MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

bioBakery tools for meta'omic profiling

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

MaAsLin2: Microbiome Multivariate Association with Linear Models

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

High-quality circular representations of taxonomic and phylogenetic trees

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).

Biobakery formulae for the Homebrew package manager

MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

Large-scale Benchmarking of Microbial Multivariable Association Methods

MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.

The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.