At one point I was involved in a Java library for Phylogentic analysis (the Phylogentic Analysis Library - PAL). Here is a copy of the source code for the last released version (I believe). I have not worked on this for a number of years, but I did do substantial work on a replacement library which has lots of nice features, and is somewhat faster. I will try and release that at some point (please email me to encourage me to do so).
This is made available according to the GPL licence (see in source code, and related paper)
A brief introduction to the Phylogenetic Analysis Library version 1.5 (paper link)