<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>

CC BY-SA 3.0
2018-01-04T11:53:57.620Z
2018-01-04T11:53:57.620Z
Devon Ryan
<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>

<phylogenetics><python><file-formats><errors>
Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?
# Why doesn't Biopython AlignIO.read() recognise the 'mauve' format?

(Asked by: username_0 on 2018-01-04)

On this Biopython tutorial, 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)  in ()
----> 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

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## 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).


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