Version 1.48.1

Enhancements:

• Adds fasta type to make.file. This allows you to generate a count or group file for a set of fasta files. For example: make.file(inputdir=./, type=fasta). Mothur will create a 2 or 3 column file file. If there are paired fasta files, a 3 column file file will be generated. group forwardFastaFileName reverseFastaFileName If there are single fasta files, a 2 column file file will be generated. group fastaFileName
• Adds file option to make.count. The file used as input here must the 2 or 3 column fasta file file created by the make.file command with fasta as the input type. (described above) Using a fastq file file will result in a read error as make.count is only designed to be used with fasta files.
• Adds constaxonomy and contigsreport files to set.current

Bug Fixes:

• Restores ability to escape '-' characters in parameters.
• Fixes segfault with pcr.seqs when all seqs are bad and keepdots=f
• Fixes bug with get.oturep if invalid cutoff given
• Fixes bug with count file compress flag
• Fixes bug in fastq.info when using checkorient with barcodes. The barcodes were ignored.
• Fixes bug in sequence class that flagged 'U' as ambiguous.

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher
Windows 10 or higher
Centos 7
RHEL 8 or greater / Ubuntu 20.
Binaries include:

Mac version - includes boost, readline, gsl, hdf5
Windows - includes boost
Ubuntu - includes boost
Linux - includes boost, readline, hdf5, gsl
NOTE: Mothur's external tools (vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

Boost 1.75.0
GSL 2.6
HDF5 1.12.0

Version 1.48.0

Enhancements:

• Adds translate.seqs command. #789
• Adds make.count command to assign groups to fasta files.
• Adds format parameter to make.group command.
• Updates fastq.info, trim.seqs, trim.flows to output count file by default.
• Significant speed improvements to commands that split by sample. ie, pre.cluster, chimera commands
• Significant speed Improvements to unifrac.weighted.
• Adds group name check to update sample names with illegal characters.
• Adds flow file to get.groups
• General speed improvement with sequence commands.

Bug Fixes:

• Fixes bug with chimera.vsearch with no groups and denovo
• Fixes bug with clearcut sequence name copy
• Fixes bug with make.contigs screening parameters if maxlength not set
• Fixes bug with split.groups flow file option with count table
• Fixes bug with sets parameter not passing to pairwise lefse calc
• Fixes bug with make.sra single-end reads

Version 1.47.0

Hello mothur users!

We are happy to announce the release of mothur v.1.47.0. There are a few significant thigns to report with this release...

First, we are happy to announce that this release is the first announced version of a mothur-based approach to open and closed reference clustering that doesn't suffer from the same problems found with other algorithms. This can be achieved using the cluster.fit function. You can read more about it in a paper we recently had accepted in mSphere. A preprint version of the paper can be found here while we wait for the official publication.

Second, over the past few months we’ve incorporated a number of significant improvements to mothur to make it easier to work with by consolidating commands. For example, we have included the ability to use screen.seqs arguments within make.contigs. This means that you can now do "make.contigs(file=stability.files, maxambig=0, maxlength=275, maxhomop=8)" as a single command rather than two commands. We are also trying to phase out the names and groups files  in place of a count file since they add confusion and extra steps. Another notable change is that, by default, the chimera commands will remove the sequences from the fasta file so that you no longer need to use the subsequent remove.seqs command. 

Third, if you've been to one of my workshops you know that the hardest step can often be getting to the correct place using the command prompt. Now, if you double click on the mothur executable it should start mothur in the directory where the executable was found. We are calling this the 'mothurhome' argument
Fourth, we found a small bug in pcr.seqs that inadvertently removed the first base from the outputted sequences. You may notice a one-base difference in the start/end coordinate positions between versions.

Finally, I continue to put a lot of effort into developing educational content that should be of interest to mothur users. I am posting two videos each week to YouTube that often uses mothur-based files as input to work within R. You can find these at the Riffomonas YouTube channel. If you are interested in upcoming R and mothur workshops be sure to check out the schedule for virtual workshops; I'll be teaching an R workshop in a couple of weeks! If you're looking for more updates on Riffomonas and resources for strengthening your R skills, I have a free weekly newsletter that you can subscribe to. I've been encouraged by the positive feedback I've received from the content on Riffomonas - let me know if there's anything you'd like me to be sure to cover.

Enhancements:

• Updated SOP to reflect change brought with this version of mothur
• Adds cluster.fit command. OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs #415
• make.contigs now outputs count file instead of group file. #793
• Adds maxambig, maxhomop, maxlength parameters to make.contigs. #793
• Sets default output for unique.seqs to count file.
• Adds removechimeras parameter to chimera commands to auto remove chimeras from files. Default=t. #795
• Adds auto name fix for sample names that include special characters like '-'.
• MOTHUR_FILES can now contain multiple paths separated by ';' #799
• Updates MOTHUR_TOOLS to allow for multiple locations separated by ';' #799
• Allows for multiple input directories separated by ';' #799
• Adds 'mothurhome' keyword #800
• Adds qfile to list.seqs #802
• Adds ability to input multiple files to list.seqs, remove.seqs and get.seqs to help resolve file mismatches. #803
• Adds ability to read *.gz fastq files in list.seqs. #804
• Adds fastq and format parameters to chop.seqs #790
• Removes BLAST from mothur. #801
• Removes search and blastlocation parameters from chimera.slayer. #801
• Removes blastlocation parameter from set.dir. #801
• Forces lefse pairwise comparisons.

