This code repository is associated with our manuscript entitled "Stable species boundaries despite ten million years of hybridization in tropical eels", which has been published in Nature Communications (Barth et al. 2020).
Sets of analyses are split into directories according to the main data source. The src subdirectory of each directory contains a script named run_all.sh that specifies in which order all other scripts need to be executed. Note, however, that the run_all.sh scripts are not intended to be executed themselves, as some of the other scripts can not run immediately one after another. In many cases, slurm jobs are triggered by those scripts, meaning that first, those scripts will need to be run on a server equipped with the slurm system (or they need to be adjusted), and second, downstream scripts can only be executed once those slurm jobs have finished. In the case of SNAPP analyses, these jobs will need to be resumed 16 times to achieve a sufficient length of the MCMC chain; the total run time of SNAPP analyses will be on the order of weeks. Without preparation, some scripts will quit immediately and provide an error message to indicate that before running them, particular input files will first need to be downloaded and placed in the correct directories.