scikit-bio¶

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

API Reference¶

Sequence collections and alignments (skbio.core.alignment)
Biological sequences (skbio.core.sequence)
Dissimilarity and distance matrices (skbio.core.distance)
Exceptions (skbio.core.exception)
Warnings (skbio.core.warning)
Genetic Code (skbio.core.genetic_code)
Tree representations (skbio.core.tree)
Constructing workflows (skbio.core.workflow)
Distribution visualizations (skbio.draw.distributions)
Format biological sequences (skbio.format.sequences)
Alpha diversity measures (skbio.math.diversity.alpha)
Beta diversity measures (skbio.math.diversity.beta)
Distance-based statistics (skbio.math.stats.distance)
Miscellaneous statistics utilities (skbio.math.stats.misc)
Ordination methods (skbio.math.stats.ordination)
Spatial Statistics (skbio.math.stats.spatial)
Gradient analyses (skbio.math.gradient)
Subsampling (skbio.math.subsample)
Parse biological sequences (skbio.parse.sequences)
I/O utils (skbio.util.io)
Miscellaneous Utilities (skbio.util.misc)
Testing utilities (skbio.util.testing)

Developer Documentation¶

The developer documentation contains information for how to contribute to scikit-bio.

Supporting Python 2 and Python 3
Coding guidelines
Adding a new module to skbio