add locus charpartitions

[roblanf]

The point is to add explicit information on every single locus in the dataset.

At the moment we have

begin SETS;

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

    CHARPARTITION loci = 1:COI_1stpos, 2:COI_2ndpos, 3:COI_3rdpos, 4:16S;

    [genomes]
    CHARSET mitochondrial_genome = 1-3037;

    CHARPARTITION genomes = 1:mitochondrial_genome;

end;

But we should have

begin SETS;

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

    [loci]
    CHARPARTITION COI = 1:COI_1stpos, 2:COI_2ndpos, 3:COI_3rdpos;
    CHARPARTITION 16S = 1:16S;

    CHARPARTITION loci = 1:COI, 2:16S;

    [genomes]
    CHARPARTITION   mitochondrial_genome = 1:COI, 2:16S;

    CHARPARTITION genomes = 1:mitochondrial_genome;

This involves:

• Change current [loci] to [partitions]
• add a [loci] section with one CHARPARTITION for each locus
• make the loci CHARPARTITION list the actual loci, not the charsets themselves
• make the mitochondrial genome (and other genome) CHARPARTITIONs list the actual loci, not the charsets themselves

[DS4B-ANU]

closing because we're going to have separate nexus files