anhima - Exploration and analysis of genetic variation data

This package is no longer under active development. Existing functionality is gradually being migrated into the `scikit-allel`_ package, where development efforts are now focused.

• Documentation: http://anhima.readthedocs.org
• Examples: http://nbviewer.ipython.org/github/alimanfoo/anhima/tree/master/examples/
• Source: http://github.com/alimanfoo/anhima
• Mailing list: https://groups.google.com/forum/#!forum/anhima
• Release notes: https://github.com/alimanfoo/anhima/releases

Installation

Install latest stable release from PyPI:

pip install -U anhima

Install from GitHub:

git clone https://github.com/alimanfoo/anhima.git
cd anhima
python setup.py install

Contents

• Locating samples and variants
• Genotypes
• Allele frequencies
• Site frequencies
• Doubleton sharing
• Linkage disequilibrium
• Genetic distance
• Principal components analysis
• Multidimensional scaling
• Trees
• Pedigrees (families and crosses)
• Input/output utilities
• HDF5 utilities
• Miscellaneous utilities
• Simulations

Indices and tables

• Index
• Module Index
• Search Page