Difference between revisions of "Archaeopteryx and Forester"
(Created page with "=Introduction = 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...") |
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= Forester usage = | = Forester usage = | ||
| − | If you get major.minor java errors, this is because f the java version. Forester is pretty | + | 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: | 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 | java -cp /usr/local/forester_1043.jar org.forester.application.phyloxml_converter -f=dummy gubbins.final_tree.tre gubbins.final_tree.xml | ||
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| + | Note how this presupposes the location for the jar-file. This will need to be modified most likely. | ||
Latest revision as of 16:56, 23 September 2016
Introduction
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.
