get.oturep with the new vsearch clustering

Commands in mothur
1

If I cluster OTUs with the new vsearch method, the absence of a .dist file prevents me to retrieve representative sequences for OTUs with get.oturep, since it won’t accept passing the fasta+name files and still asks for a phylip or column file.

am I missing something?

Thanks

2

You could use the abundance-based approach in get.oturep, which doesn’t require name file. Alternatively, you could always run dist.seqs to get the distance matrix.

Pat