PAL is designed as an object-oriented programming library, and as such it has no direct user interface. To access the methods and objects available in PAL you need to program in Java.

However, there are user-friendly programs available that rely (in part) on PAL to do their job. Be aware, however, that they will usually restrict functionality to some core features of PAL:

• Vanilla aims at providing a simple bare bones text interface to some selected features in PAL. It basically consists of a set of command line applications, most of them in PHYLIP CUI style. Best run in a UNIX (incl. MacOS X) or MSDOS shell. This package is also useful to see how you could use PAL in your own program.
• Pebble (codenamed vCEBL) is much more broadly targeted. It not only offers a GUI interface to PAL but also comes with its own functional command language. PEBBLE has an easy-to-use installation program.

• It should be rather straightforward to use features available in PAL from within the Mesquite program, a modular system for evolutionary analysis written in Java by Wayne and Dave Maddison.
• In collaboration with Andrew Rambaut (University of Oxford) it is planned to develop a general XML interface definition for evolutionary analysis, which will be implemented for PAL and for Andrew Rambaut 's Nautilus C++ libraries.
• Java provides the opportunity to write web-based applications (applets) that can be executed in a web browser. In collaboration with Andrew Rambaut it is planned to write simple applets, e.g. for skyline plot analysis, tree viewing etc.