It is often useful to identify subsets of your Alignments when creating command blocks for your PAUP analyses. For example, you amy want to identify your outgroups, or some set of taxa that do not include all of the genes in your alignment or you may want to partition your codon positions, genes or morphological sets
The best way to do this is to create a "sets" block in your NEXUS file.

The two most common sets are for characters and Taxa. To create a set of characters you will use the "charset" command and for taxa you will us the "taxset" command.

The syntax for both is - charset yourname4theset=1-500;

2. CHARSET COI=1-688;
3. CHARSET 16S=689-1250;
4. CHARSET morph=1251-1322;
6. CHARSET COIpos1=1-688\3;
7. CHARSET COIpos2=2-688\3;
8. CHARSET COIpos3=3-688\3;
10. TAXSET outgroup=taxon1 taxon2 taxon3;
11. TAXSET NoMorph=taxon33 taxon38 taxon50;
12. TAXSET COIonly=1-33;
13. TAXSET beetles=22 25 27 33 35 40;