Phylogenetically classifies variable-length DNA sequence fragments. PhyloPythia is a method that uses sequence composition to phylogenetically characterize sequence fragments. The software allows the phylogenetic classification of genomic fragments ≥ 1–3 kb for all taxonomic ranks considered (domain, phylum, class, order and genus). PhyloPythia can also achieve this for fragments originating from new organisms. It was used PhyloPythia to analyse three metagenomes: the Sargasso Sea sample and two samples of Enhanced Biological Phosphorus Removal (EBPR)-sludge used in industrial wastewater processing.