DNA barcoder

Similarity matrix

How to use this page

On this page a similarity matrix can be generated of a FASTA file. The similarity matrix can be used for the similarity cutoff calculation and the visualization. Using a precomputed similarity matrix significantly reduces the computing time of these calculations when run multiple times. The sequences in the FASTA file will be compared and a similarity score between 0 and 1 will be given for each comparison. For the calculation of the similarity matrix a minimum sequence alignment length is required. 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.