[Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes
Chris Fields
cjfields at illinois.edu
Thu Jul 8 02:36:22 UTC 2010
It is possible our NEXUS parser doesn't do this for some reason, but we would need a sample file to work out the problem. You could try Rutger Vos's Bio::Phylo, which may have this working.
chris
On Jul 7, 2010, at 9:41 AM, Greg Baillie wrote:
> Hi.
>
> I'm trying to extract information (eg. posterior values) from nodes of trees generated using BEAST/treeannotator/FigTree.
>
> The trees, which are in nexus format, seem to load OK, but when I iterate through the nodes looking for posterior values (/if ( $node->has_tag('posterior') ) {.../), none of the nodes seem to have posteriors.
>
> In fact, none of the nodes have any tags (/my @tags = $node->get_all_tags(); print join ',', @tags/). And when I dump an entire tree using Data::Dumper, there is no sign of any of the node values.
>
> Does TreeIO handle these values? If so, should I be looking somewhere other than the tags for the values?
>
> Thanks.
>
> Greg.
>
>
>
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