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Difference between revisions of "Mothur v.1.8.0"

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* added average neighbor and nearest neighbor methods to [[hcluster]] command
 
* added average neighbor and nearest neighbor methods to [[hcluster]] command
 
* added random parameter to [[unifrac.weighted]] and [[unifrac.unweighted]] commands that allows you to shut off the comparison to random trees.
 
* added random parameter to [[unifrac.weighted]] and [[unifrac.unweighted]] commands that allows you to shut off the comparison to random trees.
 +
* you can now input multiple fasta files to the [[align.seqs]] and [[classify.seqs]] commands by separating filenames with dashes. i.e. fasta=abrecovery.fasta-amazon.fasta

Revision as of 16:14, 8 January 2010

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 as well as a progress indicator 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, so you can choose not to report the confidence scores with the bayesian method.
  • added iters parameter to classify.seqs command.
  • 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.
  • added pca command
  • corrected error in help for align.seqs and classify.seqs which gave incorrect defaults for the gapopen and gapextend defaults.
  • you can now use a distance matrix as input for the heatmap.sim command.
  • added distance parameter to unifrac.weighted and unifrac.unweighted commands that allows you to output a distance matrix from the command.
  • added average neighbor and nearest neighbor methods to hcluster command
  • added random parameter to unifrac.weighted and unifrac.unweighted commands that allows you to shut off the comparison to random trees.
  • you can now input multiple fasta files to the align.seqs and classify.seqs commands by separating filenames with dashes. i.e. fasta=abrecovery.fasta-amazon.fasta