Non-model organisms represent an exciting avenue for exploration in an evolutionary context. The diversity at both the regulatory and genome level is extensive in the animals and plants studied so far though much remains to be understood about many aspects of evolution. One example of this is how animals and plants make use of the specific features of their genomes to adapt and respond to the changing features of their environments. In this project, the aim is to develop Snakemake pipelines for the analysis of NGS datasets. These include DNA, RNA and methylation sequence data from non-model organisms (e.g. insects and worms). Some of the data is from long-running experiments in evolution while the other datasets are to establish a baseline in an animal lineage where little is know about gene regulation including methylation. Here, the goal is to better understand how experimental evolution can influence change and the genome and gene expression levels. While some aspects of the data handling can be handled by existing pipelines, many parts of the data analysis need to be adjusted depending on the species and the research goal. These include adjustments that need to be made for the processing, filtering and interpretation of the data. One objective of this project is to generate pipeline components in modular forms so that parts of pipelines can be used future analyses. Furthermore, the results from analyzing the non-model organism datasets can be used for helping to target experimental approaches using model species (e.g. humans, mice). That is, by better understanding how non-model organisms make use of their genomes, we can often find good gene candidates for functional testing.