I have many genes for many bacteriophage with precomputed secondary structures such as:
I want to align each gene's secondary structure with the SSE (secondary structure elements) of the other bacteriophages. So for instance, I may also have
for another gene. I would like to be able to align these genes so that I can find the evolutionary relationships between the bacteriophages.
Does anyone have a suggestion for the algorithms I should use for this project?