I've run into an error when attempting to pipe raxml trees into phylonet. I can successfully use phylonet to construct inferred species trees based on many raxml bestTrees files which have been catenated together as one tree file. However, when I try to pass the catenated bootstrap trees (i.e., bipartition files) into phylonet, I receive the following error. Has anyone dealt with this previously and if yes, have you found a solution? Thanks!
[jturner8@compute-0-29 phylonet]$ java -jar /home/jturner8/bin/ phylonetv24.jar inferstbootstrap -n 100 -m MDC -i cat.bipartitions.phy -o bootstrap.test.newick Error when parsing the Newick representation from input file. Duplicate node 0 phylonet.tree.io.ParseException: Duplicate node 0 at phylonet.tree.io.NewickReader.readNode(NewickReader.java:415) at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399) at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399) at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399) at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399) at phylonet.tree.io.NewickReader.readNode(NewickReader.java:399) at phylonet.tree.io.NewickReader.readTree(NewickReader.java:374) at phylonet.tree.io.NewickReader.readTree(NewickReader.java:95) at phylonet.coalescent.Bootstrap.main(Bootstrap.java:49) at phylonet.cmdline.tool.BootstrapCmdLineTool.performCalculation(BootstrapCmdL ineTool.java: 43) at phylonet.cmdline.CommandLineApp.setUpAndRunTool(CommandLineApp.java: 54) at phylonet.cmdline.CommandLineApp.main(CommandLineApp.java:45) at phylonet.app.PhyloNetApp.main(PhyloNetApp.java:45) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImp l.java: 25) at java.lang.reflect.Method.invoke(Method.java:597)
From the developers of PhyloNet: I looked at your file. The gene trees are not in the right format of what PhyloNet accepts. Your format has (... , ...)A:B for internal nodes where A is the bootstrap value and B is the branch length. PhyloNet interprets it as A is the name of that internal node and B is the branch length. In PhyloNet v2.4, the right format is (... , ...):B:A.
Currently searching for an easy way to switch (... , ...)A:B to read (... , ...)B:A for many tree files.
put that as an answer and accept it, so that its easy to find for other people having the same problem
Can you see if you find two node 0's in your catenated tree file? Just a wild guess from only seeing the error lines, but it might be that when it's putting them together it's not changing the node id's and that is why you get Duplicate node 0