Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences

• Incompleteness of reference sequence databases and unresolved taxonomic
relationships complicates taxonomic placement of fungal sequences. We
developed PROTAX-fungi, a general tool for taxonomic placement of fungal
ITS sequences, and implemented it into the PlutoF platform of the UNITE
database for molecular identification of fungi. • PROTAX-fungi
outperformed the SINTAX and RDB classifiers in terms of increased accuracy
and decreased calibration error when applied to data on mock communities
representing species groups with poor sequence database coverage. • With
empirical data on root- and wood-associated fungi, PROTAX-fungi identified
reliably (with at least 90% identification probability) the majority of
sequences to the order level but only ca. one fifth of them to the species
level, reflecting the current limited coverage of the databases. • When
applied to examine the internal consistencies of the Index Fungorum and
UNITE databases, PROTAX-fungi revealed inconsistencies in the taxonomy
database as well as mislabelling and sequence quality problems in the
reference database. The according improvements were implemented in both
databases. • PROTAX-fungi provides a robust tool for performing
statistically reliable identifications of fungi in spite of the
incompleteness of extant reference sequence databases and unresolved
taxonomic relationships.