some bootstrap values are missed

[Evgen S]

Hi everybody,

sometimes some bootstrap values are missing on the tree. Screenshot with an example is attached. The best ML tree and the 'bipartitions' tree have identical topology, but bootstrap value  for one node is absent. I have checked it by a text editor and found that this value is really absent in the file generated by raxml. RAxML  8.2.4  was called as follows:  -s cytb.phy -n cytb -m GTRGAMMA -f a -q partition_rag -x 31857372 -N 1000 -p 758742  on Ubuntu 14.04. 

Any suggestions? 

[Alexandros Stamatakis]

Please read this paper here:

http://biorxiv.org/content/biorxiv/early/2016/09/07/035360.full.pdf

you should also urgently update your dendroscope version (see page 3 of
that preprint).

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Evgen S]

Alexis, thanks for the prompt reply and thanks for the paper. I read it and updated the Dendroscope. But it solves the problem only for mid-point rooting (for the node highlighted in my initial post). But when I want to root with any branch I got the 'empty' bootstrap values again. I usually use Archaeopteryx and never had such a problem before, but now it doesn't work in Archaeopteryx too. 

[Evgen S]

I re-ran the analysis with RAxML version 7.2.8 and got the tree with all bootstrap values displayed correctly. I also re-ran it with v.8.2.9 and got the same problem as with 8.2.4. I've tried several programs for tree viewing and results are the same. Screenshot with both trees is attached.  Surely, I can stick with 7.2.8, but I would like to understand what is going on. 

On Friday, 2 December 2016 14:37:41 UTC+7, Alexis wrote:

[Alexandros Stamatakis]

which is which on the screenshot? the tree on the right is actually
correctly displayed ... keep in mind that BS supports always and only
refer to inner branches of the tree

alexis

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> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>