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Biopython Molecular Biology Toolkit

Gives Claude a domain-organized Biopython playbook for sequences, NCBI/Entrez, BLAST, structures, and phylogenetics.

Dev & CodingIntermediate★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

Packages practical Biopython 1.87 guidance into a skill: Claude identifies the task domain, reads the matching file in references/ (sequence I/O, alignment, databases, BLAST, structure, phylogenetics, advanced), and writes working Python.

  • Parse and convert FASTA, GenBank, FASTQ, PDB, mmCIF
  • Query PubMed/GenBank/Protein/Gene via Bio.Entrez with proper email, tool name, and rate limits
  • Run web or local BLAST and filter XML hits by E-value/identity
  • Bio.PDB structure traversal, distances, RMSD, DSSP secondary structure
  • Bio.Phylo tree building, pruning, and visualization; motifs, PopGen, restriction analysis
  • Migration notes for modules removed in 1.86 and the changed PairwiseAligner gap score

Who it's for

  • Researchers and grad students batch-processing sequence data
  • Developers building custom bioinformatics pipelines in Python
  • Data analysts automating NCBI data collection
  • Instructors who need vetted Biopython example code

Example uses

  1. "Convert every GenBank file in this folder to FASTA and give me a GC-content table" → SeqIO.convert + gc_fraction script
  2. "Pull titles and abstracts for 200 PubMed hits on a keyword into CSV using my API key" → batched Entrez esearch/efetch code
  3. "Build a neighbor-joining tree from this alignment and export Newick plus an ASCII tree" → DistanceCalculator + DistanceTreeConstructor pipeline

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/biopython folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/biopython/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/biopython ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Confirm Python 3.10+ and Claude Code are installed.
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/biopython ~/.claude/skills/
  4. Install the library: pip install "biopython==1.87" (or uv pip install "biopython==1.87").
  5. For NCBI access, export credentials: export NCBI_EMAIL="you@example.com" and optionally export NCBI_API_KEY="...".
  6. Install local BLAST or MUSCLE separately if you plan to use the local-tool examples.
  7. Restart Claude Code and try a prompt like "use biopython to summarize this FASTA file" to verify the skill loads.
View source on GitHub ↗License: MIT