epa tree > invalid branch length

[Jan Finke]

Hello,

I tried out placing 700 OTUs on a reference tree using the "raxmlHPC -f v ..." option. While all worked well, I get error messages when trying to open the RAxML_labelledTree.

FigTree v1.4.2 says: Error reading tree file: Number format error: For input string: "0.08338312920260704153[I0]"

iTOL says: Invalid branch length 0.08338312920260704153[I0]

BTW This is referring to the first node in the nwk file, but all nodes have that many digits which I suspect to be the issue.


Is there a way to restrict the branch length in the output format when running raxml or is there a way to display the tree? I could not find the issue on the discussion board, any advice would be great!


Thanks

Jan

[Jan Finke]

If it makes a difference, the server I am using has raxmlHPC version 8.0.0

[Alexey Kozlov]

Hi Jan,

I think the problem is not the brlen precision but the branch labels - "[I0]" - which might be not recognized by all
tree viewers.

Not sure about FigTree, but with iTOL you can load a .jplace file instead, which contains both reference tree and the
placements:

http://itol.embl.de/upload.cgi

As a bonus, you will see all the placements with corresponding weights, and not just a single most likely placement per
query as in RAxML_labelledTree.

Hope this helps,
Alexey

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[Alexandros Stamatakis]

Thanks Alexey :-)

> I think the problem is not the brlen precision but the branch labels -
> "[I0]" - which might be not recognized by all tree viewers.

Yes, that's it, Dendroscope can vizualize this though, but as Alexey
pointed out, it's much better to use the iTOL viewer that has support
for the .jplace format.

You should also urgently upgrade your RAxML version, the latest release
is 8.2.9 at https://github.com/stamatak/standard-RAxML/releases

alexis

--
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

[lucas...@h-its.org]

Hi Jan,

also, for working with EPA data (particularly the jplace format), you can try our library/toolkit genesis: http://genesis-lib.org/

For example, if you want to visualize the number of placements per branch, there is an out-of-the-box setup for this: http://doc.genesis-lib.org/demos_visualize_placements.html
But also for many other tasks, there might be something in there for you.

What questions do you want to answer using the EPA data / what tasks do you want to do with it? Maybe I can give you some further hints or help.

All the best
Lucas

[Jan Finke]

Thank you all very much for the help!

iTOL worked and I have started to look into genesis...

I think I was also just expecting a different output, I thought it would generate a new tree with new branches added to the reference tree.

Thanks,

Jan

[Adam Witney]

I am posting this a bit late, but might be useful to others finding the thread. You can filter the tree file so that it loads in FigTree using

perl -pe "s/\[I\d+\]//g"  RAxML_labelledTree.epa-mytree > new-tree-file 

[Alexandros Stamatakis]

thank you :-)

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

www.exelixis-lab.org