Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-30T17:02:42.523Z
Answers.LastActivityDate: 2021-03-30T17:32:12.700Z
Answers.LastEditDate: 2021-03-30T17:32:12.700Z
Answers.UserDisplayName: Bioinfomrat
Body: <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>
  
Tags: <phylogenetics><multiple-sequence-alignment><substitution-model>
Title: File format of substitution matrix in clustalw
ThreadText: # 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
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-03-30. Score: 3 | Accepted answer
  
  This [example](https://www.biostars.org/p/133912/) 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!
  
  
  ---
  
  