Finally got this working:

Inline with the SplitsTree way of thinking (that is the representation of the different nexus blocks being part of a continuous pipeline, i.e. unaligned > character > network) you have to write in an st_assumption block into your .nex file (the file that you want to perform the operation on in the first place) and SplitsTree will then use this information to update your nexus file. To 'update' your nexus file you can run EXECUTE FILE on your .nex that now contains the st_assumption block (by creating a command file providing this as the -c flag). Splits tree will detect the fact that there are nexus blocks missing according to what you have put in your st_assumption block and it will 'update' the file.

An example is helpful. Let's say you have a .nex file which simply contains a single multiple sequence alignemtn (DNA). Let's say you want to run the MedianJoining method on this alignment. At the end of the .nex file you would append the following:

begin st_assumptions;

CHARTRANSFORM=MedianJoining Epsilon=5 SpringEmbedderIterations=10 LabelEdges=false ShowHaplotypes=true SubdivideEdges=false ScaleNodesByTaxa=true;

end;

You will see that I have added the MedianJoining information as an argument to the CHARTRANSFORM variable, this is because it is a method that acts to transform a nexus character block. If you want to do a method that works on, for example, an unaligned set of sequences you would use the UNALIGNTRANSFORM instead. Other options can be found in the documentation.

To get Splits tree to then create the network, you need to execute your new .nex file. To do this you create a new file (we'll call it to_exe). It contains, for example:

begin SplitsTree;

IMPORT FILE=/Users/humebc/phylogenetic_software/splitstree/SplitsTree/infasta_splitstree.fasta;

EXPORT FILE=/Users/humebc/phylogenetic_software/splitstree/SplitsTree/test_out.nex FORMAT=new nexus REPLACE=yes;

QUIT;

end;

The list of different 'commands' that are recognised are listed in the documentation.

Finally you can run ./SplitsTree -g -c to_exe

This will generate the network.

N.B. the command line version appears to be more format sensitive than the GUI version unfortunately.

I hope this can save somebody the time it cost me.

I'm sure it's pretty simple – does this page help: https://www.biostars.org/p/345347/ ?

The manual (http://ab.inf.uni-tuebingen.de/data/software/splitstree4/download/manual.pdf) Section 23 seems to provide an answer for you. Hope it helps!