# Conservation Map

> Compute per-position conservation/entropy for an aligned peptide MSA (aligned sequences).

- Skill: `lamm-mit/conservation-map` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add lamm-mit/conservation-map`
- Raw SKILL.md: https://api.skillmd.com/api/skills/lamm-mit/conservation-map/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/conservation-map

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# Conservation Map

Compute conservation for each alignment column from an MSA.

Accepts either:
- `--aligned-json` (preferred): a JSON list of aligned sequences (safe even if sequences contain `-`)
- `--query`: JSON list or `;`-separated raw/aligned sequences (raw sequences will be aligned internally)

## CLI
```bash
python3 scripts/run.py --aligned-json '["AGC--K","AGCFFK"]'
python3 scripts/run.py --query "AGCKNFFWKTFTSC;FCFWKTCT"
```