Overview

SeqSift is a python package for vetting, manipulating, and converting molecular sequence data.

The package is written by Jamie Oaks of the University of Kansas Department of Ecology and Evolutionary Biology.

Requirements

SeqSift has only been tested on version 2.7 of Python.

It requires the Biopython: http://biopython.org/wiki/Biopython

Some components of Biopython require NumPy (http://numpy.scipy.org). However, none of the Biopython code currently used by SeqSift requires NumPy. Thus, SeqSift will work if you intall Biopython without NumPy.

Installation

You should have Python 2.7 and Biopython installed.

Clone Git repository and install using:

$ git clone git://github.com/joaks1/SeqSift.git
$ cd SeqSift
$ python setup.py install

If the install fails due to a permission error, try:

$ sudo python setup.py install

To run the test suite, use:

$ python setup.py test

If you plan to develop the code, install via:

$ python setup.py develop

Citing SeqSift

Please cite the Biopython library upon which SeqSift depends.

Acknowledgements

This software greatly benefited from funding provided to Jamie Oaks from the National Science Foundation (DEB 1011423 and DBI 1308885), University of Kansas (KU) Office of Graduate Studies, Society of Systematic Biologists, Sigma Xi Scientific Research Society, KU Ecology and Evolutionary Biology Department, and the KU Biodiversity Institute.

License

This program is distributed under the GPL license in the hope that it will be useful, but WITHOUT ANY WARRANTY. See the GNU General Public License for more details.