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.
User manual || TutorialIdentify and prioritize potentially bioactive (and often uncharacterized) gene products in microbial communities.
User manual || TutorialIntegrates gene sequence homology and taxonomic provenance to identify metagenomic contigs explained by pairs of microbial clades
User manual || TutorialA system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data.
User manual || TutorialViral community profiling on metagenomic, metatranscriptomic, or metavirome sequencing data
User manual || TutorialA 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 || TutorialMelonnPan is a computational method for predicting metabolite composition from microbiome sequencing data.
User manual || TutorialA computational pipeline to prioritize microbial genes based on their metagenomic properties (e.g. prevalence and abundance).
User manual || TutorialAnalysis/Statistics Tools
Determining multivariable association between clinical metadata and microbial meta’omic features.
User manual || TutorialA hierarchical model of microbial ecological population structure capable of simulating metagenomic data with known correlation.
User manual || TutorialCCREPE is an R package designed to detect significant correlations in compositional datasets.
User manual || TutorialA computational tool enabling sample selection in two-stage (tiered) studies.
User manual || TutorialDetermines 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 || TutorialA method to find multi-resolution associations in high-dimensional, heterogeneous datasets.
User manual || TutorialA package for analyzing compositional covariance while accounting for the compositional structure.
User manual || TutorialA 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 || TutorialA 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