PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins

Abstract Ancient proteins from fossilized or semi-fossilized remains can yield phylogenetic information at broad temporal horizons, in some cases even millions of years into the past. In recent years, peptides extracted from archaic hominins and long-extinct mega-fauna have enabled unprecedented insights into their evolutionary history. In contrast to the field of ancient DNA - where several computational methods exist to process and analyze sequencing data - few tools exist for handling ancient protein sequence data. Instead, most studies rely on loosely combined custom scripts, which makes it difficult to reproduce results or share methodologies across research groups. Here, we present PaleoProPhyler: a new fully reproducible pipeline for aligning ancient peptide data and subsequently performing phylogenetic analyses. The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. We describe the various steps of the pipeline and its many functionalities, and provide some examples of how to use it. PaleoProPhyler allows researchers with little bioinformatics experience to efficiently analyze palaeoproteomic sequences, so as to derive insights from this valuable source of evolutionary data.