[Biojava-l] It is possible to parse phylogenetic trees with bootstrap/posterior probabilities

Martin Jones martin.jones at ed.ac.uk
Mon Jan 31 10:40:51 UTC 2011

Hi all,

I am using BioJava to parse MrBayes NEXUS files containing consensus
trees, using code that looks like this:

NexusFileBuilder builder = new NexusFileBuilder();
NexusFileFormat.parseFile(builder, new File('2fin3-4.nex.con'));
NexusFile nexus = builder.getNexusFile();
def tree = getTree(nexus, 'con 50 majrule')

The parser constructs a weighted graph where the edge weights are the
branch lengths. It is possible to parse the tree so that posterior
probabilities are included in the resulting object?


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