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Difference between revisions of "Mothur v.1.8.0"

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* 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.
 
* added [[mgcluster]] command which incorporates the functionality of the mgdotur program.
 
* added [[mgcluster]] command which incorporates the functionality of the mgdotur program.
* added [[pca]] command
+
* added [[pcoa]] command
 
* corrected error in help for [[align.seqs]] and [[classify.seqs]] which gave incorrect defaults for the gapopen and gapextend defaults.
 
* 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.
 
* you can now use a distance matrix as input for the [[heatmap.sim]] command.

Revision as of 11:19, 29 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 distance search method to classify.seqs
  • 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 large parameter to get.oturep command, so if your distance matrix is too large to fit in ram you can still run the command.
  • 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 pcoa 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.
  • mothur now recognizes ./ and ../ in file names
  • added unclassified bins to classify.seqs command output.
  • summary.shared(all=false) by default
  • added warning about average neighbor clustering near cutoff.
  • fixed a bug in how the morisitahorn index was being calculated
  • mothur's logfiles are now time stamped and not overwritten with each execution of mothur.
  • fixed bug in aligner that caused a bus error if your candidate sequence had more bases than your longest template sequence.
  • 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.
  • added distance parameter to unifrac.weighted and unifrac.unweighted commands that allows you to output a distance matrix from the 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 read a shared file and then run the .single commands.
  • added set.dir command allowing you to set an input file directory and / or redirect the output files generated by mothur.
  • get.oturep command now outputs a .rep.names file.
  • get.oturep command - when selecting the rep, if there are multiple sequence with the minimum maximum distance to other members in the bin the sequence with the smallest average distance is selected. This is a change that may produce different results from those calculated by previous mothur versions. previously the first sequence found with the minimum maximum distance was selected.


  • added average neighbor and nearest neighbor methods to hcluster command
  • 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
  • added otu.hierarchy command which relates otus at different distance levels