Individual skill

protein-sequence-msa

Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.

skills/protein_sequence_msa/SKILL.md

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Last checked: Nov 9, 2026

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Repository stars (not skill ratings): 3,439
Repository last updated: Oct 23, 2026
License: Apache-2.0

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scripts/msa_align.pyruns · 4,953 bytes

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## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **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.
3.  **`.env` file**: Make sure the `.env` file exists in your home directory.
    Create one if it does not exist.
4.  **`USER_EMAIL`**: Required by the wrapper script for Clustal Omega job
    tracking (recommended by the EBI). You **MUST** use the safe credentials