mothur v.1.16.0

We are happy to announce the release of mothur v.1.16.0, aka the “Brett who?” version in celebration of the Green Bay Packers beating the Pittsburgh Steelers. This release contains a number of new features related to multivariate data visualization including implementations of tools to generate PCA and nmds, both of which complement the earlier pcoa command. Another new command corr.axes allows you to determine how well the relative abundance of your OTUs/phylotypes or metadata correlate with the axes generated by PCoA, NMDS, or PCA. These are the data that are commonly plotted to generate biplot diagrams. In addition we have added commands that allow you to remove rare OTUs and merge groups in a shared file. In addition to these commands we have added a large number of features to the existing commands most notable are the additions to the indicator and chimera.slayer commands and the inclusion of an additional 18 beta-diversity estimators. Finally, we also added a mothur-compatible version of the RDP training set to the wiki that you can use to reproduce the output provided by the RDP website.

In the next several days you will be receiving an additional email or two from us with information about several exciting developments. First, we are going to change the way that this email system works. We are still ironing out the kinks, but the new system will give you more flexibility in joining and quitting the list. Second, we will be sending out information about a survey we have pulled together to ask you guys for some valuable information. Finally, two weeks ago we announced that Pat will be hosting a workshop at a hotel near the Detroit International Airport - that workshop is full, but we anticipate holding a second workshop in April, if you are interested please email Pat (pdschloss gmail com).

As always, we appreciate your enthusiastic use of mothur and ideas. Within one year of publishing mothur, it received over 60 citations - thank you! Feel free to keep the six packs and Russian vodka coming...

New commands

  • corr.axes - correlation of data to axes
  • pca - generate principle components plot data
  • nmds - generate non-metric multidimensional scaling data
  • remove.rare - remove OTUs that are below a threshold of abundance
  • merge.groups - merge lines in shared file that are grouped by a design file.

Feature updates

  • indicator - added the design parameter
  • classify.otu - added reftaxonomy, group and basis options to build a summary file for the results.
  • trim.seqs - added keepfirst and removelast options as alternative ways of trimming sequences
  • get.lineage and remove.lineage - allows users to make use of confidence scores
  • chimera.slayer - can now use the template file as it’s own reference to look for chimeras specific to your data
  • chimera.slayer - added a trim parameter to only include the portion of the sequence that corresponds to the largest parent
  • parse.sff - removed; but implemented in sffinfo
  • pcoa - added R2 metric to output
  • sub.sample - added persample parameter to command
  • cluster.fragments - added percent and diffs parameters to command
  • normalize.shared - added zscore method

Bug fixes

  • added headings to the .indicator.summary file
  • fixed weird characters outputted in trim.seqs merging.
  • fixed memory leak in chimera slayer
  • fixed bug with order of printing the distances in the distance file output for unifrac.unweighted and unifrac.weighted
  • fixed bug in trim.seqs with qtrim=T

Other stuff

  • added our version of the RDP reference files to the wiki; should give very similar output to that generated by the RDP website