raw_competition_data

Text file containing raw data from all competition experiments. All competitions were performed over 2 transfer cycles. Fitness values from this file are summarized in 'genotype_fitness.txt', which is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population

genotype_fitness

Text file containing all replicate fitness measurements of each constructed genotype. Includes columns: strain, strain number; genotype, beneficial mutations present where r = rbs, t = topA, s = spoT, g = glmUS and p = pykF; mutations, number of beneficial mutations in the genotype; w, fitness estimate; block, experimental block; Plate, physical container used for the competition. This file is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population

Khan_etal_Fig4

R script to generate figure 4 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt

Khan_etal_analysis

R script used to: estimate beneficial mutation effects and epistasis parameters, perform statistical tests and generate all figures presented in Khan et al. (2011), except figures 1 and 4. Takes as input the file: genotype_fitness.txt

fig1.b R script

R script to generate figure 1

fig4_mutations_in_founder_also_in_replay

Input file for fig. 4 R script. Summarizes mutations present in founders that also occurred in some replay clones. These mutations are omitted from calculation of the convergence metric

Khan_etal_Fig1

R script to generate figure 1 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt

fig3_anc-ev

Input data required to generate figure

fig4_replay_clone_mutations

Input to fig4 R script. Summary of mutated genes in clones isolated from replay populations

fig1.b input data

Input data necessary to generate figure 1