Scripts and functions generated in the framework of GenSal project, financed by the University of Udine. They were used to analyze dd-RAD sequencing data of Salmo trutta samples and obtain information on polymorphisms, genetic structure and signatures of selection. The relevant paper is "ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout" and has been published in Genetics Selection Evolution. You can freely access it from the publisher.
We tried to put all the scripts and functions in the correct order. The prefix a denotes the analysis devoted to genetic structure and detection of signatures, and the prefix b denotes analysis performed for the functional annotation of regions under selection and testing for enrichment in functional classes. As a general rule, scripts are executed first, and they usually call R functions. You will need to create a few path variables. Scripts and functions are generally commented, and you should be able to walk your way throusgh them. If this is not the case, drop us a line.