MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
HUMAnN: The HMP Unified Metabolic Analysis Network, version 3
HAllA: Hierarchical All-against All Association Testing
LEfSe determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
bioBakery workflows: A collection of meta'omic analysis workflows
AnADAMA2: Another Automated Data Analysis Management Application 2
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and *in-vivo* transcriptional activity of individual strains in metagenomic samples. PanPhlAn’s ability for strain-tracking and functional analysis of unknown pathogens makes it an efficient tool for culture-free infectious outbreak epidemiology and microbial population studies.
ShortBRED: a system for profiling protein families of interest at very high specificity in shotgun meta’omic sequencing data
HUMAnN2: The HMP Unified Metabolic Analysis Network 2
PPANINI: Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration.
WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events