95%HDP and FigTree

[EDG]

I can not display height 95% HDP for some nodes in my tree in FigTree.
I saw that Marcin posted the same problem, and as him, I can not find
the value for node ages in the .tree text file. His question "Does
FigTree extrapolate these values using other node heights?" was not
answered, and I would also really like to get an answer to that
question. I have also tried to change the "posterior probability
limit" in TreeAnnotator to 0, but I can still not display the height
95% HDP values in FigTree.

Best,
EDG

[Joseph W. Brown]

The key to your problems lie in the "Posterior probability limit" in
TreeAnnotator. Nodes that receive posterior clade probabilities lower
than what is specified here (default = 0.5) will not be annotated. You
should notice, for example, that the non-annotated nodes that are
revealed in FigTree all involve nodes of ambiguous relationships. I
think this is a reasonable approach: why would you want to annotate
something with little support? However, if you *really* need estimates
for those nodes you can reduce the "Posterior probability limit"
threshold when summarizing your tree distributions in TreeAnnotator to
something <0.5. However, if doing this I think you should acknowledge
this in any resulting manuscript.

Hope this helps.
Joseph.

Quoting EDG <ellen...@gmail.com>:

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Joseph W. Brown, PhD Candidate, Rackham Predoctoral Fellow
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[EDG]

Hey Joseph and thanks for your reply.

I did did reduce the Posterior probability limit to 0 and I still didn
´t get the 95%HDP. I have done 3 runs of 90 million simulations for
complete mtDNA sequences and looking at the results in Tracer they
look fine (EES values etc). I guess the problem is not the poor
support, since it does not matter if I reduce the Posterior
probability limit to 0 in TreeAnnotator, what else could be the
problem?

Best,
EDG

On Feb 12, 2:25 pm, "Joseph W. Brown" <josep...@umich.edu> wrote:
> The key to your problems lie in the "Posterior probability limit" in  
> TreeAnnotator. Nodes that receive posterior clade probabilities lower  
> than what is specified here (default = 0.5) will not be annotated. You  
> should notice, for example, that the non-annotated nodes that are  
> revealed in FigTree all involve nodes of ambiguous relationships. I  
> think this is a reasonable approach: why would you want to annotate  
> something with little support? However, if you *really* need estimates  
> for those nodes you can reduce the "Posterior probability limit"  
> threshold when summarizing your tree distributions in TreeAnnotator to  
> something <0.5. However, if doing this I think you should acknowledge  
> this in any resulting manuscript.
>
> Hope this helps.
> Joseph.
>

> Email: josep...@umich.edu