pyrad has now been superceded by ipyrad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.

pyrad

Assembly and analysis of RADseq data sets

Tutorials

Detailed information and a number of example tutorials are available here <http://www.dereneaton.com/software/pyrad/>_.

Downloads

Stable release versions can be downloaded here <https://github.com/dereneaton/pyrad/releases>_, 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

Python requirements ^^^^^^^^^^^^^^^^^^^ You will need the following two Python dependencies with pyrad.

• numpy
• scipy

In addition to the programs

• muscle <http://www.drive5.com/muscle/downloads.htm>_
• vsearch <https://github.com/torognes/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 <[email protected]>_.