I would like to get some suggestions for relatively simple visual tools for aligning and examining Sanger sequencing data. All I am trying to do is align a bunch of traces to the mRNA/cDNA sequence for the gene. Any assistance would be much appreciated.
I currently primarily use Consed. However, it is a UNIX tool and that confuses other people. The alignment is not especially helpful either because it does not give you codons or position within a gene.
Mutation Surveyor is fairly simple to use. It aligns the traces and then tells you exactly where each position falls within the gene. It also does mutation calling, which is not very good and not even necessary for me. It's also fairly expensive."