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MANTIS: an R package that simulates multilocus models of pathogen evolution.

José Lourenço1, Paul S Wikramaratna2, Sunetra Gupta3

  • 1Department of Zoology, University of Oxford, South Parks Road, Oxford, UK. jose.lourenco@zoo.ox.ac.uk.

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Summary
This summary is machine-generated.

Researchers developed the Multilocus ANTIgenic Simulator (MANTIS) software for R, enabling simulations of host-pathogen evolutionary dynamics. This free, open-source tool aids in understanding pathogen evolution and immune responses.

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Area of Science:

  • Epidemiology
  • Evolutionary Biology
  • Computational Biology

Background:

  • Host immunity drives pathogen evolution through competition between genetic variants.
  • Cross-protective responses lead to pathogen-specific dynamic behaviors.
  • Computational epidemiological models are crucial for understanding these evolutionary forces.

Purpose of the Study:

  • To develop a free, accessible software tool for simulating and analyzing host-pathogen dynamics.
  • To provide a user-friendly platform for researchers studying pathogen evolution.

Main Methods:

  • Developed the Multilocus ANTIgenic Simulator (MANTIS) software package within the R statistical environment.
  • Integrated a C/C++ ordinary-differential equations system with a Runge-Kutta solver.
  • Created user-friendly R functions for simulation, analysis, visualization, and data export.

Main Results:

  • MANTIS simulates and analyzes epidemiological time-series based on the strain theory of host-pathogen systems.
  • The package includes specialized functions for time-series plotting and exportation.
  • MANTIS is designed as a ready-to-use academic software tool.

Conclusions:

  • MANTIS serves as a free, open-source academic software for simulating host-pathogen evolutionary dynamics.
  • The software facilitates the study of pathogen evolution and immune system interactions.
  • MANTIS is available under the GPL license, with potential for user expansion.