mothur v.1.34.0

After a long delay, we are very happy to announce the release of mothur_v.1.34.0 ! We’re anxious to get back on our normal release schedule of a new version ever month or two. In the current release, we’ve added a new machine learning algorithm classify.svm and added a bunch of new features that you all have requested. There are also a number of bug fixes that have also been incorporated into the release. Some of the feature updates that you might find most interesting is the addition of the shannon range calculator that was published last year in ISMEJ by Haegeman and colleagues and the addition of the Jensen-Shannon Divergence calculator. You may notice that we don’t quite have the make.sra command up and running yet. It’s still very much in the works and we have a lot of the components in place to make it happen. We are working with the folks at the SRA to make it as seem less as possible for you all and so this has required a bit of iteration. We were really hoping to have something for you by this release, but all we can do is hope that we’ll have it for the next release. SRA is very excited about this, but they just need to make sure all their ducks are in a row first.

There’s also a few other things going on that you should know about...

  • We’ve launched a blog. Of course, we’re only 10 years behind, but hey! The plan is to use the blog to discuss how to use mothur to do different things beyond the analysis examples and how we generate various reference files. You’ll see a nice mix of mothur, R, and bash commands getting play in the posts.
  • There will be a mothur workshop in Detroit from December 17-19. The next workshop will be in March and I’m still not sure whether it will be a mothur or R workshop. Email Pat if you are interested.

We’re plugging away at continuing to make mothur a great program, as always, if you have questions, ideas, or code to contribute, please don’t hesitate to shoot us a note!

New commands

  • get.mimarkspackage - create blank mimarks package form for sra command
  • make.sra - create submission ready files
  • classify.svm - Rank OTUs using the support vector machine learning algorithm

Feature updates

Bug fixes