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multiple-alignment

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

When to use

• aligning three or more homologous sequences
• phylogenetics
• conservation analysis
• evolutionary studies
• tool and algorithm selection
• cross-aligner sensitivity check
• large dataset alignment
• fragmentary input alignment

When not to use

• aligning fewer than three sequences

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