Archaeopteryx and Forester

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These are two tree handling tools from Christian Zmasek.

Forester usage

If you get major.minor java errors, this is because f the java version. Forester is pretty up-to-date, so it will want java version 8.

To convert a newick tree to phyloxml:

java -cp /usr/local/forester_1043.jar org.forester.application.phyloxml_converter -f=dummy gubbins.final_tree.tre gubbins.final_tree.xml

Note how this presupposes the location for the jar-file. This will need to be modified most likely.