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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<meta name="KeyWords"
content="PAL, phylogenetic analysis library, molecular phylogenetics,
molecular evolution, phylogeny,
tree reconstruction, maximum likelihood">
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<title>The PAL Project</title>
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<a href = "index.html">About</a>
<br>
<a href = "people.html"> People Involved </a>
<br>
<a href = "features.html">Features</a>
<br>
<b>User Interfaces</b>
<br>
<a href = "related.html">Related Projects</a>
<br>
<br>
<a href = "download.html">Downloads and Installation</a>
<br>
<a href = "history.html">History</a>
<br>
<br>
<a href = "contributing.html">Contributing</a>
<br>
<a href = "acknowledgments.html">Acknowledgements</a>
<br>
<br>
<a href = "online.html">Pal Online</a>
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<img src=pal.gif hspace=10 align=left ALT="PAL icon">
<strong><font size="+2">PAL: Phylogenetic Analysis Library</font></strong>
<br>
<br>
<em><strong>
<center>User Interfaces</center>
</em></strong>
<p>
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.
<p>
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:
<ul>
<li>
<strong><a href="http://www.stat.uni-muenchen.de/~strimmer/pal-project/vanilla/">Vanilla</a></strong>
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.
</li>
<li>
<strong><a href="http://www.cebl.auckland.ac.nz">Pebble</a></strong>
(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.
</li>
</ul>
Three other ways of accessing the functionality in PAL without requiring
Java programming experience are planned:
<ul>
<li>
It should be rather straightforward to use features available in PAL from
within the
<a href="http://mesquite.biosci.arizona.edu/mesquite/mesquite.html">Mesquite</a>
program, a modular system for evolutionary analysis written in Java by Wayne and Dave
Maddison.
</li>
<li>
In collaboration with Andrew Rambaut (University of Oxford) it is planned to
develop a general <a href="http://www.xml.org">XML</a> interface definition for evolutionary analysis, which will be
implemented for PAL and for Andrew Rambaut 's
<a href="http://evolve.zoo.ox.ac.uk/projects/BBSRC-Nautilus/Nautilus.html">Nautilus C++
libraries</a>.
</li>
<li>
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.
</li>
</ul>
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