Which bioinformatics file formats are compatible?

The skill supports over 19 formats with automatic detection, including FASTA, FASTQ, GenBank, Newick, Clustal, and BIOM tables.

What types of biological sequences does this skill support?

It supports DNA, RNA, and protein sequences with specialized classes that provide alphabet validation and biological operations like transcription and translation.

Can I use this skill for microbiome research?

Yes, it is highly optimized for microbiome analysis, offering UniFrac distances, alpha/beta diversity metrics, and PCoA ordination methods.

Does it include statistical testing for ecological data?

Yes, it provides specialized non-parametric tests like PERMANOVA, ANOSIM, and Mantel tests for comparing biological distance matrices.

Scikit-bio (Biological Data Analysis)

Name: Scikit-bio (Biological Data Analysis)
Author: K-Dense-AI

byK-Dense-AI

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3,719

Data Science & ML

Performs comprehensive biological data analysis including sequence manipulation, phylogenetics, and microbial ecology statistics.

About

Scikit-bio is a specialized skill that empowers Claude to handle complex bioinformatics workflows directly within Python environments. It provides a robust toolkit for processing biological sequences, performing sequence alignments, constructing phylogenetic trees, and calculating ecological diversity metrics like UniFrac. By integrating these domain-specific capabilities, this skill enables researchers and developers to perform advanced multivariate statistics, ordination (PCoA), and microbiome analysis using high-level abstractions for common biological file formats.

Key Features

3,719 GitHub stars
Support for 19+ biological file formats including FASTA, Newick, and BIOM
Advanced sequence alignment using global and local dynamic programming algorithms
Phylogenetic tree construction, manipulation, and distance calculation
Calculation of alpha and beta diversity metrics for microbial community ecology
Sequence manipulation for DNA, RNA, and protein data with grammar validation

Use Cases

Constructing and visualizing phylogenetic relationships between species or strains
Processing and converting high-throughput sequencing data across various bioinformatics formats
Analyzing microbial community diversity and composition from OTU/ASV tables

About

Key Features

3,719 GitHub stars
Support for 19+ biological file formats including FASTA, Newick, and BIOM
Advanced sequence alignment using global and local dynamic programming algorithms
Phylogenetic tree construction, manipulation, and distance calculation
Calculation of alpha and beta diversity metrics for microbial community ecology
Sequence manipulation for DNA, RNA, and protein data with grammar validation

Use Cases

Constructing and visualizing phylogenetic relationships between species or strains
Processing and converting high-throughput sequencing data across various bioinformatics formats
Analyzing microbial community diversity and composition from OTU/ASV tables