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Mothur v.1.9.0

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Revision as of 11:40, 10 March 2010 by Westcott (Talk | contribs) (Bug fixes)

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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

Bug fixes

  • 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.