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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?
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!
