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Revision as of 15:42, 29 March 2018 by Westcott (Talk | contribs) (processors)

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The metastats command is based on the Metastats program, White, J.R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5, e1000352 (2009). The metastats command outputs a .metastats file.

See: http://metastats.cbcb.umd.edu/ for more information on Metastats.

Default Settings

mothur > metastats(shared=temp.job2.shared, design=temp.job2.design)



The iters parameter allows you to set number of bootstrap permutations for estimating null distribution of t statistic. The default is 1000.


The threshold parameter allows you to set the significance level to reject null hypotheses (default 0.05).


The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.


The label parameter allows you to select what distance levels you would like, and are also separated by dashes.


The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.


The sets parameter allows you to specify which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in the designfile.


The processors parameter allows you to specify how many processors you would like to use. Default processors=Autodetect number of available processors and use all available.


  • 1.25.0 - modified to more closely follow results from metastats website.
  • 1.25.0 - OTU numbers in metastats should correspond to the column names in the shared file.
  • 1.22.2 - fixed bug.
  • 1.23.0 - Added qvalues.
  • 1.24.0 - paralellized for Windows.
  • 1.29.1 - Bug Fix: error with output filename
  • 1.32.0 - Bug Fix: generate p values for sparse data using fisher's exact test instead of permutted values
  • 1.33.0 - improved work balance load between processors.
  • 1.36.0 - Remove qvalues. Also removes fortran source from mothur.
  • 1.36.0 - Bug Fix: Infinite loop with certain datasets - http://www.mothur.org/forum/viewtopic.php?f=3&t=3701
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347