PAL: Phylogenetic Analysis Library
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:
Three other ways of accessing the functionality in PAL without requiring
Java programming experience are planned:
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.
(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
program, a modular system for evolutionary analysis written in Java by Wayne and Dave
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
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.