The benefit of pyRAD over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (vsearch) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.
pyRAD is intended for use with any type of restriction-site associated DNA. It currently supports RAD, ddRAD, PE-ddRAD, GBS, PE-GBS, EzRAD, PE-EzRAD, 2B-RAD, nextRAD, and can be extended to other types. Below is the download link as well as a number of tutorials. There is a “general use” pyRADtutorial which explains how to install and setup input files, and also tutorials with example data sets for different data types and analyses. pyRAD was initially described in the following publication (preprint, journal)