Phylociraptor – A unified computational framework for reproducible phylogenomic inference

Abstract

AbstractMulti-stage phylogenomic analyses require complex computational environments. A unified framework for software- and parameter space exploration, data organisation and -deposition is currently lacking. We present phylociraptor (https://github.com/reslp/phylociraptor), a pipeline facilitating fast, reliable, portable (containerized), and reproducible phylogenomics. We demonstrate phylociraptor’s utility and uncover topological discrepancies associated with software and parameter choices in large-scale datasets (31-101 species, 241-2894 genes) addressing enigmatic questions in fungal and vertebrate evolution.