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 joins (merges) multiple single-sample output files into a single table with multiple samples. It can also be used to join multiple multi-sample output files into a single table.