text: user9815: 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?
  
  user11856: 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!
  
original_text: 9815: <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>
   11856: <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>
  