scikit-bio

Overview

scikit-bio is a comprehensive Python library for biological data analysis, spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics. It provides specialized data structures (DNA, RNA, Protein, DistanceMatrix, TreeNode, TabularMSA) that integrate with the broader Python scientific stack.

When to Use

• Calculating alpha/beta diversity and running PERMANOVA on microbiome data
• Building phylogenetic trees from distance matrices (NJ, UPGMA)
• Performing PCoA ordination on community composition data
• Reading/writing biological formats (FASTA, FASTQ, Newick, BIOM)
• Pairwise sequence alignment (Smith-Waterman, Needleman-Wunsch)
• Computing UniFrac distances for phylogenetic beta diversity
• Statistical testing on ecological distance matrices (ANOSIM, Mantel)
• Working with QIIME 2 artifacts and microbiome pipelines
• For high-throughput NGS alignment/variant calling, use STAR/BWA instead
• For protein structure prediction, use AlphaFold/ESMFold instead