# Peptide Msa

> Perform a simple multiple-sequence alignment (MSA) for short peptides and return aligned sequences + consensus.

- Skill: `lamm-mit/peptide-msa` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add lamm-mit/peptide-msa`
- Raw SKILL.md: https://api.skillmd.com/api/skills/lamm-mit/peptide-msa/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: lamm-mit (https://skillmd.com/u/lamm-mit)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/lamm-mit/peptide-msa

---


# Peptide MSA

Lightweight MSA intended for peptides (≈6–40 aa). Produces:

- `aligned_sequences` (list of gapped strings)
- `aligned_json` (JSON string of `aligned_sequences`, safe to pass via argv)
- `consensus` (gapped consensus string)

## CLI

```bash
python3 scripts/run.py --sequences AGCKNFFWKTFTSC FCFWKTCT
python3 scripts/run.py --query "AGCKNFFWKTFTSC;FCFWKTCT"
```