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. 2016 Oct 15;32(20):3190-3192.
doi: 10.1093/bioinformatics/btw368. Epub 2016 Jun 17.

TADtool: Visual Parameter Identification for TAD-calling Algorithms

Free PMC article

TADtool: Visual Parameter Identification for TAD-calling Algorithms

Kai Kruse et al. Bioinformatics. .
Free PMC article


Eukaryotic genomes are hierarchically organized into topologically associating domains (TADs). The computational identification of these domains and their associated properties critically depends on the choice of suitable parameters of TAD-calling algorithms. To reduce the element of trial-and-error in parameter selection, we have developed TADtool: an interactive plot to find robust TAD-calling parameters with immediate visual feedback. TADtool allows the direct export of TADs called with a chosen set of parameters for two of the most common TAD calling algorithms: directionality and insulation index. It can be used as an intuitive, standalone application or as a Python package for maximum flexibility.

Availability and implementation: TADtool is available as a Python package from GitHub ( or can be installed directly via PyPI, the Python package index (tadtool).

Contact:, jmv@mpi-muenster.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.


Fig. 1.
Fig. 1.
(A–D) TADtool window. (A) Hi-C plot, (B) TADs (black bars) called with current window size (WS: 2.5 × 105) and cutoff (2.7 × 10-3), (C) insulation index plot for current window size, (D) heatmap of insulation index for all window sizes. (E) Modifying TAD-calling parameters changes the identified TADs. (F) TADs called from Dixon et al. (2012) data with window size used in the original publication (bottom) and modified (top)

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