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scikit-bio Bioinformatics Assistant

Guides Claude to write correct, up-to-date scikit-bio code for sequence analysis, alignment, phylogenetics, and microbiome diversity statistics.

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

What it does

  • Reads/writes biological sequences and 19+ formats (FASTA, FASTQ, GenBank, Newick, BIOM) and handles reverse complement, transcription, translation, and regex motif search.
  • Runs pairwise/multiple alignment with the modern pair_align engine (global/local/semi-global, affine gaps, BLOSUM62/NUC.4.4), CIGAR paths, and TabularMSA.
  • Builds and compares phylogenetic trees (NJ, UPGMA, GME, BME, NNI), patristic distances, Robinson-Foulds comparisons.
  • Computes alpha/beta diversity (Shannon, Chao1, Faith's PD, weighted/unweighted UniFrac), ordination (PCoA, CA, CCA, RDA), and tests (PERMANOVA, ANOSIM, PERMDISP, Mantel, ANCOM, dirmult_ttest).
  • Handles feature tables from BIOM/pandas/polars/AnnData via the 0.7 dispatch system, plus protein language-model embeddings.

Who it's for

  • Microbiome and community-ecology researchers and grad students.
  • QIIME 2 users who want to continue analysis in Python.
  • Bioinformatics engineers prototyping sequence or phylogenetic pipelines.

Example uses

  1. "From table.biom and tree.nwk, compute unweighted UniFrac, run PCoA, and plot colored by bodysite."
  2. "Test group differences with PERMANOVA (999 permutations) and pair it with PERMDISP to check dispersion."
  3. "Stream a large FASTQ, quality-filter it, write FASTA, and report ATG motif positions."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/scikit-bio/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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/scikit-bio folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/scikit-bio/.
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 && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/scikit-bio ~/.claude/skills/

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

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills folder: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/scikit-bio ~/.claude/skills/
  4. Install the library in your Python env: uv pip install scikit-bio (or conda install -c conda-forge scikit-bio). Requires Python 3.10+ and NumPy 2.0+.
  5. Optional extras for plotting and table interop: uv pip install matplotlib seaborn plotly biom-format polars anndata
  6. Restart Claude Code and try a prompt such as "Use scikit-bio to compute beta diversity and run PERMANOVA on my OTU table."
View source on GitHub ↗License: MIT