Mothur-py

Feature Updates
* Adds contigsreport to current files saved by mothur. 291
* Improves randomization functions
* Sets method driven cutoffs in cluster commands. For methods opti, agc and dgc (cutoff=0.03) which will create OTU for distance 0.03. For methods average, nearest, furthest and weighted (cutoff=0.15) which may be adjusted down due to the sparse matrix, [Why does the cutoff change?](https://mothur.org/wiki/Frequently_asked_questionsWhy_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F)

Bug Fixes
* Fixes [make.lefse](https://mothur.org/wiki/Make.lefse) output. 314
* Fixes [make.file](https://mothur.org/wiki/Make.file) segfault. 316
* Fixes "couldn't find OTUID" [make.biom](https://mothur.org/wiki/Make.biom) error.
* Fixes Windows subsampling issue. 317

Binaries
* Mac Version requires OSX 10.12 or higher
* Windows 10 or higher
* All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64_static.zip contains a statically linked copy of mothur. The Mothur.linux_64.zip contains a dynamically linked copy of mothur. The Mothur.linux_64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

Feature Updates
- Updates mothur to use seeded mersenne_twister_engine to randomize. This improves random distribution and resolves the Windows subsampling discrepancies. 311

Binaries
- Mac Version requires OSX 10.12 or higher
- Windows 10 or higher
- Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.


v.1.39.3
Feature Updates
- Adds contigsreport to current files saved by mothur. 291

Bug Fixes
- Fixes bug with shortcut files in [classify.seqs](http://www.mothur.org/wiki/classify.seqs) command. 307

Binaries
- Mac Version requires OSX 10.12 or higher
- Windows 10 or higher
- Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

Feature Updates:
- Adds file mismatch check to [summary.seqs](http://www.mothur.org/wiki/summary.seqs)

Bug Fixes:
- [chimera.vsearch](http://www.mothur.org/wiki/chimera.vsearch) removing last character of sequence names when processing with a reference. Not an issue with denovo method. 306
- Fixes [summary.tax](http://www.mothur.org/wiki/summary.tax) summary file printing issue.
- Fixes bug on start "[ERROR]: basic_string::substr: __pos (which is 18446744073709551615) > this->size()..."
- Fixes bug with the [rename.file](http://www.mothur.org/wiki/rename.file) command that occurs if outputdir is used and multiple files are provided.
- Fixes ls bug for Windows users in [make.file](http://www.mothur.org/wiki/make.file) command.

Binaries
- Mac Version requires OSX 10.12 or higher
- Windows 10 or higher
- Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

Feature Updates:
- Adds runsensspec parameter to [cluster.split](http://www.mothur.org/wiki/cluster.split). Default=T.

Bug Fixes:
- [pre.cluster](http://www.mothur.org/wiki/pre.cluster) (without groups) not clustering properly. 301
- [make.contigs](http://www.mothur.org/wiki/make.contigs) fixes "off by one" name mismatch error. 303
- [rename.file](http://www.mothur.org/wiki/rename.file) unable to automatically rename with output directory specified.
- [cluster](http://www.mothur.org/wiki/cluster) and [cluster.split](http://www.mothur.org/wiki/cluster.split) improper printing of list file when using name file option. Does not effect printing of the list file when clustered with count file.
- [cluster](http://www.mothur.org/wiki/cluster) and [cluster.split](http://www.mothur.org/wiki/cluster.split) improper printing of list file when using phylip file option. Does not effect printing of the list file when clustered with column file.
- Incorrect taxlevel printed in *.tax.summary file.

Binaries
- Mac Version requires OSX 10.12 or higher
- Windows 10 or higher

New Commands

Feature Updates
- Changes default clustering method to opti.
- Adds agc and dgc vsearch clustering methods for Windows users. 215
- Adds [chimera.vsearch](http://www.mothur.org/wiki/chimera.vsearch) command for Windows users. 215
- Major speed improvement for [pre.cluster](http://www.mothur.org/wiki/pre.cluster) command with aligned files. 220
- Major memory requirement reduction for [pre.cluster](http://www.mothur.org/wiki/pre.cluster) command with by group option. 220
- Adds constaxonomy file to current files saved by mothur.
- Control-C handling: In script or batch mode exit mothur. In interactive mode exit command. 212 http://www.mothur.org/forum/viewtopic.php?f=5&t=4102&p=12431p12431
- Adds blastdir parameter to [set.dir](http://www.mothur.org/wiki/set.dir) command. 223
- Taxonomy files can now contain spaces in the taxon names. 265
- Makes refasta and repnames parameters optional for [create.database](http://www.mothur.org/wiki/create.database) command. 32
- Removes cutoff adjust in [dist.seqs](http://www.mothur.org/wiki/dist.seqs) command. 274
- Adds trim parameter to [make.sra](http://www.mothur.org/wiki/make.sra) command for use with sff files.

Bug Fixes
- Fixes Windows multiple processors with groups crash - [chimera.uchime](http://www.mothur.org/wiki/chimera.uchime) command.
- Fixes Windows bug with [make.file](http://www.mothur.org/wiki/make.file) command. 255
- Creates unique group names for 3 column format [make.file](http://www.mothur.org/wiki/make.file) command. 270
- Fixes bug with number of "taxon"_unclassifeds appended to taxonomy in [classify.seqs](http://www.mothur.org/wiki/classify.seqs).
- Eliminates zero abundance OTUs created by some floating point biom files converted to shared files [make.shared](http://www.mothur.org/wiki/make.shared).
- Floating point exception in [sparcc](http://www.mothur.org/wiki/sparcc) command.
- Fixes bug where mothur was not finding matches for sequence names "off by one character" in the name. [make.contigs](http://www.mothur.org/wiki/make.contigs)
- Fixes bug with "find" command for Linux user in [make.file](http://www.mothur.org/wiki/make.file)
- Fixes bug with optimize parameter using alignreport file in [screen.seqs](http://www.mothur.org/wiki/screen.seqs) command. 288

Download

Registered Users

Binaries
- Mac Version requires OSX 10.12 or higher

New Commands
- [merge.count](http://www.mothur.org/wiki/merge.count) command combines count files. 259

Feature Updates
- Removes hard parameter from [cluster](http://www.mothur.org/wiki/cluster), [cluster.classic](http://www.mothur.org/wiki/cluster.classic) and [cluster.split](http://www.mothur.org/wiki/cluster.split) commands. All commands now use hard=T.
- Improved [help](http://www.mothur.org/wiki/help) command. 257
- [Make.file](http://www.mothur.org/wiki/make.file) command is more flexible with filenames. 243
- Adds prefix parameter to [Make.file](http://www.mothur.org/wiki/make.file) command. 251
- Changes bad character in group names error to warning. Modifies group names with '-' characters in output filenames to avoid downstream issues.

Bug Fixes
- Fixes bug with output directory in [make.group](http://www.mothur.org/wiki/make.group) command.
- Fixes filename expansion issue [make.contigs](http://www.mothur.org/wiki/make.contigs). http://www.mothur.org/forum/viewtopic.php?f=3&t=5869&p=14857p14857
- Fixes group name issue with oligos file option in [get.mimarkspackage](http://www.mothur.org/wiki/get.mimarkspackage) command.

Download

Registered Users

Binaries
- Mac Version requires OSX 10.11 or higher