Tools
Microbial Community Profiling Tools
Profiling presence/absence and abundance of microbial pathways in a community from metagenomic sequencing.
Prediction of unobserved character states in a community of organisms from phylogenetic information about the organisms.
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Identify and prioritize potentially bioactive (and often uncharacterized) gene products in microbial communities.
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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 system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data.
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Viral community profiling on metagenomic, metatranscriptomic, or metavirome sequencing data
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A computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
A computational pipeline for reconstructing highly accurate phylogenetic trees based on whole-genome sequence
Strain-level resolution on single nucleotide polymorphisms conserved and unique species marker genes.
User manual || Tutorial
MelonnPan is a computational method for predicting metabolite composition from microbiome sequencing data.
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A computational pipeline to prioritize microbial genes based on their metagenomic properties (e.g. prevalence and abundance).
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Analysis/Statistics Tools
Determining multivariable association between clinical metadata and microbial meta’omic features.
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A hierarchical model of microbial ecological population structure capable of simulating metagenomic data with known correlation.
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CCREPE is an R package designed to detect significant correlations in compositional datasets.
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A computational tool enabling sample selection in two-stage (tiered) studies.
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Determines the features most likely to explain differences between classes by coupling standard tests for statistical significance.
Bioconductor package implementing meta-analysis methods for microbial community profiles.
User manual || Tutorial
A method to find multi-resolution associations in high-dimensional, heterogeneous datasets.
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A package for analyzing compositional covariance while accounting for the compositional structure.
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A command-line tool to easily fetch 'omics data from multiple heterogeneous repositories and processing.
User manual || TutorialInfrastructure/Utilities
A collection of workflows for executing common microbial community analyses using validated tools and parameters.
Create reproducible workflows and execute them efficiently allowing tasks to run locally or in a grid computing environments.
User manual || Tutorial
A tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments.
A software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.
User manual || Tutorial