Huttenhower Lab Galaxy Server 2.0

Francois-Xavier Bagnoud Building, Harvard School of Public Health

Please consider using MaAsLin2 as a long term alternative for LEfSe.

Important note: Files will be cleaned/removed from the servers after 60 days without access. Please do not leave any important datasets on the server for long term storage.

Legacy galaxy URL: https://huttenhower.sph.harvard.edu/galaxy

Thanks for visiting our lab's tools and applications page, implemented within the Galaxy web application and workflow framework. Here, we provide a number of resources for metagenomic and functional genomic analyses, intended for research and academic use. Please see the menus and folders to the left for an overview of available tools including documentation, sample data, and publications.


The tools are available here without account creation. However, you are strongly invited to create an account for having access to history, saved analyses, datasets, and workflows. You can create an account and/or log in using the User menu in the top-right corner.


If you’re interested in hearing more about our work, please visit the lab web site or the Harvard Chan Microbiome in Public Health Center.


If you have any comments, questions, or suggestions on the tools themselves, feel free to reach out to our bioBakery support Forum.



Galaxy tools

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A hierarchical model of microbial ecological population structure capable of simulating metagenomic data with known correlation.

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A computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

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Determining multivariable association between clinical metadata and microbial meta’omic features.

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Profiling presence/absence and abundance of microbial pathways in a community from metagenomic sequencing.

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Bioconductor package implementing meta-analysis methods for microbial community profiles.

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A method to find multi-resolution associations in high-dimensional, heterogeneous datasets.

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Prediction of unobserved character states in a community of organisms from phylogenetic information about the organisms.

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Integrates gene sequence homology and taxonomic provenance to identify metagenomic contigs explained by pairs of microbial clades.

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A software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.

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Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance.