pyrad
Assembly and analysis of RADseq data sets
GPL-3.0 License
pyrad has now been superceded by ipyrad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]>_.