

HUMAnN 3.0
Profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing.
User manual || Tutorial
MetaPhlAn 3.0
A computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

StrainPhlAn
Strain-level resolution of species across large sample sets, on single nucleotide polymorphisms (SNPs) within conserved and unique species marker genes.
User manual || Tutorial
MaAsLin 2
R package for efficiently determining multivariable association between clinical metadata and microbial meta’omic features.
User manual || Tutorial
MMUPHin
Bioconductor package for microbial community profiles providing interfaces for covariate-controlled batch and study effect adjustment.
User manual || Tutorial