BaseFinder is a tool for processing trace data for DNA sequencing, or for analysis of SHAPE data. It was written primarily by Morgan Giddings and Jessica Severin at the University of Wisconsin-Madision, in Lloyd Smith's lab. The program was started in 1991 by Morgan, and continued refinements were made through 1997. From 2005-2008, Suzy (Vasa) Stiegelmeyer added tools and support for SHAPE analysis and TRFLP.
The code was last built in 2008 and supported OSx 10.4 and 10.5. It no longer builds in 10.9 and likely earlier OSx releases, but I'm (Suzy) working on that in my spare time. Please read the BaseFinder README and ShapeFinder README for more details, how to build it in Xcode and history information.
BaseFinder is written in Objective-C.