[Bioperl-l] bootstrap values in cladogram
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.
Alexander Donath wrote, On 3/9/10 10:00 AM:
> 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:
> <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?
> By the time you've read this, you've already read it!
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