• Medientyp: E-Artikel
  • Titel: AsymmeTree : A Flexible Python Package for the Simulation of Complex Gene Family Histories
  • Beteiligte: Schaller, David [Verfasser:in]; Hellmuth, Marc [Verfasser:in]; Stadler, Peter F. [Verfasser:in]
  • Erschienen: Basel: MDPI, [2024]
  • Erschienen in: Software ; 1 (2022), Seite 276-298
  • Sprache: Englisch
  • Schlagwörter: species tree ; sequences ; gene tree ; horizontal gene transfer ; gene family histories ; simulation ; rate heterogeneity
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  • Beschreibung: AsymmeTree is a flexible and easy-to-use Python package for the simulation of gene familyhistories. 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 acidsequences (optionally with indels, among-site rate heterogeneity, and invariant sites) can be simulatedalong the gene phylogenies. For all steps, users can choose from a spectrum of alternative methodsand parameters. These choices include most options that are commonly used in comparable tools butalso some that are usually not found, such as the innovation model for species evolution. While outputfiles for each individual step can be generated, AsymmeTree is primarily intended to be integrated incomplex Python pipelines designed to assess the performance of data analysis methods. It allows theuser to interact with, analyze, and possibly manipulate the simulated scenarios. AsymmeTree is freelyavailable on GitHub.
  • Zugangsstatus: Freier Zugang
  • Rechte-/Nutzungshinweise: Namensnennung (CC BY)