The complexities of viral mutation rates (Peck and Lauring 2018)

Data for generating Figure 1 for The complexities of viral mutation rates (Peck and Lauring 2018).

Figure_1_mu_and_K_data.csv

Contains data compiled from Sanjuan 2012 (for evolutionary rates), Sanjuan and Domingo-Calap 2016 (mutation rates), and additional references for estimates of evolutionary and mutation rates. Data file also includes group, family, and genome size for each viral species.

Figure_1_mu_and_K_references.docx

Full references for the mutation rate and evolutionary rate data in Figure_1_mu_K_data.csv. References are for values reported in Sanjuan 2012, Domingo-Calap and Sanjuan 2016, as well as a few additional reference (post-2016 estimates).

Lynch_2016_mu_data.csv

Data from Lynch et al. 2016 (Supplemental Table 1) which includes the genome size and mutation rate estimates for a number of multicellular, unicellular, and eubacteria taxa.

Figure_1_plots.R

R code to read in the above .csv files and output:

• Figures 1A: viral evolutionary rates, K, vs. mutation rates, mu, for each Baltimore class (data from Figure_1_mu_and_K_data.csv)
• Figure 1B: viral evolutionary rates, K, vs. mutation rates, mu, for individual viruses (ones that include an estimate for both K and mu) (data from Figure_1_mu_and_K_data.csv)
• Figure 1C: mutation rate, mu, vs. genome size, G, for viruses (data from Figure_1_mu_and_K_data.csv) as well as eubacteria, unicellular, and multicellular taxa (data from Lynch_2016_mu_data.csv)

Shiny app (server.R and ui.R)

To run the shiny app displaying Figures 1A-1C, open R or RStudio and run:

install.packages("shiny")

library(shiny)

runGitHub("JVI_Gem_2018", "lauringlab")

Alternatively, download the files, open them in RStudio and click on "Run App".