anhima
- Exploration and analysis of genetic variation dataΒΆ
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