Fig. 1: PhyloPhlAn 3.0 phylogenetically places microbial isolate or metagenomic assemblies.

PhyloPhlAn 3.0 provides strain-to-phylum level phylogenies built from newly generated microbial genomes (isolate or metagenomic assemblies) in the context of over 80,000 existing isolate genomes and 150,000 metagenomic assemblies. It automatically selects the most informative loci on a clade-specific basis, handles incomplete or fragmented assemblies, and can be configured to provide the resulting multiple-sequence alignment, estimated mutation rates (optionally), and phylogenetic tree.