BEAST XML

[Chong Kai Ng]

Hi all, 

I am using BEAST X, continuing some work my colleague left behind. 

Long story short, I would like to replace the sequences he used with some other sequences, so I figured I had to recreate the XML file. I used BEAUTi to help me. 

However, I ran into some problems. For example, I have the following code block in my XML, while he didn't.

<!-- Generate a coalescent likelihood for the subtree defined by taxon set, Alpha -->

<coalescentLikelihood id="subtree.coalescent">

<model>

<constantSize idref="subtree.constant"/>

</model>

<populationTree>

<treeModel idref="treeModel"/>

</populationTree>

<include>

<taxa idref="Alpha"/>

</include>

</coalescentLikelihood>

I was thinking it could be because of the options I have selected in BEAUTi. While using the GUI, I created some taxon sets as per my ex-colleague's instructions. I also checked mono, and unchecked stem. Under trees, I unchecked "use separate prior for subtree", as I did not see him defining any prior for sub-tree. 

However, under the "Priors" tab, I kept seeing the prior for subtree. I tried to play around the options, and found out that this happens when I select mono. 

So the following is my qn: Is there anyway to remove the subtree prior and still retain mono? If it helps, I am using beast version="10.5.0">, while he used <beast version="10.5.0-beta2">. I would also like to surface that I know nothing about phylogenetic tree analysis, but I need to replicate his work because of his sudden departure. So honestly I am merely trying to trace his steps.

Thank you!

If I am not posting correctly or I need to post somewhere else, please let me know. Thank you!