Mothur with COI reference sequence

Commands in mothur
1

Is there a way for me to run my analysis using COI reference sequence like MIDORI (http://reference-midori.info/download.php#)?

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.

2

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

1 Like
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This works for me. Thank you!

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