Hey mothur users,
We’re happy to announce the long awaited v.1.37.0! There are some pretty sweet features in the new release that I’d like to highlight for you. _First_, for the mac and unix users, we’ve added two methods to [cluster](http://www.mothur.org/wiki/cluster) and [cluster.split](http://www.mothur.org/wiki/cluster.split) to allow you to use abundance and distance-based greedy clustering using the free and open source VSEARCH program. This release was a bit delayed because we’ve been trying to get the windows version to work, but haven’t gotten as far as we’d like. The next release should include it. I would point out that if you are doing 16S rRNA gene sequencing you want to stick with the defaults - this is mostly for those doing ITS. You can see two of our recent papers published in [PeerJ](https://peerj.com/articles/1487/) and [mSystems](http://biorxiv.org/content/biorxiv/early/2016/03/26/042812.full.pdf) for more discussion of this. _Second_, we’ve added a [make.file](http://www.mothur.org/wiki/make.file) command that will allow you to generate a files file for use in make.contigs. This command should significantly simplify the process of generating the file. _Third_, we've created a [biom.info](http://www.mothur.org/wiki/Biom.info) command that will convert a biom formatted file to mothur-formatted shared and assorted taxonomy files. There have also been a number of other new features and bug fixes that you should check out on the [release page](https://github.com/mothur/mothur/releases/tag/v1.37.0).
In addition to improvements to mothur, since the last release we've also published several papers and blog posts that you should definitely check out.
_Blog:_
- [mothur and QIIME](http://blog.mothur.org/2016/01/12/mothur-and-qiime/)
- [No, greengenes' reference alignment hasn't improved](http://blog.mothur.org/2015/08/04/No-greengenes-hasnt-improved/)
- [README for SILVA v123 reference files](http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/)
- [Suck until you don't](http://blog.mothur.org/2016/01/04/Suck-until-you-dont/)
_Papers:_
- [Application of database-independent approach to assess the quality of OTU picking methods](http://biorxiv.org/content/biorxiv/early/2016/03/26/042812.full.pdf)
- [De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units](De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units)
- [Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system](https://peerj.com/articles/1869/)
That's all until next time, enjoy! As always, feel free to let us know what you think or if there are additional features you'd like to see in mothur...
New Commands
- [biom.info](http://www.mothur.org/wiki/Biom.info) - reads biom file and creates shared, taxonomy, constaxonomy and tax.summary files. 82
Feature Updates
- Adds agc and dgc methods to the [cluster.split](http://www.mothur.org/wiki/cluster.split) and [cluster](http://www.mothur.org/wiki/cluster) commands from the vsearch software package. Not available for Windows. 169
- [merge.groups](http://www.mothur.org/wiki/Merge.groups) - adds count option. http://www.mothur.org/forum/viewtopic.php?f=5&t=3698 88. Adds method and fasta parameter. Method options are sum, average and median. Default=sum. 105
- [get.groups](http://www.mothur.org/wiki/Get.groups) / [remove.groups](http://www.mothur.org/wiki/Remove.groups) - adds phylip and column options. 79
- [get.seqs](http://www.mothur.org/wiki/Get.seqs) / [remove.seqs](http://www.mothur.org/wiki/Remove.seqs) - Checks for repeat sequences names and eliminates them. Allows users creating their own templates to easily remove duplicate sequences from their reference files. 159
- Remove MPI source code - MPI version is slower than non-MPI version. No advantage to using it. 144
- [unique.seqs](http://www.mothur.org/wiki/Unique.seqs) - adds format parameter. Options are name and count. 125
- Simplify makefile 157
- [make.file](http://www.mothur.org/wiki/Make.file) - adds numcols parameter. Options 2 or 3. Default=3, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first '_' or if no '_' is found then the root of the forwardFastq filename. 162
- Output number of warning and errors detected.
