I have used several programs like MEGA7, Mesquite, and even tried a python script that allows me to edit MSA by deleting very gapped columns (by codon). Now, I need to do this for well over 200 different MSAs for different species and I cannot find a program or an R package or even python package that will keep a record of which columns were removed. It is hard for me to edit the python script because every time one column is removed, the indices change. Is there a program that will keep track of the columns removed so that I can go back and see why it was removed?
For example, assuming these are in codons:
And say based on the rest of the alignment, I delete the last 4 columns here. I would need it tracked in some way. An idea is below:
sp1 Codon 3: - Codon 4: - Codon 5: - Codon 6: Y
Or anything similar