<p>This <a href="https://www.biostars.org/p/133912/" rel="nofollow noreferrer">example</a> seems to have information on this, looks like it should have this format:</p>
<pre><code>   A   G   C   T   U   *
A  1   -1  -1  -1  -1  -1
G  -1  1   -1  -1  -1  -1
C  -1  -1  1   -1  -1  -1
T  -1  -1  -1  1   -1  -1
U  -1  -1  -1  -1  1   -1
*  -1  -1  -1  -1  -1  -1
</code></pre>
<p>However, the page I linked is specifically about a bug regarding ClustalW <strong>ignoring</strong> custom made matrices. It's a pretty old post so it might have been fixed since. However, if you encounter that bug, that same page thankfully does contain a workaround!</p>

CC BY-SA 4.0
2021-03-30T17:02:42.523Z
2021-03-30T17:32:12.700Z
2021-03-30T17:32:12.700Z
Bioinfomrat
<p>I need to set the substitution matrix used by command line CLUSTALW when comparing DNA sequences to:</p>
<pre><code> 0 -1 -1 -1
-1  0 -1 -1 
-1 -1  0 -1
-1 -1 -1  0
</code></pre>
<p>from my understanding I need to pass the location of a file with the matrix to the <code>-dnamatrix</code> parameter, however, I cannot find out what format the file is supposed to be in. Any idea?</p>

<phylogenetics><multiple-sequence-alignment><substitution-model>
File format of substitution matrix in clustalw
# File format of substitution matrix in clustalw

(Asked by: username_0 on 2021-03-30)

I need to set the substitution matrix used by command line CLUSTALW when comparing DNA sequences to:
 0 -1 -1 -1
-1  0 -1 -1 
-1 -1  0 -1
-1 -1 -1  0

from my understanding I need to pass the location of a file with the matrix to the -dnamatrix parameter, however, I cannot find out what format the file is supposed to be in. Any idea?

**Tags:** phylogenetics, multiple-sequence-alignment, substitution-model

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## 1 answers

### Answer by username_1 on 2021-03-30. Score: 3 | Accepted answer

This example seems to have information on this, looks like it should have this format:
   A   G   C   T   U   *
A  1   -1  -1  -1  -1  -1
G  -1  1   -1  -1  -1  -1
C  -1  -1  1   -1  -1  -1
T  -1  -1  -1  1   -1  -1
U  -1  -1  -1  -1  1   -1
*  -1  -1  -1  -1  -1  -1

However, the page I linked is specifically about a bug regarding ClustalW ignoring custom made matrices. It's a pretty old post so it might have been fixed since. However, if you encounter that bug, that same page thankfully does contain a workaround!


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