Cite the software that was used in your research, including all software that was used to generate and analyze data. The Force11 recommendations: "citation is partly a record of software important to a research outcome". "Software should be cited on the same basis as any other research product such as a paper or a book; that is, authors should cite the appropriate set of software products just as they cite the appropriate set of papers."
Where to put software citations?
Where software and data citations should go may vary from publisher to publisher; check with the author guidelines if writing for publication. Where no more specific guidance exists, consider following the Force11 recommendations to put software citations in the reference list: "Software citations should be accorded the same importance in the scholarly record as citations of other research products, such as publications and data, they should be included in the metadata of the citing work, for example in the reference list of a journal article, and should not be omitted or separated."
How to cite software?
If guidelines from your publisher or citation style exist, follow them, or if writing for publication check with your editor. Some guidelines on citing software from publishers and manuals of style are included here. Many software packages also give guidance on how they want to be cited. If no guidance exists, best practices for software citation elements are below.
As described in the AAS Journal's software policy, software can be cited in two ways:
Citing the paper describing the software (e.g. "galpy: A python Library for Galactic Dynamics", Bovy 2015, ApJ, 216, 29);
Citing a DOI for the software, for example, obtained via Zenodo or FigShare (e.g. Foreman-Mackey et al. 2014, corner.py, v0.1.1, Zenodo, doi:10.5281/zenodo.11020, as developed on GitHub).
Ideally, both forms of citation should be included; alongside these formal references, authors may also want to include footnote URLs to appropriate code repositories, such as GitHub, or metadata indices, such as the Astrophysics Source Code Library.