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CrossClassify is a tool for mapping results of metagenomic analyses from one taxonomy onto another. It is packaged with five taxonomies:

  1. SILVA 128 (29 Sep 2016)
  2. RDP release 11, update 5 (30 Sep 2016)
  3. Greengenes (May 2013)
  4. NCBI (5 Oct 2016)
  5. OTT version 2.10 draft 11 (10 Sep 2016)


Click here to download CrossClassify.

Command line options

Short Full Description Default
-i --in input BIOM1 file.
-r --reference reference taxonomy [ncbi/rdp/silva/gg/ott]. ncbi
-o --out output BIOM1 file.
-d --dictionary use synonim dictionary as provided by ncbi. Off
-s --strict performs strict mapping (default mapping procedure is loose). Off
-n --nwk print reference taxonomy as a newick file.Creates files <taxonomy>.tre and <taxonomy>.map for MEGAN. Off
-hm --heatmap heatmap file. Saves summary of the cross mapping as a heatmap in a pdf file.
-ps --parallelsets parallel sets file. Saves summary of the cross mapping as a parallel sets diagram in a pdf file.
-v --values prints values of all parameters as set by the user or by default. Off
-h --help prints this message. Off

Usage examples

We recommend allocating more heap space when running CrossClassify (e.g. with -Xmx6G, see here for more details).

Saving a whole taxonomy for viewing with MEGAN

java -Xmx6G -jar CrossClassify.jar -n -r rdp

Will produce rdp.tre, and files.

Mapping taxonomic assignments onto another taxonomy

java -Xmx6G -jar CrossClassify.jar -i <input>.biom -r silva -o <output_on_silva>.biom

Will map taxonomic paths in <input>.biom onto SILVA taxonomy and save results to <output_on_silva>.biom. Use -s or --strict for strict mapping and -d or --dictionary if you want to use NCBI's synomin dictionary to correct for possible misspellings.

Mapping results are summarised as normalised dissimilarities and visualized as

  • parallel sets (-ps/--parallelsets <ps_file>.pdf) and
  • heatmaps (-hm/--heatmap <hm_file>.pdf).

For more details please see paper.


If you use CrossClassify please cite:

Balvočiūtė M. & Huson D. H. SILVA, RDP, Greengenes, NCBI and OTT --- How do these taxonomies compare? 2016 Under Revision

CrossClassify is distributed under AGPL lisence

Taxonomic classifications in the data folder (packaged together with CrossClassify.jar) are under the following licences:


CrossClassify uses itext library for generating PDF files and json-simple for handling BIOM1 files.