This directory is often installed in the location /usr/ncbi/blast/matrix.
If a different location is desired, use the BLASTMAT environment
variable to instruct the BLAST programs where to look for scoring matrix
files.

The aa/ subdirectory contains scoring matrix files appropriate for
amino acid scoring.  BLOSUM62 is the default matrix used.

The nt/ subdirectory contains scoring matrix files appropriate for nucleic acid
scoring (used by BLASTN only).  The default scoring system used by BLASTN is
+5,-4.  That is M=5 N=-4 on the command line, or a +5 reward for a match and -4
penalty for a mismatch.  Internal to the program, BLASTN uses a matrix to score
alignments, but the default matrix -- and any other matrix specified with the M
and N command line options -- is actually computed internally by the program at
run-time, precluding the need to read a scoring matrix file.  Only when the
"matrix=<filename>" option to BLASTN is used is a scoring matrix file read.


