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Difference between revisions of "Mothur v.1.8.0"

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* added iters and name parameters to [[classify.seqs]] command.
 
* added iters and name parameters 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.
 
* 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.
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* removed the groups parameter from [[get.sharedseqs]] and in its place added the unique and shared parameters.
 
* 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 file checking to read.dist to fix error that occured in the libshuff command if the files did not match.

Revision as of 21:00, 26 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 list.seqs, 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 and name parameters 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
  • fixed bug in merge.files command that gave a "cannot open file" error in the windows version.
  • added formatting to mothur to make phylip formatted distance files compatible with other software tools.
  • you can now read a shared file and then run the .single commands.
  • added large parameter to get.oturep command, so if your distance matrix is too large to fit in ram you can still run the command.
  • get.oturep command now outputs a .rep.names file.
  • fixed bug in aligner that caused a bus error if your candidate sequence had more bases than your longest template sequence.
  • mothur's logfiles are now time stamped and not overwritten with each execution of mothur.
  • added warning about average neighbor clustering near cutoff.
  • fixed a bug in how the morisitahorn index was being calculated
  • summary.shared(all=false) by default
  • added otu.hierarchy command which relates otus at different distance levels
  • mothur now recognizes ./ and ../ in file names
  • added unclassified bins to classify.seqs command output.
  • added set.dir command allowing you to set an input file directory and / or redirect the output files generated by mothur.