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>java -jar $PHYLONET PATH/jar/PhyloNet_X.Y.Z.jar charnet.nex

Charnet net -m tree
((a,(b,c)),(e,d));
((a,b),((d,c),e));

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Note how the Charnet command identifier and its parameters are first displayed followed by the output of the command. This feature becomes very helpful for reading results when many commands are listed in a single NEXUS file.

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Each command that supports the optional file output command parameter in a given NEXUS file can be given its own unique file parameter value resulting in the generation of distinct output files for each command. Alternatively, one may specify the file output parameter for only some commands in a NEXUS file. In this case those commands without the optional parameter would continue to utilize the default behavior and display their results on the console. Repeating a file output parameter value for many commands in a NEXUS file is not advisable as each command's output will overwrite the previous command's output with the same parameter value. One can however send the entire output of a PhyloNet execution to one file by using most operating systems' redirection operators.

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PhyloNet provides a special command called Nexus_Out that allows the user to instruct instructs PhyloNet to additionally create an output NEXUS file containing a copy of each tree result generated by all commands within the script. For example, executing the following NEXUS script:

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in addition to the usual console output of a similar file without the Nexus_Out for the Charnet command.

All trees recorded in the TREES section will be of the form:

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