The Joint Alignment and Tree Inference (JATI) project is a main pillar of the Applied Computational Genomics Team (ACGT). Its long-term aim is the joint inference of all parameters of current models of molecular sequence evolution (i.e. phylogenetic tree, homology mapping, ancestral sequences, substitution/insertion/deletion model parameters).In this context we have developed and implemented an algorithm to compute the likelihood of a sequence alignment and phylogenetic tree under a classical model of sequence evolution. The model exists since the 1990’s, but despite the model being important, this is the first and only available implementation (due to the complexity of the problem). It allows us to exclusively study the limitations of the model. To this end, we have designed the concept for a simulation study. The goal of the present Anschub project is to1.Optimise the implementation of the algorithm,2.to execute the simulation study, and3.to publish both results in scientific journals.