News and Announcements » – A workflow script for performing jackknifed UPGMA clustering and building jackknifed Emperor PCoA plots.


To directly measure the robustness of individual UPGMA clusters and clusters in PCoA plots, one can perform jackknifing (repeatedly resampling a subset of the available data from each sample).

Usage: [options]

Input Arguments:



-i, --otu_table_fp
The input OTU table in biom format [REQUIRED]
-o, --output_dir
The output directory [REQUIRED]
-e, --seqs_per_sample
Number of sequences to include in each jackknifed subset [REQUIRED]
-m, --mapping_fp
Path to the mapping file [REQUIRED]


-t, --tree_fp
Path to the tree file [default: None; REQUIRED for phylogenetic measures]
-p, --parameter_fp
Path to the parameter file, which specifies changes to the default behavior. See . [if omitted, default values will be used]
Method for computing master trees in jackknife analysis. “consensus”: consensus of trees from jackknifed otu tables. “full”: tree generated from input (unsubsambled) otu table. [default: consensus]
-f, --force
Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]
-w, --print_only
Print the commands but don’t call them – useful for debugging [default: False]
-a, --parallel
Run in parallel where available [default: False]
-O, --jobs_to_start
Number of jobs to start. NOTE: you must also pass -a to run in parallel, this defines the number of jobs to be started if and only if -a is passed [default: 1]


This scripts results in several distance matrices (from, several rarefied OTU tables (from, several UPGMA trees (from, a supporting file and newick tree with support values (from, and Emperor PCoA plots.


These steps are performed by the following command: Compute beta diversity distance matrix from otu table (and tree, if applicable); build rarefied OTU tables by evenly sampling to the specified depth (-e); build UPGMA tree from full distance matrix; compute distance matrics for rarefied OTU tables; build UPGMA trees from rarefied OTU table distance matrices; build a consensus tree from the rarefied UPGMA trees; compare rarefied OTU table distance matrix UPGMA trees to either (full or consensus) tree for jackknife support of tree nodes; perform principal coordinates analysis on distance matrices generated from rarefied OTU tables; generate Emperor PCoA plots with jackknifed support. -i otu_table.biom -o bdiv_jk100 -e 100 -m Fasting_Map.txt -t rep_set.tre