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Excepti= on in thread "main" java.lang.UnsupportedClassVersionError: edu/rice/cs/bio= info/programs/phylonet/Program : Unsupported major.minor version 51.0
If your g= ene trees have support values as node labels, PhyloNet cannot read them cor= rectly. See Rich Newick Format for the format of phylogenies that PhyloNet r= eads. For example, if your gene tree is (((A:1.0,B:1.0)100:1.0,<= /span>(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 in= dicated below
Duplica= te node 100
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 res= ulting gene trees.
>jav= a -jar PATH/TreeConversion.jar inputFile outputFile
Some commands require a l= arge amount of memories, like InferNetwork_ML. If your dataset is large, you might run in= to memory issue indicated below
java.l= ang.OutOfMemoryError: Java heap space
When you launch PhyloNet from command line, add -Xmx followed b= y the memory size you want to allocated to Java. For example, if you want t= o increase the memory to 4G for running PhyloNet, run the following command=
>jav= a -jar -Xmx4G PATH/jar/PhyloNet_X.Y.Z.jar script.nex