Codes for "Most synonymous mutations in yeast are strongly non-neutral"

Codes for the article "Most synonymous mutations in yeast are strongly non-neutral"

All_fitness_values_of_genes.tar.gz:

        The folder contains fitness data of 19 genes in four environments, separated by genes.

All_mutations_four_env_SNF6_two_replicates-fitness.csv:

        A merged table contains all fitness data of 19 genes in four environments.

Fitness_simulation.ipynb:

        Simulations to show that fitness estimates are the same (1) when strains are grown together and (2) when strains are grown individually. The simulation is to respond to a reviewer's question.

dNdS-Nenv_curve.ipynb:

        Simulation of the impact of environmental changes on dN/dS.

empirical_dNdS.ipynb:

        Calculation of expected dN/dS in the four environments.