The emergence of cutting-edge bacterial culturing techniques, driving the discovery of novel bacteria at an increasingly rapid rate, is revolutionizing our understanding of the microbiome. The ability to rapidly generate extensive amounts of new data from this research has created a need to develop sound analysis techniques and software, that can efficiently process these vast datasets and deliver biologically meaningful and interpretable outcomes. Phylogenetic Analysis of Metagenomes (PAM) is a software package that implements distance-based comparison between sequenced metagenomic data and reference genomes, to estimate with precise resolution the phylogenetic distribution of species within a sample. The integration of vast genome sequenced isolate collections with the application of sequence based distance trees to metagenomic analysis presents an alternative to the traditional taxonomic classification, relying solely on high quality sequence data to determine read abundance and infer phylogenetic prevalence. The PAM approach provides the potential to perform high resolution metagenomic analysis, aid in the identification of novel bacterial species and determine key functional capabilities, crucial to our understanding of microbial activity.