Hey mothur users,
We’re happy to announce the release of v.1.38.0! This release primarily has a bunch of random bug fixes that we were anxious to get out to you. Two new commands should strike your interest. First, we have introduced [rename.file](http://www.mothur.org/wiki/rename.file), which renames files so that you don't have to worry about using your system commands and updates the "current" files. Second, building off the introduction of VSEARCH functionality in the last release, we've created [chimera.vsearch](http://www.mothur.org/wiki/chimera.vsearch) to detect chimeras using VSEARCH. Their benchmarking indicates that it performs similar to UCHIME, which is available as [chimera.uchime](http://www.mothur.org/wiki/chimera.uchime).
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:_
- [The mothur AMI for work on Amazon's Web Server](http://blog.mothur.org/2016/07/12/mothur-AMI/)
- [How to customize your reference alignment for non-V4 data](http://blog.mothur.org/2016/07/07/Customization-for-your-region/)
_New Commands_
- [rename.file](http://www.mothur.org/wiki/rename.file) - renames file and updates current files saved by mothur.
- [chimera.vsearch](http://www.mothur.org/wiki/chimera.vsearch) - detects chimeras using vsearch software package. 239
_Feature Updates_
- Removes [hcluster](http://www.mothur.org/wiki/Hcluster) command. It is really really slow and we don't recommend it. 208
- Removes save option which kept references in memory. 208
- Removes [clear.memory](http://www.mothur.org/wiki/clear.memory) command which worked with the save option. 208
- Removes [pds.pipeline](http://www.mothur.org/wiki/pds.pipeline) command. 208
- Command line mode returns exit-code to indicate failure. 151
- Removes reftaxonomy parameter from [classify.otu](http://www.mothur.org/wiki/classify.otu) and [summary.tax](http://www.mothur.org/wiki/summary.tax). 241
- Removes large parameter from [count.seqs](http://www.mothur.org/wiki/count.seqs) command. 203
- Allows [make.biom](http://www.mothur.org/wiki/make.biom) with picrust option to handle mothur's new parentTaxon_unclassified format. 241
- Adds mothur's location as a default file location to check. Reduces unable to open file errors. 231
- Adds count parameter to [sens.spec](http://www.mothur.org/wiki/sens.spec) command. 225
- Clarifies [seq.error](http://www.mothur.org/wiki/seq.error) command output. 175
- Adds sets parameter to [lefse](http://www.mothur.org/wiki/lefse) command. 234
- Removes indexFile requirement for using NONE option in oligos file. [make.contigs](http://www.mothur.org/wiki/make.contigs). 193
- [make.contigs](http://www.mothur.org/wiki/make.contigs) command will skip blank file pairs. 233
- Warn about illegal characters in group names to prevent downstream analysis issues. 37
- Adds rdiffs to [pcr.seqs](http://www.mothur.org/wiki/pcr.seqs) command to allow for setting different diffs for the forward and reverse primers. 244
_Bug Fixes_
- Mothur can handle whitespace in command lines. 191
- Fixes gradient bar on [heatmap.sim](http://www.mothur.org/wiki/heatmap.sim) command. 237
- Fixes bug with [classify.otu](http://www.mothur.org/wiki/classify.otu) persample option.
- Fixes bug with agc method in [cluster](http://www.mothur.org/wiki/cluster) and [cluster.split](http://www.mothur.org/wiki/cluster.split)
- Fixes bug with [summary.tax](http://www.mothur.org/wiki/summary.tax) command not including name file counts in *tax.summary.
- Fixes RAM output for linux [get.current](http://www.mothur.org/wiki/get.current). 232
- Error generated when filenames are too long for uchime program. 226
- Fixes cutoff adjust for agc and dgc clustering methods. 254
Binaries
- Mac Version requires OSX 10.11 or higher