The followings are some of the problems you might run into when running PhyloNet:

  1. Outdated Java version


    Exception in thread "main" java.lang.UnsupportedClassVersionError: edu/rice/cs/bioinfo/programs/phylonet/Program : Unsupported major.minor version 51.0

    Solution: Update your Java to 1.7.0 or later

  2. Wrong format of gene trees


    If your gene trees have support values as node labels, PhyloNet cannot read them correctly. See Rich Newick Format for the format of phylogenies that PhyloNet reads. For example, if your gene tree is (((A:1.0,B:1.0)100:1.0,(C:1.0,D:1.0)100:1.0)90:1.0,E:1.0), PhyloNet will read the support values as the names of nodes so that you will get error indicated below

    Duplicate node 100

    Solution: Download the executable TreeConversion.jar and run it on your gene trees 

    TreeConversion.jar runs from command line as follows. It takes two parameters, including inputFile which contains your gene trees and outputFile which is the file for the resulting gene trees.

    >java -jar PATH/TreeConversion.jar inputFile outputFile



  3. Not enough memory


    Some commands require a large amount of memories, like InferNetwork_ML. If your dataset is large, you might run into memory issue indicated below

     java.lang.OutOfMemoryError: Java heap space

    Solution: Increase the memory by using -Xmx

    When you launch PhyloNet from command line, add -Xmx followed by the memory size you want to allocated to Java. For example, if you want to increase the memory to 4G for running PhyloNet, run the following command

    >java -jar -Xmx4G PATH/jar/PhyloNet_X.Y.Z.jar script.nex