[Biojava-l] Quicktree

[Scooter Willis]

I am searching for a Java implementation of Quicktree or other accepted 
methods for reconstructing phylogenies from aligned sequence data. I am 
currently using quicktree but it requires sequence data to be in 
stockholm format which requires a conversion step, followed by running 
quicktree in cygwin on windows and then parse the Newick/Hew Hampshire 
format. I use quicktree because it is fast against large sequences. I 
would like to integrate the tree construction step as part of my Java 
application. Anyone know of an accepted Java library for building trees? 
Plenty of tree viewers just can't seem to find anything to construct 
from aligned sequence data.

Thanks

Scooter