Measurement of selection coefficients from genomic samples of adapting populations by computer modeling

The existing protocols of measuring the selection coefficients of loci neglect linkage effects existing between loci. This protocol is free from this limitation. The protocol inputs a set of DNA sequences at three time points, removes conserved sites, and estimates selection coefficients. If the user wishes to test the accuracy, it can ask the protocol to generate mock data by computer simulation of evolution. The main limitation is the need for sequence samples isolated from 30–100 populations adapting in parallel. For complete details on the use and execution of this protocol, please refer to Barlukova and Rouzine (2021).