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conservation-map

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

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Source SKILL.md: https://github.com/lamm-mit/scienceclaw/blob/HEAD/skills/conservation-map/SKILL.md

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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

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