Version 1.44.2

Enhancements:

• Adds shared file conversion to make.shared #716
• Updates uchime makefile and adds uchime build to mothur #711

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 trim.flows empty *flow.files issue.
• Fixes rarefaction.shared groups output bug. #729
• Fixes indicator command pvalues. #729
• Removes "paired" tag from make.file command.
• Fixes bug with oligos file trimming when several barcodes match same read.
• Fixes bug with align.seqs 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.

Version 1.44.1

Enhancements:

• Adds ability to run batch files from interactive mode.

Bugs:

• Fixes segfault crash.
• Fixes bug with remove.lineage and get.lineage not handling taxon definitions with multiple levels.
• Fixes bug with spaces in path.
• Rebuilds uchime for Catalina.

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.

Version 1.44.0

Enhancements:

• Adds sra.info command to download and extract samples from NCBI using prefetch and fasterq-dump written by NCBI. #27
• Adds make.clr command. #695
• Adds clr file type to metastats command. #695
• Expands batch files. #601 #658
• Adds environment variables to mothur. #601
• Adds MOTHUR_TOOLS option to allow you to set the location of mothur's external tools at compile time or through the set.dir command at run time. #682
• Adds uchime parameter to chimera.uchime. #682
• Adds vsearch parameter to chimera.vsearch, cluster, cluster.split commands. #682
• Improves mothur's checkorient option in make.contigs. Also sets checkorient=t by default.
• split.abund command 's cutoff parameter can now be a percentage. Removes fasta file requirement. #263
• Adds contigsreport to get.seqs and remove.seqs commands. #660
• Adds processors option to split.groups. #685
• Adds sets to remove.groups and get.groups commands. #277
• Adds parallelization to chimera.vsearch when using denovo method. #700
• Changes filter.seqs fasta file delimantor from '-' to '|' to allow for '-''s in filenames.
• Adds list file output for make.shared with count table.

Bugs:

• Fixes tree.shared distance being used instead of similarity.
• Fixes bug with remove.seqs not removing empty groups from the count table. #675
• Fixes bug with trim.seqs if no name file is given and allfiles=T. #696
• Fixes corr.axes bug when metadata files contain zeroed columns.

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.

Version 1.43.0

• Adds list to split.groups #624
• Adds estimator.single command. #164
• Passes CXX variables to uchime makefile. #614
• Modifies output files from dist.shared, summary.single and summary.shared. You may run with or without rareification, but not both. #607
• Improves speed and resource management for align.seqs command. #647
• Improves mothur's logging features.
• Adds qfile option to make.contigs. #650
• Adds auto decompress feature to make.contigs if gz read fails. #634
• Improves speed of dist.seqs and pairwise.seqs. #653
• Adds 2 column pacbio file option to fastq.info. #649
• Windows users can now run make.contigs with *.gz files.

Bugs:

• Removes empty groups before printing count table. #641
• Changes datatype for opti method to correct overflow.
• Makes current file class thread safe. Caused random crashes in pre.cluster. #643
• get.oturep command wasn't handling multiple labels. Removed labels parameter and modifies cutoff to act like cluster commands. ie. cutoff=0.01-0.03. Also failing with abundance method using count file without group information #656 #575
• Trim.seqs was not removing paired primers. #667
• get/remove.lineage not producing a accnos file.

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 and uchime) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

Version 1.42.3

• BUG FIX: Issues with count files

Version 1.42.2

• Fixes bug in count table removeGroups functions #626
• Fixes definitions #633

Version 1.42.1

• Updates vsearch version to resolve Windows output format bug.
• Improves removeOTU functions to increase processing speed.

Version 1.42.0

Enhancements:

• Sets random seed to 19760620 at start of mothur. #600
• Adds constaxonomy file to list.otus command. #581
• Adds rename option to the get.oturep command. #555
• Adds ability to comment out lines in the file file. #560
• Adds merge.otus command. #558
• Adds processors option to rarefaction.single and rarefaction.shared. #544
• Expands make.shared to allow for count files with no groups. #563
• Adds fastq to split.groups command. #499
• Adds Oligos class and split.groups commands fastq.info. #499
• Merge.count command ignores duplicate names. #259
• Removes catchall dependency. #164
• Improves help command. #183
• Adds tree parameter to sub.sample command.
• Adds withreplacement parameter to sub.sample command. #262
• Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262
• Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583
• Adds taxonomy parameter to rename.seqs.
• Removes multiple inputs from mothur. #379
• Reduces memory needed for pre.cluster #589
• Adds count parameter to count.seqs to inflate or deflate count tables.
• Updates vsearch version to 2.11.1 #585
• Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586
• Adds constaxonomy file to subsample command. #582

Bug Fixes:

• Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true.
• Fixes file extensions of output files in pcr.seqs.
• Fixes sub.sample with multiple labels bug. #559
• Fixes bug with otu.association metadata file.
• Fixes pcr.seqs end issue with keepdots=f.
• Fixes bug in remove.lineage with cons.taxonomy and shared files. #580
• Removes extra space from output. #603
• Fixes output filename for make.group. #602

Version 1.42.0 Beta Release

Enhancements:

• Adds rename option to the get.oturep command. #555
• Adds ability to comment out lines in the file file. #560
• Adds merge.otus command. #558
• Adds processors option to rarefaction.single and rarefaction.shared. #544
• Expands make.shared to allow for count files with no groups. #563
• Adds fastq to split.groups command. #499
• Adds Oligos class and split.groups commands fastq.info. #499
• Merge.count command ignores duplicate names. #259
• Removes catchall dependency. #164
• Improves help command. #183
• Adds tree parameter to sub.sample command.
• Adds withreplacement parameter to sub.sample command. #262
• Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262
• Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583
• Adds taxonomy parameter to rename.seqs.
• Removes multiple inputs from mothur. #379
• Reduces memory needed for pre.cluster #589
• Adds count parameter to count.seqs to inflate or deflate count tables.
• Updates vsearch version to 2.11.1 #585
• Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586
• Adds constaxonomy file to subsample command. #582

Bug Fixes:

• Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true.
• Fixes file extensions of output files in pcr.seqs.
• Fixes sub.sample with multiple labels bug. #559
• Fixes bug with otu.association metadata file.
• Fixes pcr.seqs end issue with keepdots=f.
• Fixes bug in remove.lineage with cons.taxonomy and shared files. #580

Version 1.41.3

Enhancements

• Adds timing to pre.cluster deconvolute steps.

Bug Fixes

• classify.seqs and filter.seqs command may eliminate reads causing file mismatches.
• get.oturep bug with abundance method.