References that are not literature or qualified sources
As a computer scientist, I often encounter this as well. I have seen three main approaches used, in decreasing order of preference


Cite the paper about the software, if one exists: academic software is often the subject of papers, and the authors very much appreciate those citations, often explicitly requesting them in the software documentation.
Cite the software as a miscellaneous reference: most citation styles will have an explicit recommended means for doing so, (e.g., this post on APA software citations)
The first time the software is mentioned, put a link to the software in a footnote or parentheses.


The earlier ones are better for the authors of the software, but I have sometimes had journals refuse to allow me to give a proper citation.