This is the pal library source and api docs, version 1.5.1  downloaded from 
www.cebl.auckland.ac.nz/pal-project/download.html.

I (Terri) added the pal_test directory and modified the code that reads
newick strings to handle quotes and special characters in taxa names.
The files I changed are pal/Tree/ReadTree.java and pal/io/FormattedInput.java.
I'm calling our version pal-1.5.1-modified-1.  I also modified the ant build.xml
to give the jar the name we expect.

We use the pal library in the cipres framework and in the cipres web app.
Both uses are pretty minor.  In the web app, it's used by the treeimage
servlet to read in a newick file, reroot the tree and write out the new
newick tree.

The cipres framework expects to find the pal jar checked into svn and the
web app looks for the jar in the maven repo.