Protein Sequence Msa

This handles protein sequence multiple sequence alignments through Clustal Omega via EBI's web service. You'll need to provide an email for job tracking (it uses the credentials skill to request this safely), and it'll check that you've seen EBI's terms of use before running anything. From Google DeepMind's science skills collection, so it's built for real computational biology work rather than demos. The setup is straightforward if you already have uv installed. One thing to note is that you're hitting external EBI infrastructure, so you're subject to their rate limits and availability. Good for when you need MSA without maintaining your own Clustal installation.

skills.sh installs: 2.2K
GitHub stars: 3.4K
last updated: Aug 21, 2026

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Install

$ npx -y skills add google-deepmind/science-skills --skill protein-sequence-msa --agent claude-code

Installs into .claude/skills of the current project.

Files

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If .licenses/protein_sequence_msa_LICENSE.txt does not already exist in the workspace root 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.
.env file: Make sure the .env file exists in your home directory. Create one if it does not exist.
USER_EMAIL: Required by the wrapper script for Clustal Omega job tracking (recommended by the EBI). You MUST use the safe credentials protocol in the credentials skill to check for and request this credential if this skill looks relevant to the user's request.