An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

We introduce an open source software utility to extract the highly variable ITS1 and ITS2 subregions from fungal nuclear ITS sequences, the region of choice for environmental sampling and molecular identification of fungi. Inclusion of parts of the neighbouring, very conserved, ribosomal genes in the sequence identification process regularly leads to distorted results. The utility is available for UNIX-type operating systems, including MacOS X, and processes about 1 000 sequences per minute.