Bug Fixes:

• Fixes crash with split.groups when running with fasta and group files without a names file. Effects allfiles options in other commands.
• Fixes bug with pcr.seqs If keepdots=f, and start and end are used, then first base was removed by mistake.
• Fixes bug with get.sharedseqs if no groups are provided.
• Fixes bug with remove.groups phylip file option.
• Fixes formatting issue with chimera.vsearch with a reference
• Fixes bug in sens.spec when name file is used
• Fixes crash with sort.seqs if multiple seqs present with the same name
• Fixed segfault caused by logger.

Amazon Machine Image:

• 1.47.0_ID = ami-097205064a488a028

Version 1.46.1

Bug Fixes:

• Fixes crash with split.groups when running with fasta and group files without a names file. Effects allfiles options in other commands.
• Fixes pcr.seqs crash when run without oligos file.

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher
Windows 10 or higher
Centos 7
RHEL 8 or greater / Ubuntu 20.
Binaries include:

Mac version - includes boost, readline, gsl, hdf5
Windows - includes boost
Ubuntu - includes boost
Linux - includes boost, readline, hdf5, gsl
NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.
External library requirements (if building from source):

Boost 1.75.0
GSL 2.6
HDF5 1.12.0

Version 1.46.0

Enhancements:

• Reduces time to run pairwise.seqs by up to 99% using kmer distances. #763
• Adds ability to cluster unaligned sequences in cluster.split. #763
• Reduces time of cluster.split through improvements in the splitting process. #778
• Removes split by distance option from cluster.split.
• Adds jtt, pmb, pam and kimura calculators to dist.seqs to find distances between protein sequences. #776
• Adds pairwise parameter to lefse command. #781
• Adds checkorient parameter to pcr.seqs. Change Includes functions to reorient and reverse unpaired primers. #768
• Rework of rename.seqs file option. #772
• Simplifies system command. #782
• Adds ASV to OTU mapping for otu.hierarchy command. #777
• Adds check to shared file read for incorrect numOtus column. This error can occur if the shared file is modified outside of mothur.
• Adds warning in remove.seqs for dereplicate. See http://mothur.org/wiki/chimera_dereplicate_example/ for detailed explanation.

Bug Fixes:

• Fixes uchime command construction. (v.1.45.2)
• Fixes bug with sra.info threads option. (v.1.45.3)
• Fixes bug with OTU priority printing with file option in cluster.split
• Fixes segfault in metasats if abundance of one treatment is 0
• Fixes bug with get.sharedseqs shared file option
• Removes duplicate column headers for align.report #785
• Adds error message for missing headers in design file. Prevents addition of dummy group or removal of valid group. #779

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher
Windows 10 or higher
Centos 7
RHEL 8 or greater / Ubuntu 20.
Binaries include:

Mac version - includes boost, readline, gsl, hdf5
Windows - includes boost
Ubuntu - includes boost
Linux - includes boost, readline, hdf5, gsl
NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.
External library requirements (if building from source):

Boost 1.75.0
GSL 2.6
HDF5 1.12.0

Version 1.45.3

Fixes bug with sra.info threads option.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost
• Linux - includes boost, readline, hdf5, gsl
  NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

Version 1.45.2

Bug Fixes:

• Fixes uchime command construction.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl
  NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

Version 1.45.1

Bug Fixes:

• Fixes bug with assembly of command string for chimera.uchime and chimera.vsearch. #771

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl
  NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

Version 1.45.0

Enhancements:

• Adds shared file conversion to make.shared #716
• Updates uchime makefile and adds uchime build to mothur #711
• Adds clump parameter to pre.cluster #749
• Rework of rename.seqs for added flexibility
• Removes requirement for inputdir to be writable #747
• Adds multiple processors for chimera.vsearch when using reference instead of denovo. #757
• Adds functions to read and write HDF5 biom files. #752
• Adds RELEASE_DATE to makefiles. #761
• Removes "paired" tag from make.file.
• Adds ability to run batch files from interactive mode.
• Rebuilds uchime for Catalina.
• Removes clear screen command from mothur's initial startup. #748
• Updates vsearch to 2.16.0. https://github.com/torognes/vsearch/releases/tag/v2.16.0

Bugs:

• Fixes bug with split.abund when run with names file. #715
• Fixes bug with sff.info parsing with oligos. Effects make.sra command as well because make.sra calls sff.info with an oligos file. #726 #727
• Fixes bug with chimera.uchime assembly of accnos file.
• Fixes trim.flows empty *flow.files issue.
• rarefaction.shared groups output bug. #729
• indicator command pvalues off. #729
• Fixes bug with qfile option in make.contigs. #745
• Fixes bug with pre.cluster's unoise method.
• Fixes Windows mkDir bug. Use boost filesystems if available. #754
• Fixes bug with make.contigs not making group file for *.gz files with oligos file. #753
• Fixes bug where inputdir is attached to the floworder parameter.
• Fixes lefse screen output.
• Fixes bug with trim.seqs that required name or count file.
• Fixes make.contigs segfault.
• Fixes bug with oligos file trimming when several barcodes match same read.
• Fixes bug with align.seqs segfault.
• Fixes bug with remove.lineage and get.lineage not handling taxon definitions with multiple levels.
• Fixes bug with spaces in path.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl
  NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

Version 1.44.3

Bugs:

• Fixes bug with trim.seqs that required name or count file.
• Fixes make.contigs segfault.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5
  NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.