Geneious will pick up whatever dye(s) are listed in the microsatellite trace file. However, note that Geneious requires the ladder to be in the last dye of your trace. So if you have done a 4 dye run, then your trace should only have 4 dyes and the ladder should be in the last dye. If you have done a 4 dye run but your traces are configured as if 5 dyes are used, then the last dye is likely to be empty so Geneious will not be able to call a ladder.
