[Biojava-l] Phylogenetic Trees

[Richard Holland]

The package you found in biojavax was written with the intention of
parsing existing tree structures from NEXUS files, and to perform basic
analyses of them (neighbour joining, etc.). The code can represent trees
regardless of their source, and can output them as NEXUS files, but
there are no algorithm implementations in that package for constructing
new trees and so you'd probably have to write those from scratch.

cheers,
Richard

Scooter Willis wrote:
> I was looking for Java code to construct a phylogenetic tree from
> aligned sequence data. I came across org.biojavax.bio.phylo as an
> experimental package in the latest release of BioJava. The docs were
> thin and couldn't find any code examples so was wondering if anyone
> has used the package with success.
> 
> I also couldn't decide if the package is intended to load
> pre-constructed trees as Java objects or could be used to construct a
> tree from aligned sequence data.
> 
> Does anyone know of an accepted Java package for tree construction
> besides what is in JalView?
> 
> Thanks
> 
> Scooter
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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/