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Mothur v.1.5.0

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Revision as of 19:59, 30 July 2009 by Westcott (Talk | contribs) (Updates)

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Updates

  • list.seqs - reads one of the following file types: fasta, name, group or alignreport file and writes out the names of the sequences found within it.
  • get.seqs - reads an .accnos file and one of the following file types: fasta, name, group or alignreport file. It outputs a file containing only the sequences in the .accnos file.
  • remove.seqs - reads an .accnos file and one of the following file types: fasta, name, group or alignreport file. It outputs a file containing the sequences NOT in the .accnos file.
  • system - Allow the user to enter system commands from within mothur.
  • added sorted option to get.rabund.
  • improved clustering algorithm to increase speed with marginal memory cost [thanks to Gerhard Thallinger]
  • mothur can now read trees that include internal node labels (e.g. bootstrap values), but can only take in bifurcating trees.
  • read.otu with list and groups now outputs .rabund files instead of .list files.

Bug fixes

  • fixed windows unable to open file error with filter.seqs.
  • fixed bug with help command.
  • fixed bug with batchfile input.
  • fixed bug that resulted in an infinite loop if user forgot ; in ScriptBatchEngine.
  • fixed bug in venn with 4 groups that gave inflated values.
  • fixed bug with aligner that occurred when template sequence names contained spaces.
  • fixed bug in simpson calculator that occurred whenever the number of sequences exceeded the maximum size of an int