Protein Sequence Msa

Prerequisites

1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.

2. User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/jdispatcher/msa/clustalo and https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file recording the notification text and timestamp.

3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist.

4. USER_EMAIL (optional but recommended): Recommended by the EBI for Clustal Omega job tracking, but the skill works without it. If the variable is missing from .env, do NOT ask the user to paste it into the chat (this would leak the value into the agent's context). Instead, give the user this command — substituting ENV_FILE with the resolved literal path to the .env file:

   printf "Enter contact email: " && read email && echo "USER_EMAIL=$email" >> "ENV_FILE" && echo "Saved."
   

   The scripts load credentials automatically via dotenv. NEVER read, print, or inspect the .env file or its variables (e.g. no cat, grep, echo, printenv, or os.environ.get on keys). Credentials must stay out of the agent's context.

Core Rules

• Use the Wrapper: ALWAYS execute the alignment using scripts/msa_align.py rather than writing your own curl or custom Python requests. The script automatically enforces the required rate limit to respect EBI's Terms of Use.
• Notification: If this skill is used, ensure this is mentioned in the output.

• Always state the method: Every report must clearly state that the alignment was performed using EBI Clustal Omega.

• No Hallucinations: Do NOT invent alignments or conservation metrics. Report only what is present in the alignment file.