No way to export from python newick readable by raxml

[Andrea Gasparin]

Hello everyone,

I've been trying to call raxml.PTHREAD from python using several strategies: by hand functions, Biopython, ete3 and dendropy, but nothing seems to be working.

I have this example

((Victoria:1.00000,(Galphimia:1.00000,Oenothera:1.00000)4:1.00000)5:1.00000)Nicotiana:0.00000;

and I get:

ERROR: Expecting ',' in tree; found: character ')'

)4:1.00000)5:1.00000)Nicotiana:0.00000;
                    ^

RAxML may be expecting to read a tree that contains branch lengths

Any help?

[Oleksiy Kozlov]

Dear Andrea,

you have unifurcation in the tree, which probably causes the problem.
So just remove it, e.g.:

> (Victoria:1.00000,(Galphimia:1.00000,Oenothera:1.00000)4:1.00000)Nicotiana:0.00000;

Also, please consider using raxml-ng instead:

https://github.com/amkozlov/raxml-ng

Best,
Oleksiy

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[Alexandros Stamatakis]

To add to this, you are indeed calling and executing raxml from within
python as this error message is generated by RAxML :-) so it's the input
file and not calling raxml from python that is generating trouble,

Alexis

--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Lucas Czech]

Another addition: The error seems to happen in a named branch. It could be that you are running into issues with that, if the parser does not understand labels of inner branches and nodes, see https://academic.oup.com/mbe/article/34/6/1535/3077051 for details.

Cheers
Lucas

Dr. Lucas Czech

Postdoctoral Fellow

 

University of Copenhagen

Faculty of Health and Medical Sciences

Globe Institute, Section for GeoGenetics

 

lucas...@sund.ku.dk