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scikit-bio

Analyze biological data with scikit-bio for sequence manipulation, phylogenetics, and diversity analysis.

48|6|Updated Mar 9, 2026
Search Tags:#bioinformatics#genomics#phylogenetics#sequence-analysis#diversity-metrics#data-io
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill scikit-bio-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scikit-bio
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/05-%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E4%B8%8E%E5%9F%BA%E5%9B%A0%E7%BB%84%E5%AD%A6/scikit-bio
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill scikit-bio-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Provides a comprehensive Python toolkit for biological data analysis, enabling researchers to manipulate sequences, build phylogenetic trees, compute diversity metrics, and read/write standard bioinformatics formats without switching between tools.

Core Features & Use Cases

  • Sequence manipulation and translation across DNA, RNA, and protein data (read, write, slice, reverse-complement, translate)
  • Phylogenetic analysis and tree manipulation (construct trees, compute distances, inspect cophenetic distances and Robinson-Foulds distances)
  • Diversity metrics and ordination (alpha/beta diversity, PCoA, ordination plots) with BIOM compatibility
  • File I/O and format conversion for FASTA, FASTQ, GenBank, Newick, and BIOM

Quick Start

Install scikit-bio using pip and load a FASTA file to begin sequence exploration.

Frequently Asked Questions about scikit-bio

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I parse and manipulate FASTA and FASTQ sequences in Python?▼

Sequence manipulation of FASTA and FASTQ files in Python is done by reading data into scikit-bio sequence objects, allowing you to slice, reverse-complement, and translate DNA, RNA, or protein sequences.

Can I compute alpha and beta diversity metrics from BIOM tables?▼

Yes, you can compute alpha and beta diversity metrics and perform ordination like PCoA directly from BIOM format tables to analyze ecological diversity across biological samples.

How do I construct and compare phylogenetic trees using Newick format?▼

Phylogenetic trees in Newick format can be read into scikit-bio to construct trees, inspect cophenetic distances, and compute Robinson-Foulds distances for tree comparison.

Does scikit-bio support reading and writing GenBank files for genomics workflows?▼

Yes, scikit-bio supports file I/O and format conversion for GenBank, alongside FASTA, FASTQ, Newick, and BIOM formats, enabling seamless data loading for genomics workflows.

What's the best way to translate DNA sequences into proteins for proteomics analysis?▼

Translating DNA sequences into proteins for proteomics analysis is handled by scikit-bio's sequence translation APIs, which process biological sequences loaded from standard file formats.

Do I need to install scikit-bio separately to use these bioinformatics APIs?▼

Yes, scikit-bio installation is required to use its APIs for sequence manipulation, phylogenetics, diversity analysis, and format I/O across genomics, metagenomics, and proteomics workflows.

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