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MEGAN6 Ultimate Edition

The world’s only interactive tool for functional and taxonomic whole genome shotgun metagenomics analysis and visualization. Developed by our co-founder Professor Daniel Huson.

Test MEGAN6 UE for free now!

Comprehensive Functional Analysis

Includes an up to date version of KEGG, the most comprehensive biochemical pathway database. Harness the power of this database without having to perform additional analysis steps, right after importing your alignments.

Accurate Taxonomic Classifications

Our award-winning weighted Lowest Common Ancestor (LCA) algorithm makes taxonomic classification more precise than any alternative approach.

Reproducible Analysis Workflows

Intuitively develop scripts of your analysis workflows based on the commands displayed in the message window while performing your interactive analysis.

New Visualizations

MEGAN6 offers new visualization techniques to facilitate interpretation and data-driven decisions.

To make your visualizations stand out, MEGAN6 provides user friendly color presets for every visualization in the program.

New Samples Viewer

The new samples viewer makes it easy to manage your samples. Add study metadata, subset your data or remove samples with ease.

DIAMOND Integration

The included DAA-meganzier allows for direct import and ‚MEGANization‘ of a DIAMOND Alignment Archive (DAA), saving time and effort. DAA is now readable by MEGAN in only a fraction of the time.

Features of the Ultimate Edition

Ontologies, Databases

The Ultimate Edition comes with a KEGG license to use the KEGG Pathways and visualizations from within MEGAN. In addition to the Taxonomy, InterPro2GO, eggNOG, and SEED database mappings, the Ultimate Edition gives you access to additional databases such as KEGG, PFAM and RDP.

Functional Assignments

Besides the new InterPro2GO mapping, the Ultimate Edition supports the usage of the latest KEGG classifications and metabolic pathways (inclouded with a MEGAN Ultimate License).

Commandline Mode and Scripting

With MEGAN’s commandline tools such as Blast2RMA or the meganizer, you are able to quickly convert alignment files produced by BLAST or the fast aligner DIAMOND to a RMA or MEGAN readable DAA file. This saves you a lot of computation time. Ultimate Edition comes with a commandline mode for MEGAN preparing for using MEGAN in automated pipelines. Additionally, the Ultimate Edition provides you with NCBI taxonomy, InterPro2GO, eggNOG, DIAMOND, KEGG, SEED and Silva tailored commandline tools.


Visualizations are key in understanding your dataset. MEGAN allows you to visualize your data the best way possible, therefore you are given visualization tools to create stunning figures and charts. This includes stacked bar and stacked line charts, radial space filling trees, and word clouds. Additionally, you can create attribute correlation plots, co-occurrence plots, and heatmaps.

MEGAN6 Community Edition vs. Ultimate Edition

Download Links Community GitHub page Ultimate Edition Latest Version
Databases, Ontologies, Resources Taxonomy (NCBI, GTDB)
Taxonomy (NCBI, GTDB)
KEGG (latest)
Plots: a few examples Bar
Word clouds
Word clouds
Radial space filling trees
Attribute correlation plot
… Constantly adding new ones, submit your request
Command-Line Tools Blast2RMA Meganize Blast2RMA Meganize
NCBI taxonomy tools
InterPro2Go tools
eggNOG tools
KEGG tools
SEED tools
SILVA tools
Extensions Community-generated Latest KEGG classification and pathways (KEGG License included)
Updates Occasional bug fixes No new features Regular bug fixes All new features as they are added
Support MEGAN Community page MEGAN Community page email support
Questions answered by developers
Licensing GPL 3 Licensed by Computomics

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