mOTUs

• Quantifies known and unknown microorganisms at species-level resolution from shotgun sequencing data
• Clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs
• Profiles abundances of mOTUs in shotgun metagenomic samples
• Enables identification of novel microorganisms not previously represented in databases

eggNOG

• Provides orthologous group assignments at over 100 different taxonomic levels
• Offers multiple sequence alignments, maximum-likelihood trees, and broad functional annotations for each group
• Includes comprehensive characterization and analysis of gene families from over 2,000 complete genomes
• Enables users to explore and analyze the evolution of gene functions across different organisms

iPATH

• Visualizes and analyzes cellular pathways based on current annotations (such as KEGG)
• Provides pathway maps for primary cellular metabolism and secondary metabolite synthesis and regulatory pathways
• Allows users to map their own data onto these pathway maps
• Enables easy exploration and analysis of the functional and metabolic capabilities of (meta-)genomic data sets

iTOL

• Displays and manipulates phylogenetic trees in a variety of layouts, including circular tree layout
• Offers drawing and annotation features for tree displays
• Exports tree displays in several graphical formats, both bitmap and vector based
• Enables users to easily visualize and analyze large phylogenetic datasets

Enterotyping

• Detects and characterizes densely populated regions (enterotypes) in high-dimensional space of microbiome community composition
• Stratifies human individuals by enterotype
• Provides computational methods for detecting and characterizing enterotypes in any dataset
• Enables researchers to reproduce previous reports or determine enterotypes in new studies

SIAMCAT

• Performs statistical inference of associations between microbial communities and host phenotypes (such as disease states)
• Uses LASSO models to avoid overfitting issues and enable model interpretation and biomarker selection
• Offers a modular framework for integrating multiple data types and analysis methods
• Enables identification of potential microbial biomarkers for diseases or other conditions

proGenomes

• Provides consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes
• Enables interactive exploration and download of subsets of the database (e.g., by taxonomic clade or habitat)
• Offers customization options for subsets of organisms (e.g., representatives of each species or habitat-specific organisms)
• Facilitates research on microbial ecology and evolution

NGLess

• Provides a domain-specific language for next-generation sequencing data processing with a focus on metagenomics
• Implements the NG-meta-profiler workflow, which efficiently and reproducibly performs sequence preprocessing, mapping to reference databases, filtering of the mapping results, and profiling
• Offers flexible and customizable workflows for analyzing metagenomic data
• Enables researchers to easily integrate NGLess into their existing bioinformatics pipelines