Visualize GTDB classification

Hi,

thank you for developing this tool!
I would like to classify thousands of MAGs and therefore distribute the gtdbtk (classify_wf) computations.
In the end I would like to visualize the gtdb classification which can be found in gtdbtk.bac120.summary.tsv and gtdbtk.ar122.summary.tsv.
Can you suggest any visualization tool?
My initial plan was to generate two itol trees (one for archaea and the other for bacteria) but then I would have to merge the newick trees of my runs somehow
and maybe also trim the tree since I’m only interested in the taxonomy of my genomes and not of
all GTDB genomes.

best,
Peter

Hi Peter

I would suggest using ARB (http://www.arb-home.de/) for visualisation and any tree operations. But I acknowledge that it might take some time for you to learn how to use it. If you have time and planning on doing other ‘tree works’, I would definitely invest in it. iTOL is great for downstream beautification of the trees but it is not very handy for trimming from my experience…

Perhaps my colleagues can advice some other tools as well :wink:

cheers,

Masha

Hi Peter,

I generally use Dendroscope for visualizing large trees and FigTree for smaller trees (<100 leaves).

Cheers,
Donovan

Thank you both your answer. I decided to use dendropy.
I noticed that in newer GTDBtk versions the tree is split in multiple subtrees. Do you have a script to assemble the full tree?

best,
Peter

Hi Peter. Sorry, no script to assemble the individual trees at the moment. In general, if you need a tree where you can inspect the placement of genomes we’d recommend a de novo tree.