Different topology from starting tree

29 views
Skip to first unread message

Jose Ramirezs

unread,
Nov 15, 2022, 9:12:48 PM11/15/22
to beast-users
Dear Beast,

I am currently running an analysis with a fixed tree topology (newick). However, the resulting tree topology is different: some branches are swaped and the tips are no longer equidistant from the root. I revised the runs in Tracer and the parameters that relate to the tree (Tree-height, Tree.treeLength) have values above 200 ESS. I don’t know where the problem might be and I hope that someone could help me.

Your help would be greatly appreciated.
kind regards
José


Captura.JPG

HS

unread,
Nov 16, 2022, 2:29:24 AM11/16/22
to beast-users
Hi  José,

Did you turn off tree operators besides uploading a newick tree?

Best,
Hovhannes

Jose Ramirezs

unread,
Nov 16, 2022, 12:03:06 PM11/16/22
to beast...@googlegroups.com
Hi Hovhanne, 

Thank you for your answer,

Yes, the operators (Wide-exchange, Narrow-exchange, Wilson-Balding, Subtree-slide) that are related with the search of the tree are disabled or set to zero. But, I don`t know if I should turn off the Tree-scaler, Tree-root-scaler, Uniform, Up-down-operators, because I have "ultrametrized" the tree (topology resulting of ML analysis) by calibrating some nodes with the Chronos function of the APE package of R.

Kind regards,
José

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/beast-users/87ddb6c7-dc80-499e-b1a8-dc0cab72af14n%40googlegroups.com.


--

Shanta Hejmadi

unread,
Dec 17, 2022, 12:15:58 PM12/17/22
to beast-users
This is the same issue I am having (BEAST2.6.4).  I added an ultrametric Newick starting tree, I commented out the  Wide-exchange, Narrow-exchange, Wilson-Balding, and Subtree-slide operators. The analysis runs (suspiciously slowly for having a fixed topology), and yet my starting tree is not the same topology as the last tree in my tree.trees file.  What was the resolution to this issue, because I also need it? 
Reply all
Reply to author
Forward
0 new messages