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scikit-bio — Claude Code skill: what it does, how to install

Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. Helpful for microbiome workflows and ecology data.

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

What scikit-bio does

This skill guides coding agents through bioinformatics workflows targeting scikit-bio 0.7.4. Using bash and file editing tools, the agent handles DNA, RNA, and protein sequences. It reads standard formats like FASTA, FASTQ, or Newick, computes reverse complements, and identifies sequence motifs.

Under the hood, it applies the modern pair_align engine for pairwise and multiple sequence alignments, replacing older deprecated aligners. It also handles phylogenetic tree reconstruction through Neighbor Joining or UPGMA and computes patristic distances.

Running this requires Python 3.10+ alongside NumPy 2.0+. Without scikit-bio 0.7.4 installed, the alignment syntax and tree routines will break immediately. Optional plotting packages like matplotlib or seaborn are needed if you want figures.

What it helps with

  • construct phylogenetic trees with Neighbor Joining
  • align nucleotide sequences using pair_align
  • translate open reading frames into protein sequences
  • parse and summarize FASTA or Newick files

Example prompts for the agent

  • Read sequences from input.fasta and translate them into proteins
  • Align these two DNA sequences using pair_align_nucl
  • Build a neighbor joining tree from the distance matrix

How to install scikit-bio

1Skills CLI (Vercel)

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

2Manually: put the files in place

~/.claude/skills/scikit-bio/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/scikit-bio/

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Questions about scikit-bio

How to install scikit-bio in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill scikit-bio -a claude-code in your terminal. This registers the skill instructions for your assistant.

What does scikit-bio skill do?

It equips the agent with patterns to manipulate molecular sequences, build phylogenetic trees, and run ecological statistics using scikit-bio.

What are the dependency requirements?

You must have Python 3.10+ and NumPy 2.0+ with scikit-bio==0.7.4. Plotting requires extra libraries such as matplotlib or seaborn.

See also

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