...
Blocks in a NEXUS file start with the BEGIN keyword and terminate with the END; keyword. This example file contains two blocks--NETWORKS and PHYLONET. Contained within the PHYLONET block is the list of commands PhyloNet will execute when processing the NEXUS file. Commands in a PHYLONET block begin with a command identifier and terminate with a semicolon. In this example script, three commands are listed: Charnet, Cmpnets, and CountCoal. Appearing after the command identifier but before the semicolon are any parameters provided to a given command for its execution. For example in the script file above three parameters are provided to the Charnet command: net, -m and tree. Details Details about specific parameters for a given command can be found on the documentation page for the given command.
The NETWORKS block provides an area for defining any phylogenetic networks utilized by any command in the PHYLONET block. A network definition in the NETWORKS block must be of the form:
...