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scikit-bio

Analyze biological sequences and microbiome ecology with scikit-bio.

783|65|Updated Feb 27, 2026
Search Tags:#ordination#phylogenetics#biological data#microbiome diversity#PERMANOVA#distance matrices
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill scikit-bio-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scikit-bio
Source: https://github.com/LeonChaoX/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/LeonChaoX/qinyan-academic-skills --skill scikit-bio-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

scikit-bio solves the problem of turning messy biological sequence and community ecology data into validated analyses, distance matrices, ordination outputs, and hypothesis-test results without hand-rolling core bioinformatics logic.

Core Features & Use Cases

  • Sequence I/O & manipulation: Read/write common biological sequence formats (FASTA/FASTQ/GenBank/Newick/BIOM), then perform transformations like reverse-complement, transcription, and translation.
  • Alignments & phylogenetics: Do pairwise and multiple sequence alignment, build phylogenetic trees, and compute tree distance metrics (e.g., Robinson-Foulds, patristic distances) with Newick workflows.
  • Microbiome diversity & ecology stats: Compute alpha/beta diversity (including UniFrac), perform ordination (PCoA/CCA/RDA), and run permutation-based tests like PERMANOVA/ANOSIM/PERMDISP and Mantel tests.
  • Bioinformatics-ready data structures: Handle distance/dissimilarity matrices and microbiome tables (BIOM) with ID-based integration across steps.

Quick Start

Use the scikit-bio skill to calculate alpha and beta diversity from your BIOM feature table and visualize samples using PCoA.

Frequently Asked Questions about scikit-bio

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

FAQPage Schema
How do I calculate UniFrac beta diversity and run PERMANOVA on a BIOM table?▼

To calculate UniFrac beta diversity and run PERMANOVA, process your BIOM feature table by constructing distance matrices and applying permutation-based statistical tests to evaluate community differences across mapped sample IDs.

Can I read FASTA sequences and build phylogenetic trees in Newick format?▼

Yes, you can read FASTA sequences and build phylogenetic trees in Newick format by performing validated alignments, constructing phylogenetic trees, and computing tree distance metrics like Robinson-Foulds through Newick I/O workflows.

What is the best way to perform ordination analysis on microbiome distance matrices?▼

The best way to perform ordination analysis on microbiome distance matrices is to apply Principal Coordinates Analysis (PCoA), CCA, or RDA directly to your constructed dissimilarity matrices to visualize sample relationships.

Does scikit-bio support Mantel tests and ANOSIM for community ecology data?▼

Yes, scikit-bio supports Mantel tests and ANOSIM for community ecology data by running permutation-based statistical tests on distance matrices to assess correlations and group similarities with correctly mapped inputs.

How do I compute alpha diversity from biological sequence data?▼

To compute alpha diversity from biological sequence data, load your sequence formats into a BIOM table and utilize diversity modules to calculate within-sample species richness and evenness metrics across mapped IDs.

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