I am interested in finding a free software package to analyse sanger sequencing files (ab1).
The software needs to be able to align the sequences in the presence of indel mutations, as I am using this to validate CRISPR/Cas9 knockout of genes.
Currently I use the free version of Mutation Surveyor, but the free version cannot produce publication quality alignments as it has a watermark in the background of the alignment. I basically want a software that can perform largely the same function (alignment of sequences with indel mutations), that is open source/free/cheap.
Any recommendations would be great.