mothur v.1.9.0

We are happy to announce the release of mothur v.1.9.0! Although there are no new commands, per say, there are a number of new options available, which will hopefully make mothur more flexible. For example, when we teach workshops people are often overwhelmed by the number of files generated by mothur and are never quite sure what the output is from a command. Now each command indicates the files that are being created. Another example is the output of an accnos file from the chimera checking commands that you can use with remove.seqs to purify your sequence collection of chimeras. Perhaps the biggest update in this release is the incorporation of MPI. You can still use multiple processors without using MPI, but for those power users that have a cluster and would like to run mothur jobs across machines or nodes, it is now possible. We are curious to hear people’s experiences with the MPI version of mothur. These are just a few of the many new features that we have added to this release.

There is increased traffic on the user forum and its great to see more people are willing to try and help others. The forum has also been a great resource for users to suggest new features and ask questions. Many of the features in this release have come from users. Thanks for the great suggestions and bug reports - this feed back helps to make mothur the great program it is! We have a number of features that we are working on for v.1.10.0 and hopefully we won’t have such a long time lag before the next release.


  • added output parameter to otu.hierarchy command, options are name and number. name is default. you can output either the names of the sequences in the OTUs or the OTU numbers.
  • added dups parameter to remove.seqs command.
  • add a name option to unifrac commands
  • added output parameter so you can create a square phylip formatted matrices from dist.seqs and dist.shared
  • added parse.list command.
  • output list of files that are created at the end of each command
  • fixed problem with logfiles that occurred when multiple executions of mothur were running at the same time.
  • filter.seqs can filter multiple files by separating files names with dashes. ex. fasta=abrecovery.fasta-core_set_aligned.imputed.fasta
  • removed phylip parameter from dist.seqs and replaced with output
  • added sim parameter to read.dist
  • parallelized filter.seqs
  • added MPI code to dist.seqs, filter.seqs, classify.seqs, align.seqs, and chimera commands.
  • broke chimera.seqs up into chimera.bellerophon, chimera.ccode, chimera.check, chimera.slayer, chimera.pintail.
  • add accnos file output to the chimera.*** commands
  • added more error checking to chimera.*** commands to check query to template seqs length
  • rework the way the chimera.*** commands process seqs so only one is read at a time
  • \^C ends command instead of ending mothur.
  • \^D now ends mothur with readline

Bug fixes

  • Problem with “../” ==> align.seqs(candidate=wobus.unique.fasta, template=../DataAnalysis/silva.refalign.fasta, processors=2); Segmentation fault
  • fixed bug in merge.files that inserted the eof character in between the merged files
  • fixed bug that could cause a badalloc to occur while reading a sabund file
  • added checking for duplicate sequence names in list files which leads to file to be blank.
  • get.seqs and remove.seqs using a list file left an extra comma if you eliminated the final member in the OTU.
  • fixed bug that caused a bad alloc to occur in chimera.seqs while using bellerophon.
  • fixed bug in how ends of sequences were treated in distance calculations.
  • fixed bug that caused a bad_alloc if a sequence could not be classified to a given confidence.