DNA barcoder


DNA barcoder

This website is based on the dnabarcoder tool created by Duong Vu. Dnabarcoder is an open-source software package focused on predicting DNA sequence similarity cutoffs and classification for DNA barcodes. It also has other components such as analysis, visualization and verification. More information can be found on the GitHub page. The software was created and tested for fungal data, specifically full-length ITS, ITS1 and ITS2. It can however also be used for other data such as bacterial data.

Global vs Local Similarity Cutoffs

Most studies and metabarcoding pipelines use a singular global similarity cutoff value for sequence identification. It is however not realistic to use a singular value for all taxa, as similarity cutoffs can vary significantly between clades and taxonomy levels. This is why dnabarcoder and this website have been created. Multiple local similarity cutoffs for different clades and taxonomy levels can be calculated for a reference dataset. A global cutoff for the whole dataset can also be calculated. These similarity cutoffs can then be used for classification of DNA sequences against said reference dataset. [source]

The cutoff values can be calculated on the cutoff calculation page . The classification can be done on the classification page . More information on how to go about using these pages can be found on the pages themselves.


This website has been implemented by Ruby van der Holst. The source code can be found on the GitHub page. The original command line version of DNA barcoder was developed by Duong Vu and can also be found on GitHub.


Duong Vu, R. Henrik Nilsson, Gerard J.M. Verkley (2022). dnabarcoder: an open-source software package for analyzing and predicting DNA sequence similarity cut-offs for fungal sequence identification. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13651


Duong Vu (d.vu@wi.knaw.nl)
Ruby van der Holst (r.holst@wi.knaw.nl)