File S1

1) AlphaDrop: executable for Linux 2) macs: MaCS executable for linux 3) msformatter: MaCS executable for linux 4) Seed.txt: a file containing a random seed for initialising AlphaDrop 5) RunMacs.sh: a shell script called by AlphaDrop when it runs MaCS 6) AlphaDropSpec.txt: the specification file for AlphaDrop 7) Pedigree.txt: an example externally supplied pedigree file 8) MaCsSimulationParameters.xlsx: an excel sheet with which MaCS parameters can be calculated 9) Ne100.sh: example of what to put into RunMacs.sh (Ne100 population of Hickey et al., 2011 Genetics Selection Evolution) 10) Ne1000.sh: example of what to put into RunMacs.sh (Ne1000 population of Hickey et al., 2011 Genetics Selection Evolution)