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- added output parameter to otu.hierarchy command, options are name and number. name is default. you can output either the names of the sequences in the OTUs or the OTU numbers.
- added dups parameter to remove.seqs command.
- add accnos file output to chimera.seqs
- add a name option to unifrac commands
- rework the way chimera.seqs processes seqs so only one is read at a time
- added more error checking to chimera.seqs to check query to template seqs length
- added output parameter so you can create a square phylip formatted matrices from dist.seqs and dist.shared
- added parse.list command.
- output list of files that are created at the end of each command
- fixed problem with logfiles that occurred when multiple executions of mothur were running at the same time.
- ^C ends command instead of ending mothur.
- filter.seqs can filter multiple files by separating files names with dashes. ex. fasta=abrecovery.fasta-core_set_aligned.imputed.fasta
- removed phylip parameter from dist.seqs and replaced with output
- added sim parameter to read.dist
- ^D now ends mothur with readline
- Problem with "../" ==> align.seqs(candidate=wobus.unique.fasta, template=../DataAnalysis/silva.refalign.fasta, processors=2); Segmentation fault
- fixed bug in merge.files that inserted the eof character in between the merged files
- fixed bug that could cause a badalloc to occur while reading a sabund file
- added checking for duplicate sequence names in list files which leads to .missing.group file to be blank.
- get.seqs and remove.seqs using a list file left an extra comma if you eliminated the final member in the OTU.
- fixed bug that caused a bad alloc to occur in chimera.seqs while using bellerophon.