I get those warnings (with use warnings in effect). The problem comes from this loop.

my @lnPAM1=();
LINE: for (my $i=0; $i<20; $i++){
    for (my $j=0; $j<20; $j++){
        if ($matrix[$i][$j] > 0){
            $lnPAM1[$i][$j] = log $matrix[$i][$j];
        }else{ next LINE;
        }
    }
}
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When a matrix element equals zero, that value of @lnPAM1 remains undefined, and that undefined value is being used at line 64.

            $lnPAM1[$i][$j]= ($lnPAM1[$i][$j]) /($mutrate*100);
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For instance, $lnPAM1[0][17] and $lnPAM1[0][18] are undef. To avoid the warnings, you'll need to either assign some value to all of them or exclude matrix elements which are undef from executing line 64.