Table 3.

Species identification rates in % (correctly identified/misidentified/not identified) using two different classification methods for each of the five barcodes and their combinations.

Barcode locus/loci	TaxonDNA		BLOG
	Best match (%)	Best close match (%)
rbcL	18/23/59	18/23/58	0/25/75
matK	100/0/0	88/0/12	100/0/0
psbA-trnH	94/6/0	94/6/0	100/0/0
ITS	100/0/0	88/0/12	75/25/0
ITS2	100/0/0	100/0/0	100/0/0
rbcL + matK	82/12/6	83/12/6	100/0/0
rbcL + psbA-trnH	76/24/0	76/24/0	100/0/0
rbcL + ITS	100/0/0	88/0/12	75/25/0
rbcL + ITS2	100/0/0	100/0/0	75/0/25
matK + psbA-trnH	100/0/0	76/24/0	75/25/0
matK + ITS	100/0/0	88/0/12	100/0/0
matK + ITS2	100/0/0	100/0/0	75/0/25
psbA-trnH + ITS	82/12/6	83/12/6	75/0/25
psbA-trnH + ITS2	76/24/0	76/24/0	75/0/25
ITS + ITS2	100/0/0	88/0/12	75/25/0
rbcL + matK + psbA-trnH	100/0/0	88/0/12	100/0/0
rbcL + matK + ITS	100/0/0	100/0/0	100/0/0
rbcL + matK + ITS2	100/0/0	100/0/0	75/0/25
rbcL + psbA-trnH + ITS	100/0/0	88/0/12	100/0/0
rbcL + psbA-trnH + ITS2	100/0/0	100/0/0	75/0/25
rbcL + ITS + ITS2	100/0/0	88/0/12	75/25/0
matK + psbA-trnH + ITS	100/0/0	100/0/0	100/0/0
matK + psbA-trnH + ITS2	100/0/0	100/0/0	75/0/25
matK + ITS + ITS2	100/0/0	88/0/12	100/0/0
psbA-trnH + ITS + ITS2	100/0/0	100/0/0	100/0/0
rbcL + matK + psbA-trnH + ITS	100/0/0	88/0/12	100/0/0
rbcL + matK + psbA-trnH + ITS2	100/0/0	100/0/0	75/0/25
rbcL + psbA-trnH + ITS + ITS2	100/0/0	100/0/0	100/0/0
rbcL + matK + ITS + ITS2	100/0/0	100/0/0	75/0/25
matK + psbA-trnH + ITS + ITS2	100/0/0	100/0/0	100/0/0
rbcL + matK + psbA-trnH + ITS + ITS2	100/0/0	100/0/0	100/0/0

TaxonDNA: Best match and Best close match results. Not identified rates are summed over the “Ambiguous” and “No match” categories. Please see supplementary Table S4 for details.

BLOG: percentage correct classification for test file, using 90% slicing at species level (Refer to materials and methods for detailed analysis).

The highest success rate for preferred barcoding options in Decalepis are highlighted in grey.