[Biojava-l] Quicktree

James Procter jimp at compbio.dundee.ac.uk
Tue Aug 12 12:39:46 UTC 2008

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.

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