The bioBakery help forum

Phylophlan Tree of Life Differences

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)

Best regards,

Dear Michael,

Many thanks for using PhyloPhlAn and finding it useful in your analysis.
First of all, the phylogeny showed at the end of the tutorial is actually not built using the genomes downloaded from NCBI, but it is based on the one representative genomes for each species refined with the SGB. The tree in the tutorial is actually the tree we show in the PhyloPhlAn paper and here you can find more info about the SGBs.
However the idea is the same, but the results could be slightly different.
One thing I’m noticing looking at your tree is that it has not been re-rooted, correct? If yes, to make a better visual comparison you should find first the subtree of Archaea and the re-root the tree according to it. To do this I generally use archaeopteryx, in case you need a tool for doing that.

Many thanks,

Dear Francesco,
thank you the reply and the references to more material about the tree of life. I will have a look at these publications to get some more ideas how to use Graphlan. And yes, I have not rerooted the tree, very nice suggestion, I will try.