Data from: The fitness landscape of the codon space across environments

Mathematica Notebook Fitness landscapes statistics and adaptive walkThis notebook allows to replicate the data analyses corresponding to the section of the manuscript called "The shape of the codon fitness landscape with and without synonymous effects". Please note that the data set necessary to run the analyses is obtained through the R notebooks also available within this repository.Mathematica_notebook_finalVersionJune2018.nbR notebooks for data formatting, data normalisation and statistical analysesThese R notebooks were done using R studio. They allow 1) to format the data sets after running empiricIST; 2) to do data normalisation for all the analyses performed in the manuscript; 3) to perform all statistical analyses and create the plots for the manuscript. Please note that these notebooks assume that you have run the empiricIST in the data set (the empiricIST is available at https://github.com/Matu2083/ empiricIST). The data analysed here, as indicated in the manuscript, is available from the publication: Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD (2014). A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: Uncovering the potential for adaptive walks in challenging environments. Genetics 196: 841–852.R_notebooks.zip