Menu
Multiple sequence alignment and conservation analysis using MUSCLE
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Search and select enzyme sequence homologs from a database. Use when users provide a query sequence and want to discover sequence homologs of the query sequence in a database.
Scientific reasoning via Jnana CoScientist — hypothesis generation, evaluation, and parameter bounding
Molecular dynamics simulations using OpenMM with MDAgent-style automation and free energy calculations via MM-PBSA
Convert scientific papers into executable computational workflows and MCP tools
Protein language model embeddings, diversity sampling, and mutation prediction using ESM or GenSLM
Protein structure prediction using Chai-1 or AlphaFold with confidence scoring, quality assessment, and critic evaluation
Based on SOC occupation classification
| 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"}} |
Analyze evolutionary conservation of protein sequences using multiple sequence alignment.
Requires: MUSCLE v5 binary (muscle or muscle5) on PATH.
# 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
--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)