Over the past few years the number of available chromosome-level reference genomes for non-model organisms have increased dramatically. Efforts by the Darwin Tree of Life Project and Project Psyche to sequence all European Lepidoptera (butterflies and moths) have seen considerable early success, having now surpassed 1000 published reference genomes. Such genomes not only enable population genomic analyses for an ever growing number of species, but also are valuable data points for comparative and phylogenomic studies on the group. This compute project encompasses multiple studies utilizing these genomes, as well as the development of reproducible pipelines for the analyses. Utilizing these genomes we are investigating the evolution of Noctuid moths, using phylogenomic methods to resolve the long-standing uncertainty in their evolutionary relationships as well as using comparative genomic methods to understand genetic patterns behind dispersal ability and polyphagy, both of which contribute to the frequent pest-status of members of this clade. Additionally, using the whole genome resequencing of grassland butterfly species, we study population genomic patterns associated with land use change over the past century in Sweden, shedding light on genetic factors that may contribute to conservation concern. Finally, we focus on developing suitable analysis pipelines for processing data for taking advantage of this increase in genome availability. This compute project has previously focused on the development of PopGLen, which is designed to automate population genomic analyses on low coverage data. This pipeline has been published and will continue testing and implementing feature requests on this compute project, as well as be put in use for the butterfly conservation genomic analyses.