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.
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
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?
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.
I have been using Archaeopteryx. It’s a bit dated (development seems to have moved to the .JS version) but it has no issues at all with the massive GTDB trees.
My problem with all tree viewers/editors is learning to find my way around the controls. A 747 cockpit looks like a Zen garden by comparison.
