DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses

Thomas Hütter*, Maximilian Ganser, Manuel Kocher, Merima Halkic, Sabine Agatha, Nikolaus Augsten

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort.

DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced.

DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at ( and is open source (
Original languageEnglish
Article number151
Pages (from-to)151
Number of pages9
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 20 Apr 2020

Fields of Science and Technology Classification 2012

  • 102 Computer Sciences
  • 106 Biology


  • Algorithms
  • Bioinformatics
  • Phylogenetics
  • Taxonomy

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