scikit-bio

Topics in the source

• scikit-bio
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Sequence Manipulation
• 2. Sequence Alignment
• 3. Phylogenetic Trees
• 4. Diversity Analysis

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. 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 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

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