Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-24T06:15:45.043Z
Answers.LastActivityDate: 2021-05-24T06:15:45.043Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-25T20:57:16.383Z
Comments.Text: I would say parsimony, but thats just me
Comments.UserDisplayName: M__
Tags: <phylogenetics><fasta><samtools><covid-19><sars-cov-2>
Title: Python package or CLI tool outputting mutations of sequence with respect to reference
ThreadText: # 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  
  
  ---
  
  ## 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.
  
  
  ---
  
  