I'm importing an aligned fasta comprising 600 or so sequence of equal size. Some sequences are identical, as might be expected, and which I'll know call haplotypes. Sequences with duplicate profiles appear to be re-labelled automatically by the software to accommodate the fact that they represent duplicated haplotypes. This appears the logical thing to do. However when I import the isolate data, which has the key as the sequence identifier, although it would seem to link the isolate data with the sequence, when it comes to incorporating the actual isolate data with a network plot there appears to be some loss of information.
I've attached a figure to illustrate this, where you can see I have different colours for a field labelled POP, many of which are absent from the network which instead has lots of 'missing isolate data' based on the light blue node colour.