I have a n x n similarity matrix based on a protein sequence alignment.
(I did this using
protr::parSeqSimDisk (documentation here: https://nanx.me/protr/reference/parSeqSimDisk.html).
If I want to add a single new protein to this alignment/similarity matrix do I need to rerun everything? E.g., it's currently a 10000 x 10000 matrix. Does everything need to be rerun to obtain a 10001 x 10001 matrix?
I assume adding an additional sequence may effect the MSA, but I see that MUSCLE has profile-profile alignment (https://drive5.com/muscle/muscle.html#_Toc81224833). But since MUSCLE doesn't have similarity measure, a similarity matrix would need to be made via another program using that MSA output?
Is there simple/convenient way that I'm missing to add another protein?