text: user12272: 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?
  
  user73: 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.
  
original_text: 12272: <p>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 <code>A.fasta</code>, the other another sequence, let's call it <code>B.fasta</code>, and outputs just the mutations that <code>B</code> contains with respect to <code>A</code>.</p>
  <p>I'm open as to the output format. Is there a standard for this?</p>
  <p>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?</p>
   73: <p>If it's just a comparison of two sequences that you're looking for, then <em>diffseq</em> from the <a href="http://emboss.sourceforge.net/what/" rel="nofollow noreferrer">emboss toolkit</a> should be okay:</p>
  <p><a href="https://www.bioinformatics.nl/cgi-bin/emboss/diffseq" rel="nofollow noreferrer">https://www.bioinformatics.nl/cgi-bin/emboss/diffseq</a></p>
  <p>I think this tool requires the sequences to be oriented in the same direction. If you discover a <em>lot</em> more variants than you expect, try reverse-complementing one of the sequences.</p>
  