We are happy to announce the release of Mothur v.1.15.0 in honor of Bret Favre finally ending his consecutive game streak (and hopefully his career). Although impressive, he really should have hung up the shoulder pads back when we were postdocs. Regardless, mothur isn’t going anywhere.
Our latest release includes a number of exciting new commands to help with data processing and analysis. First, a number of people have asked for the “classic” form of the clustering algorithms that was originally implemented in DOTUR; this has been implemented as the cluster.classic command. Second, we have also created the Catchall command that wraps John Bunge’s CatchAll program for using parametric models to estimate community richness. Third, methods for performing indicator analyses have been on our radar for awhile and we are happy to finally add indicator to the stable of mothur commands. Fourth, to complement the normalize.shared command we have added the sub.sample command, which randomly selects a subsample of sequences from each group so they all have the same number of sequences. Fifth, at the suggestion of some users, we have created the consensus.seqs command to generate a consensus sequence for a list of sequences, OTUs or phylotypes. Finally, several utility commands such as remove.groups, get.groups, get.otus, remove.otus have been added to make data processing added. As always, we have also added a number of smaller features to existing commands and cured a few bugs. These are generally all suggested by users and we appreciate your continued support and feedback. We are always curious to hear how people are using the software and what we can do to make input and output more useful. Our goal is to help you take raw data and get it into a format that you can use to do science. If we aren’t doing that for you, let us know!
Once again, Pat is thinking about hosting one or two workshops this Spring in the Detroit/Ann Arbor area with a slightly different format. They would start on a Thursday evening and then go full days on Friday and Saturday. If you are interested, please let us know and suggest some weekends that would work best for you.
Be sure to pad your CV as much as possible with papers that cite mothur between now and the end of 2010 and get ready for an exciting 2011. Keep the six packs coming
- cluster.classic - clustering method from dotur
- Catchall command - wrapper for the catchall program
- indicator command - identify indicator “species” for nodes on a tree
- consensus.seqs command - finds a consensus sequence for each OTU or phylotype
- sub.sample - create a file containing a sub-sampling of sequences
- remove.groups / get.groups - get or remove sequences from a specific group or set of groups
- get.otus / remove.otus - get or remove otus containing sequences from a specified group or set of groups.
- cluster and hcluster - added weighted method
- get.seqs and remove.seqs - added qfile parameter
- make.group - added output parameter
- unifrac.unweighted and unifrac.weighted - modified the inputs for the distance parameter
- get.lineage and remove.lineage - change default for dups parameter in to true if a name file is given
- trim.seqs - added group parameter
- added strip command to mothur’s makefile to reduce the size of the executable
- parsimony - added processors option for parallelization
- get.oturep - added weighted parameter
- sffinfo - added XY coordinates and run time timestamps to the output.
- unifrac.weighted - bug introduced in version 1.14.0.
- classify.seqs - bug where summary file not printing last level’s summary info has been fixed