The "ChildApps" menu lets you link SeqPup with external sequence analysis programs that you or others may write. SeqPup can be configured to launch any other application, and to send it sequence data and command information. When the child program is finished with its analysis, SeqPup can open and display results files from the child in a variety of formats, including text, biosequence, PICT, RTF and GIF. On Macs, the ChildApps menu requires System 7 to operate.
The general design of child applications is taken to be data analysis programs that have a simple command-line user-interface, and that take input data from a file or from the system "standard input" file (stdin), and that write outputs to files and to two system standard files "standard output" (stdout) and "standard error" (stderr). This is how many existing analyses programs work, and it is very straightforward to program this basic kind of user-interface.
The value of SeqPup joined with these kinds of programs is that the SeqPup can concentrate on providing an easy-to-use interface for biologists, and the analysis application can concentrate on data analyses, without having to add a lot of software baggage to provide a more usable interface.
A desired addition to SeqPup will be a dialog to configure new and current child tasks. However, at present this needs to be done by using a text editor to change the SeqPup.prefs file.