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Updated: Nov 17, 2025

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

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TaxonTableTools: A comprehensive, platform-independent graphical user interface software to explore and visualise DNA

Till-Hendrik Macher¹, Arne J Beermann¹, Florian Leese¹

¹Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany.

Molecular Ecology Resources

|February 16, 2021

Summary

TaxonTableTools (TTT) is a new graphical user interface (GUI) that simplifies DNA metabarcoding data analysis and visualization for biodiversity assessments. This free software enables reproducible workflows for researchers with limited bioinformatics expertise.

Keywords:

OTUs biodiversity bioinformatics biomonitoring data analysis eDNA

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Area of Science:

Ecology
Bioinformatics
Genomics

Background:

DNA metabarcoding is a powerful tool for biodiversity assessment in research and environmental management.
Existing analysis software often requires significant bioinformatics expertise, creating a barrier for many users.
There is a need for user-friendly tools to translate raw sequence data into biological insights.

Purpose of the Study:

To introduce TaxonTableTools (TTT), a platform-independent graphical user interface (GUI) designed for accessible DNA metabarcoding data analysis and visualization.
To provide simple, reproducible workflows for processing and interpreting metabarcoding data.
To bridge the gap between raw sequence data and actionable biological information for a wider user base.

Main Methods:

TTT utilizes a 'TaXon table' data format, easily generated from read and taxonomy tables.
The software offers modules for generating Venn diagrams, basic statistics (e.g., read proportion per taxon), and interactive visualizations like Krona charts.
TTT supports ecological analyses such as alpha/beta diversity estimates, rarefaction plots, and data conversion for regulatory bioassessment programs.

Main Results:

TTT provides an intuitive platform for analyzing and visualizing DNA metabarcoding data, including comparative analyses and taxonomic exploration.
The software generates interactive HTML graphics viewable in web browsers, enhancing data accessibility.
TTT facilitates the conversion of metabarcoding data into formats compatible with traditional bioassessment analyses.

Conclusions:

TaxonTableTools (TTT) democratizes DNA metabarcoding data analysis by offering a user-friendly GUI.
The software supports reproducible research and environmental management through simplified visualization and ecological analysis.
TTT is freely available with comprehensive documentation, promoting wider adoption and application in biodiversity studies.