. T-COFFEE: Tree-Based Consistency Objective Function for Alignment Evaluation
Cedrik Magis, Jean-François Taly, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, José Espinosa-Carrasco, and Cedric Notredame
8. MAFFT: Iterative Refinement and Additional Methods
Kazutaka Katoh and Daron M. Standley
9. Multiple Sequence Alignment Using Probcons and Probalign
Usman Roshan
10. Phylogeny-Aware Alignment with PRANK
Ari Löytynoja
11. GramAlign: Fast Alignment Driven by Grammar-Based Phylogeny
David J. Russell
12. Multiple Sequence Alignment with DIALIGN
Burkhard Morgenstern
13. PicXAA: A Probabilistic Scheme for Finding the Maximum Expected Accuracy Alignment of Multiple Biological Sequences
Sayed Mohammad Ebrahim Sahraeian, and Byung-Jun Yoon
14. Multiple Protein Sequence Alignment with MSAProbs
Yongchao Liu and Bertil Schmidt
15. Large-Scale Multiple Sequence Alignment and Tree Estimation Using SATé
Kevin Liu and Tandy Warnow
16. PRALINE: A Versatile Multiple Sequence Alignment Toolkit
Punto Bawono and Jaap Heringa
17. PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and 3-Dimensional Structural Information
Jimin Pei and Nick V. Grishin
18. MSACompro: Improving Multiple Protein Sequence Alignment by Predicted Structural Features
Xin Deng and Jianlin Cheng
