This option allows users to select their own score matrix for protein. This is available from the "Options" menu which invokes a dialogue box. Enter the full filename of the matrix in the entry box. Clicking on the "browse" button will invoke a file browser. See section File Browser. The format for the matrices is that used by blast Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. Basic local alignment search tool. J. Mol. Biol. 215:403-10 (1990), and the default is the same as that used by the old sip program. An alternative matrix, pam250, is available in the $STADTABL directory.