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In order to run the PhyloNet toolkit, you must have Java 1.78.0 or later installed on your system. All references to the java command assume that Java 1.7 is being used.
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java -jar $PHYLONET_DIRECTORY/PhyloNet_X.Y.Z.jar script.nex |
Where $PHYLONET$PHYLONET_PATH DIRECTORY is the directory of jar file PhyloNet_X.Y.Z.jar, and script.nex is the NEXUS file containing the commands to be executed.
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Add this package to your java library, and load this library before you run PhyloNet.
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One input example: mcmc_seq.nex
All input NEXUS files: download
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Corresponding results: Fig 13 in the book chapter.
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