Quantitative analysis of gels from hydroxyl radical footprinting and other structure mapping techniques can provide a great deal of insight into the structural details of RNA molecules. We have developed and implemented a software package (SAFA v1.1) that allows rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, we estimate that an entire gel with thousands of bands can be quantified in less than 10 minutes. In general all the automated features have amanual override, such that even difficult or exceptional gels can be analyzed with the package.