mothur v.1.32.0

We have released mothur v.1.32.0 and have a number of exciting new features and updates to tell you about. The main new feature is to incorporate the LEfSe software package from Curtis Huttenhower’s lab into mothur as the lefse command. Alternatively, you could use the make.lefse command to generate a file to use as input to LEfSe. They should produce the same output, let us know if you think we’re missing anything. We also incorporated the Kruskal-Wallis non-parametric test (think ANOVA) as the kruskal.wallis command - this is part of the LEfSe algorithm. Among the new features we’ve renamed a couple of commands (see below) and improved the output generated by the classify.rf command (formerly the classify.shared command. We are putting the finishing touches on classify.svm, which will be similar to classify.rf (random forest), but uses support vector machines (SVMs). As always, there have been a number of bugs reported that we’ve addressed in this release. We also noticed that the greengenes folks expanded their database and taxonomy and we have updated the mothur-compatible versions of those. Going forward we’re looking to add a number of new commands for the next release including a SRA submission tool. If you have any suggestions for other commands or options, let us know!

Finally, there are still seats available for the R workshop in November and the mothur workshop in December. Consider coming to one or both - Detroit is beautiful that time of year.

New commands

Feature updates

Bug fixes

Changes to wiki

  • Added ITS database from Segre Lab
  • Updated the greengenes-formatted databases


Registered users