I used the following command to get the phylogenetic tree of the MAGs in the input folder which were in fasta format but I am not able to understand how it is running the analysis, I think there is something wrong with the command I have used because it is doing the same things again like mapping and cleaning of the same file created in the tmp directory.
Command used: 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
phylo_terminal_out.txt (55.6 KB)
My goal is to get the phylogenetic trees for the MAGs that I am providing phylophlan3 which are in fasta format which are coming from different samples and might be belonging to the same species. My other question is that can we get the phylogenetic tree of all the genome bins at species level. Also I am getting really confused, can anyone tell me the set of commands that I should be using for my goal?
Kindly guide me!
Thanks in Advance!