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If you want to align two protein sequences, try this:
https://web.expasy.org/sim/
This depends on what you mean by "comparison" and "interpretation". What are your goals?
i have a project im dong and I'm asked to analyse difference and similarities between TatB (gram negative) and TatC (gram negative and positive) from gram positive and negative bacteria.
I've got aligments for each but I cat compare them as I don't know how to analyse or interprete
If I understand correctly, you need to find correlations between genomic variants and gram-negativity or gram-positivity. There are a number of methods for this. I'm not a specialist, but take a look here https://en.wikipedia.org/wiki/Phylogenetic_comparative_methods. Also, this article may be of help to you: link