FGTpartitioner is a software for the rapid partitioning of full-genome sequence alignments into 'recombination-free' segments using minimal analytical assumptions. In doing so, FGTpartitioner provides a means for simple and rapid block delimitation in genome-wide datasets as a pretext for phylogenomic analysis, thus increasing accessibility of phylogenomic methods to researchers studying non-model species. Source code: https://github.com/tkchafin/FGTpartitioner