Aligned ITS reference files

Commands in mothur
1

Please suggest from where the ITS aligned reference fasta file can be downloaded?

I have tried from the link https://www.mothur.org/wiki/UNITE_ITS_database

but the mothur returns at pcr.seq command with “seqs are not aligned. When using start and end your sequences must be aligned.”

2

Hi,

I’m not sure that a global pan-ITS reference alignment is possible since ITS fragments are rarely homologous even within a genome. You probably want to do something like pairwise.seqs (https://mothur.org/wiki/Pairwise.seqs)

Pat