Answers.Body: <p>You're using version 1.68 or older. Mauve support was <a href="https://github.com/biopython/biopython/blob/master/NEWS.rst#10-july-2017-biopython-170" rel="noreferrer">added in 1.70</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-04T11:53:57.620Z
Answers.LastActivityDate: 2018-01-04T11:53:57.620Z
Answers.UserDisplayName: Devon Ryan
Body: <p>On this <a href="http://biopython.org/wiki/AlignIO" rel="noreferrer">Biopython tutorial</a>, they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module:</p>
  
  <pre><code>from Bio import AlignIO
  alignment = AlignIO.read(open("alignment.xmfa"), "mauve")
  </code></pre>
  
  <p>but I get the following error:</p>
  
  <pre><code>ValueError
  Traceback (most recent call last) &lt;ipython-input-30-396e54791d7a&gt; in &lt;module&gt;()
  ----&gt; 1 alignment = AlignIO.read(open("/Users/cr517/Documents/alignment.xmfa"),
  "mauve")
  
  /Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
  in read(handle, format, seq_count, alphabet)
      422     iterator = parse(handle, format, seq_count, alphabet)
      423     try:
  --&gt; 424         first = next(iterator)
      425     except StopIteration:
      426         first = None
  
  /Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
  in parse(handle, format, seq_count, alphabet)
      366                                                 seq_count=seq_count)
      367         else:
  --&gt; 368             raise ValueError("Unknown format '%s'" % format)
      369 
      370         # This imposes some overhead... wait until we drop Python 2.4 to fix it
  
  ValueError: Unknown format 'mauve'
  </code></pre>
  
Tags: <phylogenetics><python><file-formats><errors>
Title: Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?
ThreadText: # Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?
  
  (Asked by: username_0 on 2018-01-04)
  
  On this [Biopython tutorial](http://biopython.org/wiki/AlignIO), they describe how to import a multiple sequence alignment in the Mauve (XMFA: extensible multi fasta format). So I imported the AlignIO module:
  
  ```
  from Bio import AlignIO
  alignment = AlignIO.read(open("alignment.xmfa"), "mauve")
  
  ```
  
  but I get the following error:
  
  ```
  ValueError
  Traceback (most recent call last) <ipython-input-30-396e54791d7a> in <module>()
  ----> 1 alignment = AlignIO.read(open("/Users/cr517/Documents/alignment.xmfa"),
  "mauve")
  
  /Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
  in read(handle, format, seq_count, alphabet)
      422     iterator = parse(handle, format, seq_count, alphabet)
      423     try:
  --> 424         first = next(iterator)
      425     except StopIteration:
      426         first = None
  
  /Users/cr517/anaconda/lib/python3.6/site-packages/Bio/AlignIO/__init__.py
  in parse(handle, format, seq_count, alphabet)
      366                                                 seq_count=seq_count)
      367         else:
  --> 368             raise ValueError("Unknown format '%s'" % format)
      369 
      370         # This imposes some overhead... wait until we drop Python 2.4 to fix it
  
  ValueError: Unknown format 'mauve'
  
  ```
  
  **Tags:** phylogenetics, python, file-formats, errors
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-01-04. Score: 5 | Accepted answer
  
  You're using version 1.68 or older. Mauve support was [added in 1.70](https://github.com/biopython/biopython/blob/master/NEWS.rst#10-july-2017-biopython-170).
  
  
  ---
  
  