No taxonomy in phylogenetic tree generated by phylophlan

Hi @f.asnicar

I was trying out to get the phylogenetic tree for the MAGs generated from my metagenomic datasets. The command that I have used is :

phylophlan --input PHYLO_IN/ -d phylophlan -t a --databases_folder PHYLO_DB/ --diversity high --output_folder PHYLO_OUT -f PHYLO_OUT/supermatrix_aa.cfg --genome_extension fasta

and the final results I got are :
PHYLO_IN.tre, PHYLO_IN_resolved.tre, PHYLO_IN_resolved.tre, RAxML_bestTree.PHYLO_IN_refined.tre, RAxML_info.PHYLO_IN_refined.tre, RAxML_info.PHYLO_IN_refined.tre, RAxML_log.PHYLO_IN_refined.tre, RAxML_result.PHYLO_IN_refined.tre

  • What is the difference between these different tre files?

  • I tried to visualize the tree in ITOL web tool, but that does not give any taxonomic information of the bins. how do I get that?

Thanks in Advance!

Dear @saras22,

You can find a description of the outputs in the documentation here.
In brief, the RAxML_bestTree.PHYLO_IN_refined.tre should be your final phylogeny, in the above example.

The taxonomic information is not something you’ll get out of the tree if you don’t have other genomes in it with a known taxonomic label assigned to them.
What you can do alternatively is to run phylophlan_metagenomic that will provide you with the closest species-level genome bins (SGBs) to your input MAGs, so that you can understand whether your MAGs belong or not to an already existing SGB.

Please, let me know if something is not clear.

Many thanks,