pyrad has now been superceded by ipyrad
(http://ipyrad.readthedocs.io) <-- see here
All new development will be made on ipyrad and I recommend that pyrad users switch over. The new software offers huge speed improvements and many new features.
Assembly and analysis of RADseq data sets
Detailed information and a number of example tutorials are available here.
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
You will need the following two Python dependencies with pyrad.
In addition to the programs
Example usage (see tutorials)
>>> pyrad -n new params.txt file created >>> pyrad -p params.txt
pyrad was written by Deren Eaton.