Tools
Microbial Community Profiling Tools
![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2020/03/4-300x214.png)
Prediction of unobserved character states in a community of organisms from phylogenetic information about the organisms.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/StrainPhlAn-300x214.png)
Strain-level resolution on single nucleotide polymorphisms within conserved and unique species marker genes.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/waafle-300x214.png)
Integrates gene sequence homology and taxonomic provenance to identify metagenomic contigs explained by pairs of microbial clades
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/MelonnPan-300x214.png)
MelonnPan is a computational method for predicting metabolite composition from microbiome sequencing data.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/PPANINI-300x214.png)
A computational pipeline to prioritize microbial genes based on their metagenomic properties (e.g. prevalence and abundance).
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/ShortBred-300x214.png)
A system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2020/08/metawibele-300x214.png)
Identify and prioritize potentially bioactive (and often uncharacterized) gene products in microbial communities.
User manual || TutorialAnalysis/Statistics Tools
![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2020/03/16-300x214.png)
Determining multivariable association between clinical metadata and microbial meta’omic features.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/AREPA-300x214.png)
A command-line tool to easily fetch 'omics data from multiple heterogeneous repositories and processing.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/CCREPE-300x214.png)
CCREPE is an R package designed to detect significant correlations in compositional datasets.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/MicroPITA-300x214.png)
A computational tool enabling sample selection in two-stage (tiered) studies.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2020/03/21-300x214.png)
Bioconductor package implementing meta-analysis methods for microbial community profiles.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/BanoCC-300x214.png)
A package for analyzing compositional covariance while accounting for the compositional structure.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/HAIIA-300x214.png)
A method to find multi-resolution associations in high-dimensional, heterogeneous datasets.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2022/01/sparsedossa2-300x214.png)
A hierarchical model of microbial ecological population structure capable of simulating metagenomic data with known correlation.
User manual || TutorialInfrastructure/Utilities
![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2020/03/HUMAnN2-2-300x214.png)
Create reproducible workflows and execute them efficiently allowing tasks to run locally or in a grid computing environments.
User manual || Tutorial![](https://huttenhower.sph.harvard.edu/wp-content/uploads/2019/11/graphlan-300x214.png)
A software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.
User manual || Tutorial