The lefse command is modeled after the LEfSe program written and published by the Huttenhower lab. See make.lefse for formating files for input into the original LEfSe program.

Default Setting

The shared and design parameters are required.

mothur > lefse(shared=final.an.shared, design=mouse.sex_time2.design)

If you open the final.an.0.03.lefse_summary file, you will see:

OTU     LogMaxMean  Class   LDA     pValue
Otu001  5.21329     -
Otu002  5.06449     -
Otu003  5.08958     -
Otu004  5.06121     -
Otu005  4.82611     -
Otu006  4.76942     -
Otu007  4.81303     -
Otu008  4.69046     -
Otu009  4.71183     -
Otu010  4.77212     -
Otu011  4.63326     -
Otu012  4.80072      F003Late   4.43296     0.0363836
Otu013  4.58877      F003Late   4.02028     0.0363836
Otu014  4.5691  -
Otu015  4.42951     -



The class parameter is used to indicate the which category you would like used as the class. If none is provided first category is used.


The subclass parameter is used to indicate the which category you would like used as the subclass. If none is provided the class is used.


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 label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.


The walpha parameter is used to set the alpha value for the Wilcoxon test. Default=0.05.


The aalpha parameter is used to set the alpha value for the Krukal Wallis Anova test Default=0.05.


The lda parameter is used to set the threshold on the absolute value of the logarithmic LDA score. Default=2.0.


The wilc parameter is used to indicate whether to perform the Wilcoxon test. Default=T.


The iters parameter is used to set the number of bootstrap iteration for LDA. Default=30.


The curv parameter is used to set whether perform the wilcoxon testing the Curtis’s approach [beta version] Default=F.


The fboots parameter is used to set the subsampling fraction value for each bootstrap iteration. Default=0.67.


The strict parameter is used to set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison. Options = 0,1,2. Default=0.


The minc parameter is used to minimum number of samples per subclass for performing wilcoxon test. Default=10.


The multiclass parameter is used to (for multiclass tasks) set whether the test is performed in a one-against-one ( onevone - more strict!) or in a one-against-all setting ( onevall - less strict). Default=onevall.


The norm parameter is used to multiply relative abundances by 1000000. Recommended when very low values are present. Default=T.


  • 1.32.0 - First Introduced
  • 1.37.0 - Fixes “Skipping x iter...” warning.
  • 1.38.0 - Adds sets parameter
  • 1.40.0 - Speed and memory improvements for shared files. #357 , #347
  • 1.40.0 Bug Fix: Fixes seeded random issue. #416
  • 1.45.0 Fixes lefse screen output.