Archaeopteryx and Forester
These are two tree handling tools from Christian Zmasek.
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.