search

katylettuce / beast-mcmc

Automatically exported from code.google.com/p/beast-mcmc
0 stars 0 forks source link

Beauti defaults to coalescent tree prior regardless of selected tree prior #166

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Open Beauti
2. Load data.
3. Change to "Trees" panel
4. Change "Tree Prior" to "Speciation: Yule Process"
5. Generate xml file

The resulting xml file will have the yuleModel XML as well as the coalescent 
information, BUT the 
coalescentTree is used as the startingTree in treeModel

Using Beauti/Beast post v1.51, subversion checkout r2257, on OS X 10.6

Original issue reported on code.google.com by dev@simon.net.nz on 17 Sep 2009 at 12:01

Attachments:

GoogleCodeExporter commented 9 years ago 
This only means the random starting tree is generated under the coalescent 
process,
but Yule Model is determined in 

<speciationLikelihood id="speciation">
        <model>
            <yuleModel idref="yule"/>
        </model>
        ...
</speciationLikelihood>

Original comment by dong.w.xie@gmail.com on 17 Sep 2009 at 4:21

GoogleCodeExporter commented 9 years ago 
We can have a starting tree under the yule model, that is not hard, but I agree
should not make a diffrence.

Original comment by jhe...@gmail.com on 17 Sep 2009 at 4:24