<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>

CC BY-SA 4.0
2021-05-24T06:15:45.043Z
2021-05-24T06:15:45.043Z
gringer
<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>

CC BY-SA 4.0
2022-02-25T20:57:16.383Z
I would say parsimony, but thats just me
M__
<phylogenetics><fasta><samtools><covid-19><sars-cov-2>
Python package or CLI tool outputting mutations of sequence with respect to reference
# Python package or CLI tool outputting mutations of sequence with respect to reference

(Asked by: username_0 on 2021-05-23)

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?

**Tags:** phylogenetics, fasta, samtools, covid-19, sars-cov-2
> **Comments:**
> **username_1**: I would say parsimony, but thats just me  

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## 1 answers

### Answer by username_2 on 2021-05-24. Score: 2

If it's just a comparison of two sequences that you're looking for, then *diffseq* from the [emboss toolkit](http://emboss.sourceforge.net/what/) 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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