PSGfinder: fast identification of genes under divergent positive selection using the dynamic windows method

Abstract

SummaryOrthologous genes evolving under divergent positive selection are those involved in divergent adaptive trajectories between related species. Current methods to identify such genes are complex and conservative or present some imperfections, limiting genome-wide searches. We present a simple method, Dynamic Windows, to detect regions of protein-coding genes evolving under divergent positive selection. This method is implemented in PSGfinder, a user-friendly and flexible software, allowing rapid genome-wide screenings of regions with a dN/dS >1. PSGfinder additionally includes an alignment cleaning procedure and an adapted multiple comparison correction to identify significant signals of positive selection.\n\nAvailability and ImplementationPSGfinder is a software that implements the DWin method, is written in Python and is freely available with its documentation at: https://genev.unige.ch/research/laboratory/Juan-Montoya or at: https://github.com/joel-tuberosa/psgfinder\n\nContactjuan.montoya@unige.ch; joel.tuberosa@unige.ch