Tools

Tools

Microbial Community Profiling Tools

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

User manual || Tutorial

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

User manual || Tutorial

A computational pipeline for reconstructing highly accurate phylogenetic trees based on whole-genome sequence

User manual || Tutorial

Strain-level resolution on single nucleotide polymorphisms within conserved and unique species marker genes.

User manual || Tutorial

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

User manual || Tutorial

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

User manual || Tutorial

MelonnPan is a computational method for predicting metabolite composition from microbiome sequencing data.

User manual || Tutorial

A computational pipeline to prioritize microbial genes based on their metagenomic properties (e.g. prevalence and abundance).

User manual || Tutorial

A system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data.

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Analysis/Statistics Tools

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

User manual || Tutorial

A command-line tool to easily fetch 'omics data from multiple heterogeneous repositories and processing.

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CCREPE is an R package designed to detect significant correlations in compositional datasets.

User manual || Tutorial

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

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A computational tool enabling sample selection in two-stage (tiered) studies.

User manual || Tutorial

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

User manual || Tutorial

A package for analyzing compositional covariance while accounting for the compositional structure.

User manual || Tutorial

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

User manual || Tutorial

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

User manual || Tutorial

Infrastructure/Utilities

A collection of workflows for executing common microbial community analyses using validated tools and parameters.

User manual || Tutorial

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.

User manual || Tutorial

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

User manual || Tutorial