The Clustal Omega Multiple Alignment Package -- Phylogeny-Aware Alignment with PRANK and PAGAN -- Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI -- Aligning Protein-Coding Nucleotide Sequences with MACSE -- Cooperation of Spalm and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment -- Multiple Sequence Alignment Computation using the T-Coffee Regressive Algorithm Implementation -- Multiple Sequence Alignment for Large Heterogeneous Datasets using SATé, PASTA, and UPP -- Sequence Comparison without Alignment: The SpaM Approaches -- Lamassemble: Multiple Alignment and Consensus Sequence of Long Reads -- Automated Removal of Non-Homologous Sequence Stretches with PREQUAL -- Analysis of Protein Intermolecular Interaction with MAFFT-DASH -- Mustguseal and Sister Web-Methods: A Practical Guide to Bioinformatic Analysis of Protein Superfamilies -- Alignment of Biological Sequences with Jalview -- Evolutionary Sequence Analysis and Visualization with Wasabi -- Seaview Version 5: A Multiplatform Software for Multiple Sequence Alignment, Molecular Phylogenetic Analyses, and Tree Reconciliation -- NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data Submission -- Revisiting Evaluation of Multiple Sequence Alignment Methods.

Chapter "Alignment of Biological Sequences with Jalview" is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.