Managing individual based genetic records in a geographic context.
Python C++ Other
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README.md

geneGIS

A Python Add-in and ArcGIS toolbox for manipulating individual-based genetic records in a geographic context.

http://genegis.org

Installation

Use the install page to get a packaged release.

To get the latest source, clone this repository, and run makeaddin.py to create an installable genegis.esriaddin file.

Tools

import:

  • parse SRGD formatted CSV files into a Geodatabase Feature Class

manipulation:

  • select and filter data based on spatial and attribute queries
  • extract raster values at encounter locations

geographic analysis:

  • compute accurate geodesic distance matricies
  • generate pairwise geodesic segements between samples

genetic analysis:

  • use SPAGeDi (included) to compute a variety of genetic tests, such as F_st.

export:

  • export to GenAlEx
  • export to Genepop
  • export to SPAGeDi
  • export to SRGD formatted CSV files for use with the Shepard Project

Building from Source

git clone --recursive https://github.com/genegis/genegis.git

Development

Nose tests are included which perform basic checks. To run, the tests, use pip to install requirements:

$ pip install -r requirements-dev.txt

Then, run nose from the top-level directory:

$ nosetests

Licensing

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. See LICENSING for details or visit

http://mozilla.org/MPL/2.0/.