Re: Maximal Parsimony Problem

       # 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?

Comment on Re: Maximal Parsimony Problem Select or Download Code

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Re^2: Maximal Parsimony Problem by neversaint (Deacon) on Sep 03, 2008 at 14:28 UTC
Hi Moritz, It is based on phylogenetic tree, the substitution comparison from lower nodes must be compared to higher level. E.g. For column 11, the bases for row 3 is compared to row 1. Same result will also be given if we compare row 3 to row 2. Both row 1 and row 2 has higher level than row 3 row 4 in phylogenetic tree. --- neversaint and everlastingly indebted.......	[reply]
Re^3: Maximal Parsimony Problem by moritz (Cardinal) on Sep 03, 2008 at 14:36 UTC
I still don't quite understand. We have `human: C chimp: T mouse: T rat: C` [download] So which comparisons exactly lead to to a number of 2? With which rules? As a poor perl programmer I'm not familiar with the phylogenetic tree, so if that's relevant here please explain in which relation these four examples appear in that tree.	[reply] [d/l]
Re^3: Maximal Parsimony Problem by lidden (Curate) on Sep 03, 2008 at 15:29 UTC
Have you changed your example? `A C T G` [download] How does that become 3? And the column moritz quoted above used to bee: `C T T T` [download]	[reply] [d/l] [select]