I am using phylophlan for the first time and I am really impressed how rapidly it generates a phylogenetic tree from thousands of genome sequences. This is a tremendous piece of software and I really appreciate your work.
I started to follow the tutorial tree of life and I waited several days to get a beautiful output tree which I analyzed further with ITOL. I observed some differences in the tree to the one you show at the end of the tutorial.
My question is, what would you expect to change the order of the phylas in the tree. The number of input sequences (I considered sequences without refseq exclusion ~ 14.000) or the parameters (–diversity high, --fast)