Internal node labels -g -r option

[nwno...@gmail.com]

Hello,
I did set a constraint tree with internal node names, but the resulting tree files did no longer contain those internal node labels (here GROUP_A and GROUP_B). For further analysis this information would be quite useful. I used the -g or -r option to add more Taxa which are not part of the constraint tree and want to see at which point they will be added in the new tree. I ran it on a cluster with some testfiles. It was RAxML version 8.2.9.

This was my program call:
mpirun -np 2 /share/scientific_bin/raxml/8.2.9/raxmlHPC-MPI-SSE3 -s 10seq.fas.reduced -r test_tree.tre -m PROTGAMMABLOSUM62 -n "test_tree_internalnodes$RANDOM.tre" -p $RANDOM -N 2

The constraint tree was:
((GBCMA8813:0.25,ACS37519:0.22)GROUP_A:0.12,(ACN38049:0.33,ADG21316:0.29)GROUP_B:0.31);

The result:
(ACS37519:0.05338570684132417504,((((MYFAB022:0.12965886364545026188,ABQ01732:0.14100455074296042168):0.02894307062602749503,ACN38049:0.37491600158928534148):0.00000100000050002909,(((ADG21316:0.32594207858959156621,JF297645:0.16502641003777454576):0.04393649298407204667,GBA9958:0.20622711921721040285):0.03418216549295147871,ETBM003:0.05696661094314128815):0.04914202873093169444):0.07095249936465708451,JF821195:0.08641561743268029450):0.03537253997927671673,GBCMA8813:0.00000100000050002909):0.0;

Is it intended that there will be no longer any internal node names or did i miss an option for the tree output?

[Alexandros Stamatakis]

RAxMl doesn't store internal node labels of input trees, so this is
indeed intentional. The main reason is that under most algorithms
implemented in RAxML the tree will change, hence it does not make much
sense to preserve inner node labels.

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

[nwno...@gmail.com]

Ok, thank you!