Background Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area under active research because it could be the cause of many complex traits. The most common way to specify an epistasis interaction is through a penetrance table. Results This paper presents PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. Unlike other tools available in the bibliography, PyToxo is able to work with high-order models and realistic penetrance and heritability values, achieving high-precision results in a short time. In addition, PyToxo is distributed as open-source software and includes several interfaces to ease its use. Conclusions PyToxo provides the scientific community with a useful tool to evaluate algorithms and methods that can detect high-order epistasis to continue advancing in the discovery of the causes behind complex diseases.
The interaction among different genes when expressing a particular phenotype is known as epistasis. High-order epistasis, when more than two loci are involved, is an active research area because it could be the cause of many complex traits. The most common abstraction for specifying an epistasis interaction is through a penetrance table, which captures the probability of expressing the studied phenotype given a particular genotype.Although it is very common for simulators to use penetrance tables, most of them do not allow the user to generate them directly, or present limitations for high-order interac- tions and/or realistic prevalence and heritability values. In this work, we present PyToxo, a Python tool for generating penetrance tables from any-order epistasis models. PyToxo allows to work with more appropriate scenarios than other state-of-the-art tools. Addi- tionally, it also improves in terms of accuracy, speed and ease of use, being available as a library, through a CLI or through a cross-platform GUI.
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