mothur v.1.20.0

We are happy to announce the release of mothur v.1.20.0 in honor of Fathur’s Day and version 1’s Golden Birthday. We have a few new features and a number of small, but significant feature updates that you are sure to enjoy. First, we have heard from a lot of people about the pain of dealing with blast in chimera.slayer. As a work around that is actually better, we have ported in the source code from Robert Edgar’s latest venture UChime. It is available within mothur as chimera.uchime. The downside is that the tool is not published yet; however, based on testing, it is better than the chimera.slayer algorithm, faster, and dependency-free. We will be updating the Costello stool analysis example page to suggest a way to use chimera.uchime and chimera.slayer in a new and better way. Second, we have also added two utility functions to add the redundant sequence names back into a tree of unique sequences (deunique.tree) and a function that counts the number of sequences represented by each unique sequence (count.seqs). As for features, we have added the citation feature to every command so you can see the reference that you should cite in your paper when you use a command. This is important so people can give proper attribution to the people that developed the algorithm. We have also decided to convert all of the calculator-related output to distances to make things uniform; in addition, several of the parameters did not work as similarities. Finally, we have added column headings to the shared and relabund files. We realize this may screw up people’s scripts; however, having these headings will hopefully help people that merge mothur and R for their analysis.

This is shaping up to be a great summer as we continue to add new features to mothur. We are particularly excited about the development of mothur v.2.0. If you would like to be a beta (delta?) tester of v.2.0, please shoot us an email at mothur.bugs\ and we can get you set up. Also, I will be hosting another workshop near Detroit from August 15-17. If you are interested, please email me at pdschloss\ and I can get you more information.


Pat Schloss

New commands

Feature updates

  • citation feature: gives the reference that should be cited for each command and calculator. It’s accessed just like help for commands, example: align.seqs(citation). For calculators, just add citation to your calc string, example: collect.single(calc=sobs-chao-citation).
  • trim.seqs - added a name parameter
  • phylo.diversity - no longer requires a groupfile or at least 2 groups to run, if no group file is given mothur assumes all sequences are from the same sample.
  • get.lineage/remove.lineage = can now process multiple taxons separated by a dashes
  • dist.shared - added processors option
  • consensus.seqs - added cutoff option (
  • summary.shared and collect.shared - mothur no longer reports the similarity values, rather it now reports distances
  • Calculators - a bug was found in the spearman calculator and there was general wonkiness in how distances were converted to similarity values. The solution has been to just use distance values throughout mothur
  • added column headings to the shared/relabund files

Bug fixes

  • cluster.split - fixed an output redirect problem with fasta method (
  • summary.seqs - re-added processors option (

Minor Releases

  • 1.20.1 - fixed bug with hcluster - was not changing the cutoff with average method
  • 1.20.2 - fix chimera.uchime bug with Windows, exiting early
  • 1.20.3 - added “unclassified” bins to classify.otu summary file
  • 1.20.3 - added warning to trim.seqs for non-numeric quality scores