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.
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
AnADAMA2: Another Automated Data Analysis Management Application 2
bioBakery workflows: A collection of meta'omic analysis workflows
HUMAnN: The HMP Unified Metabolic Analysis Network, version 3
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
HAllA: Hierarchically All-against-All Association Testing