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