evolutionary-conservation

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

# From a FASTA file of homologous sequences
python skills/evolutionary-conservation/scripts/run_conservation.py \
    --input-fasta sequences.fasta --output-dir results/

# From bare sequences
python skills/evolutionary-conservation/scripts/run_conservation.py \
    --sequences MTEYKLVV... MTEYKLVVV... --output-dir results/

# With artifact DAG tracking
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)