[Bioperl-l] Posterior (and other values) from BEAST/treeannotator/FigTree tree nodes

Chris Fields cjfields at illinois.edu
Wed Jul 7 22:36:22 EDT 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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