I have a fasta file with protein sequences. I want to do a pairwise global alignment of eachThe first sequence in the fasta file againstis the top (reference)reference sequence and every subsequent sequence is something I want to align to the reference. The end goal is to identify every unique sequence and be able to compare the regions of variation.
What I have tried
I'm looking into different tools such as Clustal Omega and MAFFT, but there is no option to select the reference sequence against which all the other protein sequences will be aligned.
Q1: I want perform one pairwise global alignment of each sequence in the file against the first (reference) sequence. What software can I use to do this?
Q2: What specific commands can I use to achieve Q1? I'm looking for specific instructions on how to complete this, not just a suggestion of a tool, since I'm not able to find anything from a relatively comprehensive search of available tools.