New reference genomes and transcriptomes are becoming increasingly available across the whole tree of life, opening new avenues to tackle exciting evolutionary questions. However, there are still challenges associated with annotating genomes, aligning sequences, inferring evolutionary processes and a lack of methodological standardisation. Here, we propose a new workflow designed for evolutionary analyses to overcome these challenges, facilitating the detection of recombination suppression and its consequences in terms of rearrangements and transposable element accumulation. To do so, we assemble multiple bioinformatic steps in a single, reproducible and easy-to-use workflow. We combine state-ofthe-art tools to quickly detect transposable elements, annotate newly assembled genomes, infer gene orthology relationships, compute divergence between sequences, infer evolutionary strata (i.e. stepwise extension of recombination suppression) and their structural rearrangements, and visualise the results at different steps in the process. This workflow was called EASYstrata and was applied to reannotate a set of 42 published genomes from Microbotryum fungi. We show in case examples that we recover the same strata as previously described. While this tool was mostly developed with the goal to infer divergence between sex or mating-type chromosomes, it can be applied to any pair of haplotypes whose pattern of divergence might be of interest, e.g. supergenes in autosomes. This workflow will facilitate the study of the numerous non-model species for which newly sequenced phased diploid genomes are becoming available.