Re: Starting Tree not parsed using xml File created with BEAUTi 1.7.5 on Cipres using BEAST 1.7.4

[Andrew Rambaut]

Hi,

It makes no sense to reroot the output of BEAST. BEAST estimates the root position and the branches are in units of time. Rerooting the tree will mean there is no longer a valid timescale (and the bars will therefore have no meaning).

Andrew

On 29 Apr 2013, at 23:17, gerej...@gmail.com wrote:

I am also experiencing  problems using Beast new version. When l try to reroot my output tree after burning, in Fig tree, the node bars shift, they no longer remain in position. How best can l go over this challenge?

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[gerej...@gmail.com]

Hi Andrew

Thank you very much for your response. Does the Beast output tree topology matter most? What about if Beast ouput tree doesnt give me the expected topology? I have ran several Beast analysis trying to get a topology which is congruent with what l get from from MrBayes.

[gerej...@gmail.com]

On Tuesday, April 30, 2013 12:25:30 AM UTC+2, rambaut wrote:

Hello

I am struggling to get Beast running using a starting tree. Is there anyone who can help me out on this challenge? 

[Miller, Mark]

Hi,

 

We put BEAST 1.7.5 into production on CIPRES today. Sorry for the long delay.

 

Best,

Mark

 

From: beast...@googlegroups.com [mailto:beast...@googlegroups.com] On Behalf Of gerej...@gmail.com
Sent: Monday, April 29, 2013 3:17 PM
To: beast...@googlegroups.com
Subject: Re: Starting Tree not parsed using xml File created with BEAUTi 1.7.5 on Cipres using BEAST 1.7.4

 

On Wednesday, April 10, 2013 12:46:33 PM UTC+2, katharin...@mytum.de wrote:

Hello list,

If I try to run BEAST on Cipres (vers. 1.7.4.) I get a Parsing error 
(- poorly formed BEAST file, infile.xml:

Object with idref=startingTree has not been parsed.) for the starting tree.
My xml file (created with BEAUTi 1.7.5) reads as such:

<!-- Generate a random starting tree under the coalescent process            -->
        <coalescentSimulator id="startingTree">
               <coalescentSimulator>
                       <coalescentSimulator>
                               <taxa idref="Dactyliandra"/>
                               <constantSize idref="initialDemo"/>
                       </coalescentSimulator>
                       <coalescentSimulator>
                               <taxa idref="Trichosanthes"/>
                               <constantSize idref="initialDemo"/>
                       </coalescentSimulator>
                       <taxa idref="Ingroup"/>
                       <constantSize idref="initialDemo"/>
               </coalescentSimulator>
               <taxa idref="taxa"/>
               <constantSize idref="initialDemo"/>
        </coalescentSimulator>

        <!-- Generate a tree model                                                   -->
        <treeModel id="treeModel">
               <coalescentTree idref="startingTree"/>
               <rootHeight>
                       <parameter id="treeModel.rootHeight"/>
               </rootHeight>
               <nodeHeights internalNodes="true">
                       <parameter id="treeModel.internalNodeHeights"/>
               </nodeHeights>
               <nodeHeights internalNodes="true" rootNode="true">
                       <parameter id="treeModel.allInternalNodeHeights"/>
               </nodeHeights>
        </treeModel>

What is the problem here? Is there any way I can manipulate this part of the xml file and get it 
to run on the "older" BEAST version, availiable on Cipres?

Or does it have nothing to do with the command-lines and is instead a problem regarding 
the priors I set for the treeModel.rootHeight?

they are:
<gammaPrior shape="1.0" scale="3.4" offset="55.8">
<parameter idref="treeModel.rootHeight"/>
</gammaPrior>

I left the inital value for the treeModel.rootHeight at default (33.0) which doesn't appear in the xml file (whatever the reason for that may be).

I hope somebody can help!

Best Regards,

Kati Lindner

Hello!

[Jephris Gere]

Hello 

Thanks for the suggestion, l have now managed to run my XML file with a starting tree, however, a new challenge has risen of getting my desired topology in the output tree fromm treeannotator. The topology which l am getting doesnt tally with that of my starting tree. How can l get my desired topology after burning some of the trees in Treeannotator? If anyone can help me please 

Thank you

Jeph