If you use Toxtree, please cite the following paper:

Patlewicz, 2008
Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B. (2008) An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR QSAR Environ Res. ;19(5-6):495-524.

or/and these web sites:

JRC Computational Toxicology
https://eurl-ecvam.jrc.ec.europa.eu/laboratories-research/predictive_toxicology/qsar_tools/toxtree
Toxtree site
http://toxtree.sourceforge.net

For publications, specific to plugins, refer to the plugin page and manuals.

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