Why cite tools at all
Results depend on the software that produced them. Naming the tool, its version and its settings lets others repeat the work, and many journals now require it.
What to include
- The tool's name and, for installed software, its version.
- Where it can be found: a URL, or the paper that describes it.
- The settings you changed from the defaults, such as the genetic code, the PAM or the alignment scoring.
- The date you used it, for web tools that may change.
- An RRID, if it has one.
What an RRID is
A Research Resource Identifier is a permanent ID for an antibody, cell line, organism or piece of software, such as RRID:SCR_029096. Software and online tools have IDs starting with SCR_. Many journals ask for RRIDs because they can be searched across papers and do not break when a website moves. Find them in the SciCrunch resource registry.
Examples
Primer melting temperatures were calculated with the Toolyard Primer Tm Calculator (https://webtoolyard.com/primer-tm-calculator/, RRID:SCR_029096), accessed 5 October 2026, with the salt and primer concentrations used in the PCR.
Guide RNAs were selected with the Toolyard CRISPR Guide Finder (RRID:SCR_029096) using the NGG PAM and checked for off-target sites against the GRCh38 genome.
Every Toolyard tool, such as Reverse Complement, the CRISPR Guide Finder and the Molarity Calculator, can be cited with the same RRID.