[Bioperl-l] bootstrap values in cladogram

Jason Stajich jason at bioperl.org
Thu Mar 11 03:13:24 EST 2010


not sure if the cladogram is printing bootstraps from the internal id or 
the bootstrap function.

See the example code here  http://bioperl.org/wiki/HOWTO:Trees that 
shows how to automatically convert internal IDs to boostrap slots 
basically by using
-internal_node_id => 'bootstrap'
in the TreeIO initialization.

You may want to iterate through the tree and print $node->bootstrap 
where you think it should be so you can verify that it is working too.

-jason

Alexander Donath wrote, On 3/9/10 10:00 AM:
> Hi,
>
> using Bioperl 1.6.1, I'm reading a newick tree with branch lengths and 
> bootstrap values and try to plot the tree as cladogram. But somehow I 
> cannot print the bootstrap values.
>
> Short example:
>
> test.nwk
> ((seq_1:0.18484,seq_3:0.23183):0.17826[879],seq_2:0.36341,seq_4:0.30326);
>
>
> <code snippet>
> [..]
> use Bio::TreeIO;
> use Bio::Tree::Draw::Cladogram;
> [..]
> my $trees = Bio::TreeIO->new( -file => "test.nwk",
>                          -format => 'newick');
> my $tree = $trees->next_tree();
> [..]
> my $out = Bio::Tree::Draw::Cladogram->new( -bootstrap => 1,
>                             -tree => $tree,
>                        -compact => 0);
>
> $out->print(-file => "test.eps");
> </code snippet>
>
> I already tried it by copying the bootstrap values into the ids of the
> internal nodes - nothing. Any suggestions?
>
>
> Thanks,
> Alex
>
> ---
> By the time you've read this, you've already read it!
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 


More information about the Bioperl-l mailing list