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I was looking at this paper which talks about the miscalculations in the BLOSUM matrices and how the "wrong" BLOSUM62 matrix performs better than the corrected version. I was trying to find the corrected version they talk about to experiment with, but the link they list in the paper appears dead.

Does anyone know where I can find the corrected matrix that the authors talk about? (preferably a version listing frequencies rather than scores)

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    $\begingroup$ Either write to them asking for the files or see the images in the supplementary info (fig 4-5). They could have at least made it as a table; unfortunately you have to manually type it out. $\endgroup$
    – WYSIWYG
    Commented Sep 2, 2014 at 4:30

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Okay, I emailed Dr. Mark Styczynsk (one of the authors) to ask about a link to the matrix. Here are the links he gave me:

http://web.mit.edu/bamel/blosum/revised_blosum.c

http://web.mit.edu/bamel/blosum/original_blosum.c

http://web.mit.edu/bamel/blosum/RBLOSUM64 (isentropic with BLOSUM62)

http://web.mit.edu/bamel/blosum/RBLOSUM62 (not isentropic, but it's 62)

The first link is to the c code to generate the corrected BLOSUM. According to Mark, just replacing the original c file in the original BLOSUM tarball with the revised c file can generate the corrected matrix for any of the BLOSUMs (30, 50, 92). Haven't yet tried that myself.

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Your question made it difficult to understand what you are looking for so I hope these two links will provide you with the desired data.

0. A source link to the paper in question and its supplementary file.

1. What blast is currently using.

2. What the math calls for.

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