[Bioperl-l] branch length score - total length of the spanning subtree

[Daniel Gerlach]

Hello,

Thanks for the quick answer. I tried:

use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick',
                   -fh => \*DATA);
my $tree = $treeio->next_tree;
print $tree->total_branch_length,"\n";
$tree->splice(-keep_id => [A,B,E]);
print $tree->total_branch_length,"\n";

__DATA__
(((A:5,B:5)x:2,(C:4,D:4)y:1)z:3,E:10);

Which gives me the message "MSG: After splicing, the original root was 
removed but there are multiple candidates for the new root!" however the 
root E was not removed.

If I do it the complementary way by splicing out all unwanted nodes - 
splice(-remove_id => [C,D]) - I get what I want:

34
25

Greetings, Daniel

Sendu Bala wrote:
> Daniel Gerlach wrote:
>> Hello,
>>
>> I would like to use bioperl to calculate a branch length score for a 
>> given set of nodes and a tree. I know how to get the total branch 
>> length by using $tree->total_branch_length, but how could I get the 
>> length of the subtree spanning some given nodes which are dispersed 
>> over the whole tree (a subset of nodes from the tree which are not 
>> monophyletic)?
> 
> One 'cheat' way of doing it might be to use splice(-keep_ids => 
> \@node_ids) or similar, then run total_branch_length() on that. No idea 
> if it will actually give you the right answer though. Let us know! :)