Hi,
I am having hard time getting phylophlan work. I really need some fundamental help and where to obtain reference SGBs and genomes.
So, I have metagenome bowtie2 files from metaphlan output. first question, can I use them for phylophlan input?
Second, I want to obtain SGB4758 (Enterocloster bolteae) and map it to my metaphlan outputs and draw phylogenetic trees. I believe that is a similar approach to tutorial 4 on E.coli. In the tutorial it indicates to obtain kSGB from metagenomic output in tutorial 3. Is there any other file that we can obtain kSGB fna files because for some reason that tutorial does not work for me because it does not tar or bunzip the file ethiopian_mags.tar.bz2.