Individual skill
multiple-sequence-alignment
Multiple sequence alignment — tool choice, alignment QC, trimming, and downstream-ready alignments.
skills/multiple-sequence-alignment/SKILL.md
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## Overview
multiple-sequence-alignment covers aligning three or more sequences: choosing tools (MAFFT,
MUSCLE, Clustal Omega), alignment strategies for different data types (proteins, coding DNA,
non-coding, huge datasets), quality assessment, trimming, and producing alignments that
downstream analyses (phylogenetics, conservation, structure) can trust. Alignment error is the
silent corruptor of comparative analyses.
## When to use
- Aligning protein families: MAFFT/MUSCLE defaults and when to tune.
- Coding sequences: codon-aware alignment preserving reading frames.
- Large datasets: MAFFT FFT-NS-2, Clustal Omega for thousands of sequences.
- Non-coding RNA: structure-aware alignment (locARNA, MAFFT-Q-INS-i).