I have recently carried out a stipple sequence alignment using DECIPHER package in R. The code was fairly simple as follows:
bod_aa <- readAAStringSet("BOD_aa.fasta")
aligned_aa <- AlignSeqs(bod_aa)
This worked nicely but I would like some information on the alignment, specifically the percent homology between the different proteins? If possible percent homology to one of the sequences in particular. I.e. I really want to align all the sequences to one "query sequence" and get a percent homology to that query sequence.