DNA barcoder


How to use this page

On this page a reference dataset can be visualized three-dimensionally.

FASTA file

The reference dataset needs to be given as a file with FASTA format.
Make sure the description lines of the FASTA file have the following format:
>ID_NAME k__kingdom;p__phylum;c__class;o__order;f__family;s__species
>MH854570 k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Hypocreales;f__Nectriaceae;g__Fusarium;s__Fusarium_equiseti

Similarity matrix

To create the visualization a similarity matrix is used. When no matrix is given one will be created automatically. For this a minimum sequence alignment length is needed. The default for this setting is 400. It is however recommended lowering this when working with smaller barcodes. When using short sequences such as ITS2 sequences it is recommended to use 50.
Similarity matrices can be created separately on the analysis page.

Coordinates file

The coordinates file (.coord) is a file which is created by this visualization page. This file can be downloaded and reused for a visualization of the same dataset, but for a different rank. This will reduce the calculation time.