scikit-bio 0.6.0 documentation

scikit-bio (canonically pronounced sigh-kit-buy-oh) is a library for working with biological data in Python 3. scikit-bio is open source, BSD-licensed software that is currently under active development.

• Input and Output (skbio.io)
  • Supported file formats
  • Read/write files
  • Develop custom formats
  • Tutorial
• Biological Sequences (skbio.sequence)
  • Sequence types
  • Sequence utilities
  • Distance calculation
  • Tutorial
• Sequence Alignments (skbio.alignment)
  • Alignment structure
  • Alignment algorithms
  • Tutorial
• Trees and Phylogenetics (skbio.tree)
  • Tree structure and operations
  • Phylogenetic reconstruction
  • Tree utilities
  • Tutorial
• Community Diversity (skbio.diversity)
  • Alpha diversity
  • Beta diversity
  • Introduction
  • Tutorial
• Multivariate Statistics (skbio.stats)
  • Distance matrix statistics
  • Ordination methods
  • Composition statistics
  • Data subsampling
  • Other statistical methods
• Data Table (skbio.table)
  • BIOM table
• Metadata (skbio.metadata)
  • Sample metadata
  • Metadata columns
  • Interval metadata
• Workflow construction (skbio.workflow)
  • Classes
  • Decorators
  • Tutorial
• Utilities for Developers (skbio.util)
  • Testing functionality
  • Miscellaneous functionality
  • Developer warnings