# this heuristic seems to be faulty
        my $min_mm = scalar( uniq(@colbp) ) - 1;

[download]

To me this seems perfectly right. If you want to speed up things a bit more (this is only a micro optimization) you can use a hash in the first place: 

        my %chars;
        foreach my $site ( @{$tfbs} ) {
            my $bp = substr($site,$pos,1);
            $chars{$bp} = 1;

        }
        
       # this heuristic seems to be faulty
        my $min_mm = keys %chars - 1;
        push @mincol, $min_mm;

[download]

Instead I think that your sample output is wrong: 

# is: 
00100000302011000000100
# should be:
00100000301011000000100

[download]

If not, could you please explain how to get the 2 there?

In reply to Re: Maximal Parsimony Problem by moritz
in thread Maximal Parsimony Problem by neversaint

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