DOI: 10.5061/dryad.vk037
title: Data from: Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community

description: Sequencing of bacterial genomes has revealed an abundance of prophage
 sequences in many bacterial species. Since these sequences are accessible,
 through recombination, to infecting phages, bacteria carry an arsenal of
 genetic material that can be used by these viruses. We develop a
 mathematical model to isolate the effects of this phenomenon on the
 coevolution of temperate phage and bacteria. The model predicts that
 prophage sequences may play a key role in maintaining the phage population
 in situations that would otherwise favour host cell resistance. In
 addition, prophage recombination facilitates the existence of multiple
 phage types, thus promoting diverse co-existence in the phage-host
 ecosystem. Finally, because the host carries an archive of previous phage
 strategies, prophage recombination can drive waves of innovation in the
 host cell population.
description: Matlab run file for
 modelThis is the Matlab code
 for the main run file which calls on other function files and runs them
 based on the parameter values provided. It may be used to run
 phage_host_evolve_nested.m or
 phage_host_evolve_oneone.mrun_model.mODEs for nested modelThis file contains the Matlab code required to numerically solve the equations from the model with the nested infection pattern. It can be run using the file run_model.m (provided in the data package)phage_host_evolve_nested.mODEs for one to one modelThis file contains the Matlab code for the model with a one to one infection pattern. It can be run using the file run_model.m (provided in the data package).phage_host_evolve_oneone.mCalculating phage and host evolutionary stepsThis file contains the Matlab code for calculating the number of evolutionary steps occurring in the bacteria and phage populations at each time step of the simulation.evol_rate.mData for making Figure 1 in paperMatlab code output that can be used to generate the plots in Figure 1 in the main papermakefigure1rev.matData for making Figure 3 in paperMatlab code output that can be used to make the plots in Figure 3 in the main paper.makefigure3rev.matParameter changes for figuresThis file lists all the different parameter changes (to the values given in the table in the main paper) that are required to make all the figures in the main paper and supplementary material.Data for making Figure 2 in the paperThis file contains the Matlab code output which was used to plot the graphs in Figure 2 in the main paper.makefigure2rev.matData for making Figure S2Matlab code output used to plot the graphs in Figure S2 in the supplementary material.makefigureS2rev.matData for making Figure S3Matlab code output that was used to make the plots in Figure S3 in the supplementary material.makefigureS3rev.matData for making Figure S4Matlab code output that was used to make the plots in Figure S4 in the supplementary material.makefigureS4rev.matData for making Figure S5Matlab code output that was used to make the plots in Figure S5 in the supplementary material.makefigureS5rev.matData for making Figure S6Matlab code output that was used to make the plots in Figure S6 in the supplementary material.makefigureS6rev.matData for making Figure S1Matlab code output for making Figure S1 in the supplementary material.makefigureS1rev.mat