SeqPup uses plain TEXT type files for its primary sequence data. These files can be exchanged without modification with many other sequence analysis programs. SeqPup automatically determines the sequence format of a data file when openning it. You have an choice of several formats to save it as. As of this writing, the GenBank format is prefered (see bugs).
The program looks in the folder "tables" for text files containing various data. At present these files include "codon.table", "renzyme.table" and "color.table".
There is a "SeqPup.prefs" file which stores various user options like window positions, mail address, child tasks. This is described more in the Install and Child Apps sections.
Various temporary files are created for child tasks, generally in the :Apps: folder. Currently you cannot run the Child Tasks portion of SeqPup from a locked file server because these temporary files need to be created where the child applications reside. Otherwise, SeqPup should operate from a locked fileserver properly, and can be launched by several users at once.