News and Announcements » – This script runs any of a set of common tests to determine if a sample is statistically significantly different from another sample


The tests are conducted on each pair of samples present in the input otu table. See the unifrac tutorial online for more details (

Usage: [options]

Input Arguments:



-i, --input_path
Input otu table in biom format
-o, --output_path
Output results path
-s, --significance_test
Significance test to use, options are ‘unweighted_unifrac’, ‘weighted_unifrac’, ‘weighted_normalized_unifrac’, or ‘p-test’
-t, --tree_path
Path to newick tree file


-n, --num_iters
Number of monte carlo randomizations [default: 100]
-k, --type_of_test
Type of significance test to perform, options are ‘all_together’, ‘each_pair’ or ‘each_sample’. [default: each_pair]


The script outputs a tab delimited text file with each pair of samples and a p value representing the probability that a random sample/sequence assignment will result in more dissimilar samples than the actual pair of samples.


Perform 100 randomizations of sample/sequence assignments, and record the probability that sample 1 is phylogenetically different from sample 2, using the unifrac monte carlo significance test. The test is run for all pairs of samples. -i otu_table.biom -t rep_set.tre -s unweighted_unifrac -o unw_sig.txt