Mothur with COI reference sequence

Is there a way for me to run my analysis using COI reference sequence like MIDORI (

I tried pcr.seq and align.seq command but it says that my sequences are not aligned.

I also tried going directly to pre.cluster without aligning but encountered problem in dist.seq. So I am using pairwise.dist but it take forever to run.

Please guide me on how to proceed with my analysis.

You should use CLUSTAL or MUSCLE to align the reference sequences. You can then use that as your reference in align.seqs

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This works for me. Thank you!

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