Hi Scooter Scooter Willis wrote: > 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. You could use the neighbour joining implementation from the Jalview source - since it is GPL. It will construct a tree from aligned data, but it uses the Jalview datamodel, which may cause you problems. Alternatively, there's a library called PAL, but I'm not sure if that's actually being supported now.
Jim Procter. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l