| name | evolutionary-conservation |
| description | Multiple sequence alignment and conservation analysis using MUSCLE |
| metadata | {"openclaw":{"requires":{"env":["OPENAI_API_KEY"],"bins":["python3"],"anyBins":["muscle","muscle5"]},"primaryEnv":"OPENAI_API_KEY"}} |
Evolutionary Conservation — MUSCLE Alignment
Analyze evolutionary conservation of protein sequences using multiple sequence alignment.
Requires: MUSCLE v5 binary (muscle or muscle5) on PATH.
Capabilities
- MSA generation: Align homologous sequences using MUSCLE v5
- Conservation scoring: Per-residue conservation scores (Shannon entropy or property-based)
- Conserved region detection: Identify contiguous highly-conserved regions
- Artifact DAG integration: Results stored with full provenance tracking
Usage
python skills/evolutionary-conservation/scripts/run_conservation.py \
--input-fasta sequences.fasta --output-dir results/
python skills/evolutionary-conservation/scripts/run_conservation.py \
--sequences MTEYKLVV... MTEYKLVVV... --output-dir results/
python skills/evolutionary-conservation/scripts/run_conservation.py \
--input-fasta sequences.fasta --output-dir results/ \
--artifact-store ./artifact_store
Parameters
--input-fasta: Path to unaligned FASTA file (mutually exclusive with --sequences)--sequences: Bare protein sequences to align (space-separated)--output-dir: Directory for output files (default: conservation_output)--method: Scoring method — shannon or property (default: shannon)--conserved-threshold: Score threshold for conserved regions (default: 0.8)--min-region-length: Minimum contiguous length for a conserved region (default: 3)--muscle-bin: Explicit path to MUSCLE binary (auto-detected if omitted)--artifact-store: Root directory for artifact DAG storage (optional)
