UNITE Database

I am using the UNITE database for qiime to assign taxonomy to ITS2 sequences. I used the 12_11 release of UNITE and it gave me many more assignments than the latest version (2014-05-13). I am not sure why. Does the 12_11 version have ITS2 sequences in addition to ITS 1? Also, in the latest version of UNITE, are the INSD sequences included?
Thanks in advance!


Fellow fungal ITS person here, also working with ITS2. Did you already solve your problem? I’ve used UNITE quite often, but unfortunately I haven’t compared the versions of UNITE that you’re using, so I have no idea what the problem might be, either…

If you’re using mothur (since you’re asking on the mothur forum), is there any specific reason why are you using the qiime UNITE database? I would think that would require changing the files slightly before using them with mothur? There are mothur formatted ones available both at the mothur website (http://www.mothur.org/wiki/UNITE_ITS_database) and the UNITE website (http://unite.ut.ee/repository.php). Where did you get the latest version that you have been using, and which files are you using (at least my downloads always had three versions: 97, 99, dynamic)?

The UNITE website has separate downloads that include all unclustered, good quality UNITE+INSD sequences, also available in mothur format. The trimmed UNITE reference database downloads, which are what’s listed in mothur’s wiki, include clustered reference sequences that correspond to fungal “species hypotheses”, as described in Kõljalg et al. 2013 (http://onlinelibrary.wiley.com/doi/10.1111/mec.12481/abstract). If I understand correctly from the paper where they describe the process, all good quality UNITE and INSD sequences are used in creating the files.


I am trying to use UNITE ITS database (mothur-formatted) to run in Mothur for analysing fungal samples. While aligning, Mothur reports that the reference database is not aligned and thus aborting. I have tried with the last two versions for all three variants (97,99 and dynamic); which gave the same error message.

Kindly guide me rectify this issue.


The UNITE database is not aligned. I’m not sure why or how you could create an alignment of ITS sequences since they are non-homologous. You are probably going to be best served by using some version of UNITE with phylotype or using pairwise.seqs to generate a distance matrix.