alterlab-scikit-bio

# scikit-bio ## Overview scikit-bio is a comprehensive Python library for working with biological data. Apply this skill for bioinformatics analyses spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics. ## When to Use This Skill This skill should be used when the user: - Works with biological sequences (DNA, RNA, protein) - Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.) - Performs sequence alignments or searches for motifs - Constructs or analyzes phylogenetic trees - Calculates diversity metrics (alpha/beta diversity, UniFrac distances) - Performs ordination analysis (PCoA, CCA, RDA) - Runs statistical tests on biological/ecological data (PERMANOVA, ANOSIM, Mantel) - Analyzes microbiome or community ecology data - Works with protein embeddings from language models - Needs to manipulate biological data tables ### Does NOT Trigger | Scenario | Use Instead | |----------|-------------| | Running the full amplicon pipeline (demux -> DADA2 -> taxonomy -> diversity) as QIIME 2 artifacts | `alterlab-qiime2-amplicon` | | Inferring a phylogeny with a substitution model (IQ-TREE/RAxML, bootstrap support) | `alterlab-phylogenetics` | | General sequence record parsing, BLAST parsing, Entrez retrieval | `alterlab-biopython` | | Single-cell or bulk expression analysis rather than community ecology | `alterlab-scanpy` / `alterlab-pydeseq2` | | Generic multivariate statistics on non-composition...