Hi, I want to build a phylogenetic tree with ITS sequences of assembled genomes. For this, I need to retrieve only ITS (internal transcribed region) sequences from a genome. Genome annotations provides annotations of rRNA sequences but not ITS. Is there any tool for that?
Currently, I can only think of blasting the genome against ITS sequences and recovering blast hits as ITS sequences from the genomes. Is there a more systematic or better approach or tool for doing it?