HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.
Read more about the tool: http://huttenhower.sph.harvard.edu/humann
This tool makes strain profiles, based on the principle of detecting variable presence and absence of gene families within a species that is otherwise well-covered in multiple samples.