GTDB Forum

Add own marker for tree inference?

Dear developers,

first let me say thank you fro developing this excellent tool.We are just starting to use this in our lab and trying to figure out, what all is possible

Currently I am thinking about using GTDB tk to generate a tree for a genus of interest from a set of reference genomes and our own isolates.
The genus has a gene, that is very specific for it’s members, so I am am wondering if there is any way in GTDB tk to include an additional marker gene in the analysis. Is it somehow possible to add a protein to the marker set?

Thank you and best Wishes
Sonja

Hello Sonja,

GTDB-Tk does not support the addition of new marker gene. It is entirely based on the 120 markers for bacterial genomes and 122 markers for archaeal genomes.

Regards,
Pierre