  Precision and reliability of barcode-based biodiversity assessment can be
affected at several steps during acquisition and analysis of the data.
Identification of barcodes is one of the crucial steps in the process and can
be accomplished using several different approaches, namely, alignment-based,
probabilistic, tree-based and phylogeny-based. Number of identified sequences
in the reference databases affects the precision of identification. This paper
compares the identification of marine nematode barcodes using alignment-based,
tree-based and phylogeny-based approaches. Because the nematode reference
dataset is limited in its taxonomic scope, barcodes can only be assigned to
higher taxonomic categories, families. Phylogeny-based approach using
Evolutionary Placement Algorithm provided the largest number of positively
assigned metabarcodes and was least affected by erroneous sequences and
limitations of reference data, comparing to alignment-based and tree-based
approaches.
