Phylophlan arcahea clustering within bacteria

Hello biobackery developers and thanks very much for your amazing work you do.

I have a question for you. I binned some MAGs from some metagenomic data I have and I used phylophlan to reconstruct a phylogenetic tree among all my isolates.

Among my MAGs I have two of them that were classified as Achaea by GTDB-tk.
Nevertheless, within my tree, they still cluster among bacteria.
Speciafically I have methanobacteriota (archaea) clustering together with desulphobacterota (bacteria).I was expecting them to form a completely separate branch.

Is this correct? Why do you think it happens? Do you think it might be GTDB-tk the problem, or phylophlan?

I apologize in advance if my question is silly or ignoring certain biological knowledge necessary to answer this question.

Thanks in advance,


Dear Gabri, thank you for reaching out to us and using bioBakery!

So, to better help you with this, we would need a bit more details. For example, if your Archaea MAGs are not from the Methanobacteriota class, could it be a “visualization” issue of the tree that can be solved by re-rooting?
Additionally, did you perform quality control of your MAGs? If not, the assignment and phylogenetic placement could be biased by either a low completeness or high contamination problems.

Thanks a lot,

Ciao Francesco e grazie della risposta.
So both my Archaea are high quality ( > 95 % completeness and <5 % contamination according to checkM). In general all the genomes I used have >75% and < 10%.
And yes they are from the Methanobacteria.

I do not know about re-rooting. I have not tried. I am also not really familiar with phylogenetic trees.
How would I perform re-rooting?
I guess it would bee similar to Tree rooting with PhyloPhlan - #2 by f.asnicar
so I would have to write a configuration file with this command:

python phylophlan_write_config_file
-o custom_config_nt.cfg
-d n
–db_dna makeblastdb
–map_dna diamond
–msa muscle
–trim trimal
–tree1 fasttree
–tree2 raxml

and then open it and edit the section raxml?

Ciao Francesco,
I think it worked with the rerooting. I used ape within R:
rerooted_tree ← root(tree, node = 366, resolve.root = TRUE)

I hope it is also correct to do it in this way.


I have another question.

How come Actinobacteria are split between two groups? they should be clustering within Firmicutes?