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Mothur v.1.8.0

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Revision as of 15:13, 21 December 2009 by Westcott (Talk | contribs)

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mothur now allows for comments in fasta files in the following format:

>#=GC_SS_cons
::::::::<<<<<_______>>>>>,{{{{-{{{{{{,{{{{{{{{{-.---{{{-.{{.{.,,...
>FYV22AL02GBAKV
------------------------------------------------.-------.--.-.--...

The sequence =GC_SS_cons is ignored and only FYV22AL02GBAKV is read in.

  • added flip and threshold parameters to align.seqs command.
  • added list parameter to get.seqs and remove.seqs commands.
  • mothur uses the readline library to allow use of arrow keys and other shortcuts in Interactive mode.
  • added probs parameter to the classify.seqs command to shut off bootstrapping with bayesian method.
  • added sorted parameter to get.oturep command, so the output can be sorted by sequence name, OTU number, OTU size, or group. The default is no sorting.
  • removed the groups parameter from get.sharedseqs and in its place added the unique and shared parameters.
  • added file checking to read.dist to fix error that occured in the libshuff command if the files did not match.
  • added mgcluster command which incorporates the functionality of the mgdotur program.