- [rename.seqs](http://www.mothur.org/wiki/Rename.seqs) - adds file, map, qfile and contigsreport parameters. The map file allows you to revert sequence names back to original. Works with make.contigs to automatically rename sequences. 132
- [make.contigs](http://www.mothur.org/wiki/Make.contigs) - adds rename parameter, default=t. Renames sequences to reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream. Uses the [rename.seqs](http://www.mothur.org/wiki/Rename.seqs) command to rename which creates a map file so you can revert to original names at any time. 132
- [classify.seqs](http://www.mothur.org/wiki/Classify.seqs) - Changes cutoff parameter default to 80. This change in the bootstrap threshold reflects the default values in the 454 and MiSeq SOPs. 192
- [get.current](http://www.mothur.org/wiki/get.current) - Adds current RAM usage and total RAM available.
- Replaces '-' characters in sequences names with '_' characters to avoid downstream issues. 205
- Changes default on minlength to 10 for the [screen.seqs](http://www.mothur.org/wiki/Screen.seqs) command. 160
- Removed load.logfile command. Added output file to [get.current](http://www.mothur.org/wiki/get.current) and input/output file to [set.current](http://www.mothur.org/wiki/set.current) . These changes allow the commands to work together to keep track of current files between instances of mothur in a more direct and easy to edit manner. You can input the output file of the get.current command into the set.current command using the new current parameter.
- Adds includescrap parameter to the [make.sra](http://www.mothur.org/wiki/Make.sra) command. Default=True. http://www.mothur.org/forum/viewtopic.php?f=3&t=3750&p=11122p11122
- [get.otulabels](http://www.mothur.org/wiki/get.otulabels) removed. Functions added to [get.otus](http://www.mothur.org/wiki/get.otus) command.
- [remove.otulabels](http://www.mothur.org/wiki/remove.otulabels) removed. Functions added to [remove.otus](http://www.mothur.org/wiki/get.otus) command.
- Adds output and printlevel parameters to [classify.seqs](http://www.mothur.org/wiki/classify.seqs), [classify.otu](http://www.mothur.org/wiki/classify.otu), [biom.info](http://www.mothur.org/wiki/biom.info) and [summary.tax](http://www.mothur.org/wiki/summary.tax) commands. Output options simple and detail. Default=detail. 204 158
- Adds relabund parameter to [classify.otu](http://www.mothur.org/wiki/classify.otu) command. 101
- Adds threshold parameter to [summary.tax](http://www.mothur.org/wiki/summary.tax) command. 31
- Adds parent taxons to unclassified taxons for outputs of [classify.seqs](http://www.mothur.org/wiki/classify.seqs), [classify.otu](http://www.mothur.org/wiki/classify.otu), [biom.info](http://www.mothur.org/wiki/biom.info) commands. http://www.mothur.org/forum/viewtopic.php?f=3&t=3183&p=9003p9003 29
- Adds count parameter to [get.sharedseqs](http://www.mothur.org/wiki/get.sharedseqs) 133
Bug Fixes
- [filter.shared](http://www.mothur.org/wiki/Filter.shared) - modifies rareOtus label to prevent mothurConvert error. 137
- [make.contigs](http://www.mothur.org/wiki/Make.contigs) - File mismatch error with certain sequence name formats and multiple processors. Three column format gz file not producing group file.
- Fixes mothurConvert error if "seed" was part of filename.
- Removes OS limit on open files for cluster.split 142
- [make.sra](http://www.mothur.org/wiki/Make.sra) - Fastq.info error about no inputs selected when running make.sra with single fastq file and oligos file.
- [cluster.split](http://www.mothur.org/wiki/Cluster.split) - removes limit on number of files that can be split by cluster.split. Limit caused "[ERROR]: Cannot open yourFasta.xxx.temp" file error.
- "Illegal Instruction" error on Linux machines. Fixed in 1.29.16 release. 179
- Updates Xcode project file to fix collaboration issues.
- Fixes [filter.seqs](http://www.mothur.org/wiki/filter.seqs) issue where sequences are not the same length by setting default minlength to 10 in the [screen.seqs](http://www.mothur.org/wiki/Screen.seqs) command. 160
- Windows version - if files were used with less sequences than processors specified then empty file error. 195
- Fixes [make.contigs](http://www.mothur.org/wiki/make.contigs) name mismatch bug and gives a slight speed boost. 167
- Fixes [lefse](http://www.mothur.org/wiki/Lefse) "Skipping x iter..." warning.
Registered Users
3663