SEQSEE (Wishart et al., 1994a) and XALIGN (Wishart et al., 1994b) are two text-based, menudriven programs developed specifically for comprehensive protein sequence analysis. Originally compiled to run on SUN and SGI workstations only, SEQSEE and XALIGN have been distributed to more than 300 laboratories around the world. Both programs have been used in a variety of applications ranging from routine sequence analysis to the identification of previously unknown sequence relationships (Upton et

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... , 1992; 1993; Dulhanty & Riordan, 1994) . Since releasing these programs, we have received numerous requests asking if they could be ported to additional computer platforms (Macintosh's and PC's) or if the text-based menus could be replaced with a more friendly graphical user interface (GUI). In response to these and other requests we have integrated XALIGN and SEQSEE into a singlethreaded package with a uniform graphical user interface that is fully supported by SGI (Irix Ver. 5.0 and higher), SUN (Solaris and SunOS 4.1.3 and higher), Macintosh (Power PC OS 7.5 and higher) and PC (Windows 95) platforms. We have chosen the Smalltalk programming language to develop our graphical interface because it allows the creation of sophisticated GUI's that look and operate almost identically across all major platforms and operating systems. In many respects, Smalltalk, which was originally developed by Xerox's PARC in the late 1970's, is a more sophisticated version of the more familiar WWW language called JAVA. In particular, Smalltalk allows the facile creation of object-oriented, platform-independent graphical user interfaces. By designing the Smalltalk GUI to access the computationally intensive back-end routines through Smalltalk function calls, we were able to preserve a substantial portion of the original SEQSEE and XALIGN code (written in C). This separation between the front-end (the GUI) and the back-end has allowed for a more rapid implementation of the front-end while preserving the integrity of well-tested back-end programs. In building the SEQSEE/XALIGN interface, a total of 11 separate windows or views were constructed, including (1) a sequence editor; (2) an alignment editor; (3) a simple text editor; (4) a graph viewer/editor; (5) a dotplot viewer/editor; (6) a helical wheel viewer/editor; (7) a structure