This is an exciting day... we are happy to announce the release of mothur v.1.29.0 and the beta version of mothur v.2.0. The difference? The beta is our first public release of the GUI version of mothur that we have been developing off and on for almost two years now. You can play around with the GUI Tutorial and send feedback to mothur.bugs\@gmail.com. It is built upon the command line version, which we continue to develop and support. Please send us your feedback regarding the GUI implementation and any problems and desires you might like to see in the future for the GUI. One of the cool features of the GUI is the ability to create batch scripts that you can then either run directly from within the GUI or via the command line interface.
As for the v.1.29, we have a number of useful feature developments. First, we’ve developed filter.shared, which removes columns of OTUs based on frequency and abundance parameters. If there are other parameters you can think of, let us know. Second, although it’s been in mothur for awhile, we are publicly releasing the ability to subsample alpha and beta diversity metrics to a common number of sequences per sample. We added these parameters to the Schloss SOP with the last release. Finally, there are a number of other features and bug fixes that our loyal users have suggested via the forum - thanks for your suggestions!
Looking ahead, with the next release we should have a vetted SOP for analyzing Illumina data. Preliminary indications are that we get comparable sequence length to 454 that is just as good (or better) but a lot more reads. We’re also working with various people to generate similar SOPs for the new 454 flow structure and IonTorrent data. Sorry all of this has taken us so long.
We’re excited for 2013 and the future of mothur. Please let us know if there’s anything missing or if there’s something you think others would benefit from having in mothur!
- filter.shared - remove OTUs based on various criteria
- classify.otu - added persample option, which finds the consensus taxonomy for each sample in each otu.
- cluster.split - added cluster option (default=t). If false, mothur will split the matrix but not cluster.
- indicator - added groups to the output of the indicator values. - https://forum.mothur.org/viewtopic.php?f=3&t=1675
- summary.single, summary.shared, rarefaction.shared, dist.shared, tree.shared, unifrac.weighted, unifrac.unweighted - added subsample option
- make.fastq - added format parameter.
- venn - added sharedotus parameter (default = T). When sharedotus=t, mothur will output the otu labels of the shared species for sharedsobs.
- trim.seqs && trim.flows - you can set a barcode or primer name to “ignore”, and mothur will disregard sequences that belong to that group.
- chimera.slayer and chimera.perseus - added dereplicate parameter to
- parse.list - added count parameter
- sens.spec - increased speed and reduced memory needed to run
- chimera.uchime - added strand parameter to - https://forum.mothur.org/viewtopic.php?f=3&t=1882&p=5255#p5255
- classify.otu - if basis=sequence and count file is used, redundant sequences were not added to .tax.summary file counts.
- https://forum.mothur.org/viewtopic.php?f=3&t=1656 - ignore N’s
- classify.seqs - if input directory was given with a group file, path was incorrect.
- if tree file had random Windows newlines, mothur could not read sequence names properly.
- tree.shared - if shared file was not in alphabetical order. All shared files created by make.shared after 6/10 are sorted.
Changes to wiki
- gui tutorial and related links