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 ## Core Capabilities ### 1. Sequence Manipulation Work with biological sequences using specialized classes for DNA, RNA, and protein data. **Key operations:** - Read/write sequences from FASTA, FASTQ, GenBank, EMBL formats - Sequence slicing, concatenation, and searching - Reverse complement, transcription (DNA→RNA), and translation (RNA→protein) - Find motifs and patterns using regex - Calculate distances (Hamming, k-mer based) - Handle sequence quality scores and metadata **Common patterns:** ```python import skbio # Read sequences from file seq = skbio.DNA.read('inpu...