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!