I have a multiple sequence alignment and extract a consensus sequence from that. Now I have a new sequence and want to align that to the consensus sequence. However, the consensus sequence must not be changed as it serves as a reference (I repeat that step of aligning one sequence to the consensus several times) .
Therefore, can you recommend a software (like clustal) where you can do a pairwise alignment but tell the program to fix one sequence and align the other one in the best possible way to it?
I'm looking forward to your answers! Thank you for your help, Paula