$./phylophlan.py -u my_genomes when finished, the resulting tree will appear in the output/my_genomes folder. Example 1: Corynebacterium 'de novo' phylogenetic tree building You can try out this operation ( -u) using an example included in the PhyloPhlAn package you downloaded called example_corynebacteria and stored in the input folder. In contains a protein multifasta file for each of the 30 genomes available for the as February 2012 plus two genomes as a meaningful outgroup.
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As mentioned above, the command for obtaining the phylogenetic tree is. $./phylophlan.py -u example_corynebacteria --nproc 4 Using 4 threads (specified with --nproc 4) this operation should take no more than 4-5 minutes, but even using one processor only (default) should give you the results in 10 minutes or so. In the output/example_corynebacteria/ folder you'll find a file of the resulting tree as provided by, and a file containing the same tree rerooted with a procedure which tries to maximize the distance from the root to any leaf. The two files are available for download (, and can be inspected with and drawn with.
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Figure 3B in the reports and discuss this example. Also the full three of life reported above has been originally generated in this way. Notice that the concatenated alignment used to generate the tree with FastTree is stored in data/example_corynebacteria/aln.fna and can be used as input for other phylogenetic reconstruction software such as or among. Inserting new genomes to the tree of life PhyloPhlAn let you insert a genome (or a set of genomes) into the already built microbial tree of life (containing >3,000 genomes, see figure and tree files above). Also in this case you need to create a dedicated folder (e.g.
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