USEARCH manual > Matrix warning
Matrix is not symmetrical warning
The symptom of this bug is a message like this:

  *** WARNING *** Matrix is not symmetrical, ?->?=5, ?->?=0

A patch for this bug was kindly contributed by Robert Leach, who describes it as follows:

I found 2 bugs in the readmx.cpp code in the current version of muscle. I submitted a patch to this bioconductor repo that includes muscle. You can see the details here:

Basically, the last column of custom weight matrices being read in using the -matrix option were not being set and were generating the warnings I had asked about before.  The warnings had contained unrecognized characters (which the terminal displayed as question marks) because CharToLetter was being called instead of LetterToChar. Once I fixed the warning and eliminated the loop exit, it was clear that the last column of the matrix was unset (all zeros).  I found the loop where the matrix was being set and discovered that the `Col < HeadingCount - 1` for the for loop should have been just `Col < HeadingCount`.