mothur v.1.25.0

We are happy to announce the release of mothur v.1.25.0 with a number of new commands, features and bug fixes. First, the most significant new command is pcr.seqs, which will lift out specific regions of your gene of interest based on a number of user supplied parameters including primer sequence and alignment region. This would be most useful for creating your own reference sequence files for alignments and classification. Second, another new feature is the cooccurrence function, which will use a number of metrics and methods of testing those metrics to measure whether populations are co-occurring more frequently than you’d expect by chance. Third, at the suggestion of a user on the forum, we have begun to look at methods of synthesizing data in the create.database function. Finally, to support Greg Caporaso’s BIOM format, we have allowed for more easy formatting of data from a shared file to a biom file using the make.biom and make.shared files.

As always, we have added a number of new features and fixed several bugs that were reported to us by you through emails to mothur.bugs\ and through the user forum. We take your feedback seriously. Thank you for your continued support and suggestions. As always keep the 6 packs coming...

Pat Schloss

New commands

  • pcr.seqs - trim inputted sequences based on a variety of user-defined options
  • cooccurrence - calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance
  • create.database - synthesize sequence, group and taxonomy information (
  • make.biom - creates a .biom file from a shared file (

Feature updates

  • metastats - modified to more closely follow results from metastats website rather than the C code provided by the Pop lab
  • trim.flows and trim.seqs - allow for characters other than ATGC in reverse primers
  • make.shared - added biom parameter to create a shared file from a biom file

Bug fixes

  • phylotype - the numOtus in the list file was one to high. OTUs were clustered correctly, the count was just off.
  • phylotype - only clustering at leaf nodes, level 1.
  • metastats - OTU numbers in metastats now correspond to the column names in the shared file
  • classify.seqs segfault if no files are given. Should return error message instead (
  • rarefaction.single - groupnames that include “_” causes parsing error in the creation of the groups.rarefaction file. Fixed, workaround until release, groupmode=false.
  • filter.seqs - when run with “current”, it generated “.filter” and not “filename.filter” file.
  • sffinfo - if the sff file doesn’t end in “.sff” then the output files all end in “flow”, for example, instead of “.flow”
  • trim.seqs - windows version crash (
  • trim.seqs - fixed bug that caused seqs to go to scrap if no oligos file was given.
  • shhh.flows - outputdir didn’t put all of the files to the output directory
  • pairwise.seqs - checks for positive values for gap open, gap extend, or mismatch.
  • corr.axes - fixed OTU labels (
  • mothur can handle leading spaces in command names (

Wiki updates

  • no longer building 32 bit Mac binaries.

Registered users