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I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let's call it B.fasta, and outputs just the mutations that B contains with respect to A.

I'm open as to the output format. Is there a standard for this?

Background: I'm trying to analyse Sars-CoV-2 sequences and identify mutations with respect to the reference. I've done a google search for a tool that does what I want to but couldn't find something straightaway. Is there no standard tool for this?

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If it's just a comparison of two sequences that you're looking for, then diffseq from the emboss toolkit should be okay:

https://www.bioinformatics.nl/cgi-bin/emboss/diffseq

I think this tool requires the sequences to be oriented in the same direction. If you discover a lot more variants than you expect, try reverse-complementing one of the sequences.

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