Job ID 33938

[MARIA JOSE VALLEJO OSPINA]

Hi everyone.

I'm having trouble running GMYC analysis, it is taking too much time, and i don't really know if something went wrong, or maybe my tree input file is not the right one for the analysis. I did put a newick ultrametric tree file archive to run. Here it is.

I would appreciate any help. Thank you.

[Alexandros Stamatakis]

Dear Maria,

The tree is indeed ultrametric and properly formatted in Newick format.

Maybe the usage of the non-ASCII é ncharacter in the tree file name is
causing the issue?

Alexis

On 4/19/26 03:50, 'MARIA JOSE VALLEJO OSPINA' via PTP and GMYC species

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--
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)

[Das Grimm]

Hi Maria,

If changing the file name didn't work either, the problem may be the data. 

Being an ultrametric tree, I cannot say anything about the basic signal but from the tip naming, it doesn't look like a data/tip set suitable for delineating species at all. 

You have 18 tips labelled for 14 genera; and all genera represented by more than a single tip are forming clades. This looks like a standard phylogenetic/phylogenomic data-tip-set with a sample focussed above the species level and little coverage for within species. 

In contrast to a data set, where one would use PTP or GMYC to classify the tips into species-level taxa; which, typically, have (much) more tips than expected species (or other molecular-defined taxa in case of bulk sequencing data).

What is the question/taxonomic objective by using GMYC on this tip set?

Cheers, Guido