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?
Gabri