AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories

Abstract

AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene family histories. It simulates species trees and considers the joint action of gene duplication, loss, conversion, and horizontal transfer to evolve gene families along the species tree. To generate realistic scenarios, evolution rate heterogeneity from various sources is modeled. Finally, nucleotide or amino acid sequences (optionally with indels, among-site rate heterogeneity, and invariant sites) can be simulated along the gene phylogenies. For all steps, users can choose from a spectrum of alternative methods and parameters. These choices include most options that are commonly used in comparable tools but also some that are usually not found, such as the innovation model for species evolution. While output files for each individual step can be generated, AsymmeTree is primarily intended to be integrated in complex Python pipelines designed to assess the performance of data analysis methods. It allows the user to interact with, analyze, and possibly manipulate the simulated scenarios. AsymmeTree is freely available on GitHub.