What statistical tests are available for ecological data?

It provides specialized non-parametric tests such as PERMANOVA, ANOSIM, and Mantel tests to assess group differences and matrix correlations.

Can I use this skill for microbiome diversity analysis?

Yes, it is highly optimized for microbiome research, offering alpha and beta diversity metrics like Faith's PD, Shannon entropy, and weighted/unweighted UniFrac.

What biological file formats can this skill handle?

The skill supports over 19 biological file formats, including FASTA, FASTQ, GenBank, Newick, BIOM (HDF5 and JSON), and Clustal for seamless data integration.

Does it support phylogenetic tree construction?

Absolutely. It can construct trees using Neighbor Joining (NJ), UPGMA, and other scalable methods, while also allowing for tree pruning and rerooting.

Scikit-bio Bioinformatics

Name: Scikit-bio Bioinformatics
Author: lifangda

bylifangda

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Data Science & ML

Performs advanced biological data analysis including sequence manipulation, phylogenetic tree construction, and microbial diversity metrics.

About

scikit-bio is a comprehensive Python library designed for bioinformatics and community ecology analysis. This skill enables Claude to handle complex biological datasets with precision, offering capabilities for sequence alignment, phylogenetic tree manipulation, and the calculation of ecological diversity metrics like UniFrac and Shannon entropy. It is an essential tool for researchers and developers working on microbiome studies, molecular evolution, and genomic data processing, providing specialized support for domain-specific file formats and multivariate statistical testing.

Key Features

Extensive file I/O support for FASTA, Newick, BIOM, and GenBank formats
Microbial diversity metrics including alpha, beta, and UniFrac calculations
Comprehensive biological sequence manipulation (DNA, RNA, and Protein)
16 GitHub stars
Advanced ordination and multivariate statistics (PCoA, CCA, PERMANOVA)
Phylogenetic tree construction and evolutionary relationship analysis

Use Cases

Bioinformatics pipeline development for sequence searching and alignment
Microbiome community ecology analysis and diversity profiling
Molecular evolutionary studies and phylogenetic tree visualization

About

Key Features

Extensive file I/O support for FASTA, Newick, BIOM, and GenBank formats
Microbial diversity metrics including alpha, beta, and UniFrac calculations
Comprehensive biological sequence manipulation (DNA, RNA, and Protein)
16 GitHub stars
Advanced ordination and multivariate statistics (PCoA, CCA, PERMANOVA)
Phylogenetic tree construction and evolutionary relationship analysis

Use Cases

Bioinformatics pipeline development for sequence searching and alignment
Microbiome community ecology analysis and diversity profiling
Molecular evolutionary studies and phylogenetic tree visualization