Data from: Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community

Nadeem A, Wahl LM

Date Published: May 31, 2017

DOI: http://dx.doi.org/10.5061/dryad.vk037

 

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Title Matlab run file for model
Downloaded 2 times
Description This 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.m
Download run_model.m (4.103 Kb)
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Title ODEs for nested model
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Description This 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)
Download phage_host_evolve_nested.m (6.416 Kb)
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Title ODEs for one to one model
Downloaded 3 times
Description This 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).
Download phage_host_evolve_oneone.m (5.534 Kb)
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Title Calculating phage and host evolutionary steps
Downloaded 6 times
Description This 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.
Download evol_rate.m (2.243 Kb)
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Title Data for making Figure 1 in paper
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Description Matlab code output that can be used to generate the plots in Figure 1 in the main paper
Download makefigure1rev.mat (80.8 Kb)
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Title Data for making Figure 3 in paper
Downloaded 5 times
Description Matlab code output that can be used to make the plots in Figure 3 in the main paper.
Download makefigure3rev.mat (228.6 Kb)
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Title Parameter changes for figures
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Description This 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.
Download Parameter changes for figures.xlsx (9.014 Kb)
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Title Data for making Figure 2 in the paper
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Description This file contains the Matlab code output which was used to plot the graphs in Figure 2 in the main paper.
Download makefigure2rev.mat (277.8 Kb)
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Title Data for making Figure S2
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Description Matlab code output used to plot the graphs in Figure S2 in the supplementary material.
Download makefigureS2rev.mat (473.3 Kb)
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Title Data for making Figure S3
Downloaded 4 times
Description Matlab code output that was used to make the plots in Figure S3 in the supplementary material.
Download makefigureS3rev.mat (56.30 Kb)
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Title Data for making Figure S4
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Description Matlab code output that was used to make the plots in Figure S4 in the supplementary material.
Download makefigureS4rev.mat (179.7 Kb)
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Title Data for making Figure S5
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Description Matlab code output that was used to make the plots in Figure S5 in the supplementary material.
Download makefigureS5rev.mat (531.5 Kb)
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Title Data for making Figure S6
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Description Matlab code output that was used to make the plots in Figure S6 in the supplementary material.
Download makefigureS6rev.mat (451.2 Kb)
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Title Data for making Figure S1
Downloaded 2 times
Description Matlab code output for making Figure S1 in the supplementary material.
Download makefigureS1rev.mat (497.6 Kb)
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When using this data, please cite the original publication:

Nadeem A, Wahl LM (2017) Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community. Evolution 71(8): 2080-2089. http://dx.doi.org/10.1111/evo.13287

Additionally, please cite the Dryad data package:

Nadeem A, Wahl LM (2017) Data from: Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vk037
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