Galaxy |

Lefse (version 1.39.5.0)

shared - OTU Shared:

design - assigns groups to sets:

design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design

label - OTU Label filter:

sets - Which of the sets in your design file you would like to analyze?:

separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3

class -indicate the which category you would like used for the Kruskal Wallis analysis:

If none is provided first category is used

subclass - indicate the which category you would like used for the Kruskal Wallis analysis:

If none is provided second category is used

aalpha - alpha value for the Krukal Wallis Anova test:

walpha - alpha value for the Wilcoxon test:

lda - threshold on the absolute value of the logarithmic LDA score:

iters - number of bootstrap iteration for LDA:

fboots - set the subsampling fraction value for each bootstrap iteration:

strict - set the multiple testing correction options:

0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison

minc - minimum number of samples per subclass for performing wilcoxon test:

wilc - indicate whether to perform the Wilcoxon test:

curv - whether perform the wilcoxon testing the Curtis's approach (beta):

norm - multiply relative abundances by 1000000:

Recommended when very low values are present

Output logfile?:

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation