scikit-bio - Bioinformatics and Ecology

scikit-bio provides the data structures and statistical methods needed for rigorous biological analysis. It excels in calculating alpha/beta diversity, performing ordination (PCoA), and handling complex phylogenetic trees.

When to Use

• Analyzing microbiome data (taxonomic composition, community structure).
• Calculating ecological diversity metrics (Shannon, Simpson, UniFrac).
• Performing ordination for visualization (PCoA, DCA).
• High-level sequence manipulation (DNA, RNA, Protein with metadata).
• Reading and writing phylogenetic trees (Newick format).
• Pairwise and multiple sequence alignment analysis.
• Statistical testing of community differences (PERMANOVA, ANOSIM).

Reference Documentation

Official docs: http://scikit-bio.org/
Tutorials: http://scikit-bio.org/docs/latest/
Search patterns: skbio.sequence, skbio.stats.distance, skbio.diversity, skbio.stats.ordination