Scikit-Bio skill: what it does and how to install it

What it does. Provides Python workflows with scikit-bio for biological sequences, alignments, phylogenetic trees, microbiome diversity, ordination and statistical tests. It reads and writes formats including FASTA, FASTQ, Newick and BIOM, and connects distance matrices, feature tables and protein embeddings to downstream analyses.

When to use it. Applies to sequence processing, comparative genomics, phylogenetics and community ecology, including PCoA, PERMANOVA and UniFrac. Requires Python 3.10+, NumPy 2.0+ and scikit-bio 0.7.4; QIIME 2 artifacts need QIIME 2 separately.