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biopython — Claude Code skill: what it does, how to install

Automates computational biology workflows: parses sequence files, runs alignments, and fetches records via NCBI Entrez.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -a claude-code
Open on GitHub

What biopython does

This skill guides the agent through molecular biology routines using Biopython 1.88. It covers sequence parsing and format conversions in Bio.SeqIO, global and local alignments using Bio.Align, 3D structural analysis in Bio.PDB, and phylogenetic tree handling in Bio.Phylo.

The environment requires Python 3.10+, NumPy, and biopython==1.88. Network requests to NCBI require a contact email, while passing NCBI_API_KEY increases the Entrez throughput limit from 3 to 10 calls per second. Without standalone binaries on your machine, external tools like DSSP, local BLAST, Clustal Omega, or MUSCLE 5 cannot execute.

What it helps with

  • convert GenBank records into FASTA files
  • run global pairwise sequence alignments
  • retrieve PubMed and gene records through NCBI Entrez
  • parse and filter XML output from BLAST searches

Example prompts for the agent

  • Write a Python script using Bio.SeqIO to parse sequences.fasta and report record lengths
  • Perform a pairwise global alignment between two DNA sequences using Bio.Align
  • Search PubMed for ten recent papers via Bio.Entrez and extract their titles

How to install biopython

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -a claude-code

2Manually: put the files in place

~/.claude/skills/biopython/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/biopython/

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Questions about biopython

How to install biopython in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill biopython -a claude-code in your terminal.

What does the biopython skill do?

It provides practical code patterns for computational biology tasks, including sequence conversion, structural parsing, BLAST runs, and automated NCBI record retrieval.

What dependencies does this skill require?

You need Python 3.10+, NumPy, and Biopython 1.88. External tasks like local BLAST, DSSP structure checks, and MUSCLE 5 alignments require their own native binaries.

See also

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