Welcome to CONSTAX’s documentation!

CONSTAX (CONSensus TAXonomy) is a tool, written in Python 3, for improved taxonomic resolution of environmental DNA sequences. Briefly, CONSTAX compares the taxonomic classifications obtained from RDP Classifier, UTAX or BLAST, and SINTAX and merges them into an improved consensus taxonomy using a 2 out of 3 rule (e.g. If an OTU is classified as taxon A by RDP and UTAX/BLAST and taxon B by SINTAX, taxon A will be used in the consensus taxonomy) and the classification p-value to break the ties (e.g. when 3 different classification are obtained for the same OTU). This tool also produces summary classification outputs that are useful for downstream analyses. In summary, our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power (proportion of assigned operational taxonomic units at a given taxonomic rank) is realized by generating consensus taxonomy of available classifiers with CONSTAX.

CONSTAX 2.0.17 improves upon 1.0.0 with the following features:

  • Updated software requirements, including Python 3 and Java 8

  • Simple installation with conda

  • Compatibility with SILVA-formatted databases (for Bacteria, Archaea, protists, etc.)

  • Streamlined command-line implementation

  • BLAST classification option, due to legacy status of UTAX

  • Parallelization of classification tasks

  • Isolate matching

Developed by

Funded by

CONSTAX 1.0.0 was authored by


Liber JA, Bonito G, Benucci GMN (2021) CONSTAX2: improved taxonomic classification of environmental DNA markers. Bioinformatics doi: 10.1093/bioinformatics/btab347

Gdanetz K, Benucci GMN, Vande Pol N, Bonito G (2017) CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. BMC Bioinformatics 18:538 doi 10.1186/s12859-017-1952-x

See the menu on the left for how to install CONSTAX and how to use it.

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