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

Or

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.

• numpy
• scipy

In addition to the programs

• muscle
• vsearch

Example usage (see tutorials) ^^^^^^^^^^^^^^^^^^^ :

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


>>> pyrad -p params.txt 

GPLv3

pyrad was written by Deren Eaton.