I have a multiple sequence alignment of 48 sequences each of 3Mbp in length (large), generated using Mafft. I have generated an embl and gff file of recombination sites from Gubbins. I would like to remove these sites from each of the 48 strains. I was wondering whether there was a program to view all 48 sequences at the same time (like in Bioedit) but also show the features of the embl file (like in Artemis). I would then like to remove the same region/base, informed by the embl file, from all 48 sequences at the same time (ie, the column/set of columns).
Is there software available that can help me remove selected bases/regions informed by an embl file that I can visually inspect across an alignment?
Thank you. I look forward to hearing from you.