What biological file formats does this skill support?

The scikit-bio skill supports over 19 biological formats, including FASTA, FASTQ, GenBank, Newick for trees, and BIOM for microbiome feature tables.

Does it support phylogenetic tree building?

Absolutely. It includes robust algorithms for Neighbor Joining (NJ), UPGMA, and tree manipulation tasks like pruning, rerooting, and Robinson-Foulds distance calculations.

Can Claude use this for microbiome research?

Yes, the skill is optimized for microbiome analysis, allowing Claude to calculate alpha and beta diversity (including UniFrac) and perform ordination like PCoA.

How does it handle sequence alignment?

It provides capabilities for global and local pairwise alignments using dynamic programming (Needleman-Wunsch/Smith-Waterman) and handles Multiple Sequence Alignments via TabularMSA.

Is scikit-bio compatible with other Python data libraries?

Yes, scikit-bio is built to integrate seamlessly with the standard scientific Python stack, including NumPy, Pandas, and Scikit-learn.

scikit-bio Bioinformatics & Ecology

Name: scikit-bio Bioinformatics & Ecology
Author: jimmc414

byjimmc414

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324

Data Science & ML

Performs comprehensive bioinformatics analysis including sequence manipulation, phylogenetics, and microbial ecology statistics within Python.

About

scikit-bio is a specialized Claude Code skill designed for advanced biological and ecological data science. It provides Claude with the domain-specific knowledge required to handle complex bioinformatics workflows, ranging from sequence alignment and phylogenetic tree construction to microbial diversity analysis. This skill is particularly useful for researchers working with microbiome datasets (QIIME 2 compatible), performing ordination such as PCoA or CCA, and running non-parametric statistical tests like PERMANOVA. By integrating this skill, Claude can automate the processing of biological file formats and implement rigorous scientific analysis patterns.

Key Features

Calculates alpha/beta diversity metrics and UniFrac distances for community ecology.
324 GitHub stars
Advanced ordination methods and statistical testing including PCoA, PERMANOVA, and Mantel tests.
Support for 19+ biological file formats including FASTA, FASTQ, GenBank, Newick, and BIOM.
Comprehensive sequence manipulation for DNA, RNA, and protein data with positional metadata.
Advanced phylogenetic tree construction, manipulation, and distance calculations (NJ, UPGMA, RF).

Use Cases

Processing and converting high-throughput sequencing data between standard bioinformatics formats.
Analyzing microbiome community composition using diversity metrics and PCoA visualization.
Constructing and comparing phylogenetic trees from sequence data or distance matrices.

About

Key Features

Calculates alpha/beta diversity metrics and UniFrac distances for community ecology.
324 GitHub stars
Advanced ordination methods and statistical testing including PCoA, PERMANOVA, and Mantel tests.
Support for 19+ biological file formats including FASTA, FASTQ, GenBank, Newick, and BIOM.
Comprehensive sequence manipulation for DNA, RNA, and protein data with positional metadata.
Advanced phylogenetic tree construction, manipulation, and distance calculations (NJ, UPGMA, RF).

Use Cases

Processing and converting high-throughput sequencing data between standard bioinformatics formats.
Analyzing microbiome community composition using diversity metrics and PCoA visualization.
Constructing and comparing phylogenetic trees from sequence data or distance matrices.