Sequencher has several powerful tools to help you detect mutations and SNPs in you DNA sequences. You can use Sequencher for comparative sequence alignments among a group of sequences, or to compare 1 or more sequences to a Reference Sequence. Sequencher’s Call Secondary Peaks... function analyzes all of your sequences for potential heterozygotes. It’s easy to control the stringency that defines a heterozygote.
Map the positions of all heterozygotes in the DNA assembly Overview.
You can navigate from one heterozygote to the next; just click on the spacebar in the Bases view. View protein translations for both the consensus and the Reference sequences below the consensus. The Reference sequence ensures that the numbering of your SNPs is consistent from one DNA assembly to the next.