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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?

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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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