Use this forum to address questions about the use of various commands available in mothur
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In general, ITS evolves too quickly to be aligned. If you are working with just a small taxonomic group, you could create you own alignment. But if you are working with all fungi, you can not align ITS/ITS2
sorry, missed your followup. I do use ITS2 even though we can't align it. It gives the best taxonomic resolution that we can get for all fungi. If you are working with specific groups of fungi, you may want to choose a different target.
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