first of all I want to apologize for my lack of knowledge and unfamiliarity with the bioinformatic workflows. I'm looking for a program or online tool that allows to make annotations on individual sequences in an alignment file.
Basically, I need to compare short genomic regions from different populations of the same species, in which small variations at the DNA sequence have caused rearrangements of the exon/intron structure of the genes coded in those regions. So I need to annotate each population's sequence individually and align them so that the mutations causing the rearrangement in each population are easily noticed.
I'd be very grateful for any recommendation.