separate out nexus files

[roblanf]

At the moment we have the alignment and the SETS block all in one file. But this is annoying in terms of utility.

If we go ahead and make the partitions, loci, and genomes into a csv file, it would be better to have:

• alignment.nex
• partitions.nex
• loci.nex
• genomes.nex

partitions.nex, loci.nex, and genomes.nex all have CHARSETS only, which list the relevant sites for each element.

E.g. partitions.nex would look like:

begin SETS;

    CHARSET COI_1stpos = 1-1592\3;
    CHARSET COI_2ndpos = 2-1592\3;
    CHARSET COI_3rdpos = 3-1592\3;
    CHARSET 16S = 1593-3037;

end;

and loci.nex would look like:

begin SETS;

    CHARSET COI = COI_1stpos: 1-1592\3, COI_2ndpos: 2-1592\3, COI_3rdpos: 3-1592\3;
    CHARSET 16S = 16S: 1593-3037;

end;

etc

This lets people easily do whatever kind of analysis they are interested in.

[roblanf]

All of these files can be automatically built from the csv file