# No taxonomy in phylogenetic tree generated by phylophlan **URL:** \ **Category:** PhyloPhlAn\ **Created:** [August 20, 2022, 8:52am UTC](https://forum.biobakery.org/t/no-taxonomy-in-phylogenetic-tree-generated-by-phylophlan/3977 "2022-08-20T08:52:39Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)\ **Post date:** [August 20, 2022, 8:52am UTC](https://forum.biobakery.org/t/no-taxonomy-in-phylogenetic-tree-generated-by-phylophlan/3977/1 "2022-08-20T08:52:39Z")
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! ---
**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\ **Post date:** [August 26, 2022, 3:09pm UTC](https://forum.biobakery.org/t/no-taxonomy-in-phylogenetic-tree-generated-by-phylophlan/3977/2 "2022-08-26T15:09:26Z")
Dear @saras22, You can find a description of the outputs in the documentation [here](https://github.com/biobakery/phylophlan/wiki#output). 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, Francesco ---
**Author:** ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)\ **Post date:** [October 12, 2022, 5:38am UTC](https://forum.biobakery.org/t/no-taxonomy-in-phylogenetic-tree-generated-by-phylophlan/3977/3 "2022-10-12T05:38:53Z")
Hi @f.asnicar! Thanks for all the responses you made earlier to all the questions I had. Now I have a few more. 1. I want to confirm if I am doing everything correctly so I am mentioning all the steps that I have done for making the tree: - installed phylophlan - downloaded phylophlan config files - tree command: phylophlan --input /lustre/rsharma/PHYLO\_ANALYSIS/ALL/ -d phylophlan -t a --databases\_folder /lustre/rsharma/PHYLO\_ANALYSIS/PHYLO\_DB/ --diversity high --output\_folder /lustre/rsharma/PHYLO\_ANALYSIS/OUTPUT/ -f /lustre/rsharma/PHYLO\_ANALYSIS/OUTPUT/supermatrix\_aa.cfg --genome\_extension .fa --force\_nucleotides --nproc 50 My MAGs are in .fa format but the config file that I am using is in “aa” format, is that alright or I need to change anything? when I tried to make database using the “nt” config file it was not making the database and giving some error so I tried with this one and it started to run. 1. other question: Can I use some other tool for obtaining taxonomy like GTDBTK and then use ITOL to label the phylogenetic tree with the species? Is this the correct way of visualizing the MAGs phylogeny and taxonomy as well? One more question is that if the above-mentioned way is correct then while making the phylogenetic tree what diversity level shall I choose (low, medium, or high)? Thanks ---
**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\ **Post date:** [October 12, 2022, 11:22am UTC](https://forum.biobakery.org/t/no-taxonomy-in-phylogenetic-tree-generated-by-phylophlan/3977/4 "2022-10-12T11:22:33Z")
Hi @saras22, I’ll report the pieces so that it will be clearer to which point I’m answering to. * * * > [@saras22](#): > > - downloaded phylophlan config files Instead of downloading config files, you can use PhyloPhlAn to generate what you need so to ensure that the tools as defined in your system are correctly matched. * * * > [@saras22](#): > > My MAGs are in .fa format but the config file that I am using is in “aa” format, is that alright or I need to change anything? Your inputs can be both genomes and proteomes, so no problem at all with that. The `aa` (or `nt`) I put in the config file name, is a convenient way for me to identify config tailored for genes/nucleotides (`nt`) or proteins/amino acids (`aa`) databases. This because only with protein databases the translated search is available and can deal with both genomes and proteomes as input. * * * > [@saras22](#): > > Can I use some other tool for obtaining taxonomy like GTDBTK and then use ITOL to label the phylogenetic tree with the species? Is this the correct way of visualizing the MAGs phylogeny and taxonomy as well? Of course, you can use any other tool like those you mentioned. Alternatively, I can say that you can use `phylophlan_metagenomic` that will report the closest SGB found to your MAG and you can use this information to taxonomically characterize your MAGs. For visualization, we have GraPhlAn within bioBakery, which is very flexible but would require a bit of scripting to get colorful and annotated figures. * * * > [@saras22](#): > > One more question is that if the above-mentioned way is correct then while making the phylogenetic tree what diversity level shall I choose (low, medium, or high)? In the example above you’re running `--diversity high` and `--accurate` (the default if not specified). You can find a bit more info about the available combinations here: [Home · biobakery/phylophlan Wiki · GitHub](https://github.com/biobakery/phylophlan/wiki#accurate-or-fast-1). There are some cutoffs that differ between `--accurate` and `--fast`, but won’t be too dramatic probably in your case. I think the main difference is more on the expected diversity among the MAGs that you want to phylogenetically characterize. If you expect low genomic diversity, maybe `medium` and `high` will be too aggressive and might cut out a bit of the phylogenetic signal. * * * I hope these help, Thanks, Francesco