I have some sequence reads that go over the origin of my reference sequence and don't align properly using the alignment program I'm using (CodonCode Aligner). I want to split the .abi file into two separate .abi files and align them separately.
Importantly, I want to preserve and transfer the chromatogram information from the original .abi file to the new .abi files.
Do you know of any program or script that would do this?