pyrad

Assembly and analysis of RADseq data sets

Tutorials

Detailed information and a number of example tutorials are available here.

Downloads

Stable release versions can be downloaded here, or you can clone the current development version using git:

git clone https://github.com/dereneaton/pyrad.git

Installation (As of v.3.0.6 and newer)

With the following you can install pyrad so that it is callable as an executable from anywhere on your machine. If you have pip, then the second option will also install the dependencies numpy and scipy:

cd pyrad
sudo pip install .
pyrad -h

cd pyrad
sudo python setup.py install
pyrad -h

Or alternatively, without having to install you can simply call pyRAD.py from its location using python:

python pyrad/pyrad/pyRAD.py -h

Python requirements

You will need the following two Python dependencies with pyrad.

numpy

scipy

In addition to the programs

muscle

vsearch

Example usage (see tutorials)

>>> pyrad -n
    new params.txt file created


>>> pyrad -p params.txt

Licence

GPLv3

Authors

pyrad was written by Deren Eaton.

atcg/pyrad