This is the revised version of fhetboot that includes different ways of estimating Fst and the option of calculating p-values. It is no longer compatible with the previous pre-review version of fhetboot. This paper using these tools (fhetboot v1.0 and the scripts and programs) is currently under review. fhetboot v1.0 fhetboot_1.0.zip fhetboot_1.0.tar.gz fhetboot-manual.pdf Please see the vignette for instructions on how to use fhetboot. scripts and programs scripts scripts.tar.gz All of these scripts run the other programs. numerical analysis numerical_analysis.tar.gz This program runs a numerical analysis as described in Flanagan & Jones "Constraints on the Fst-heterozygosity approach" paper. It assumes a population size of 1000 individuals per deme, 2000 replications (genes), and 5000 generations. 50 individuals are sampled from each sampled populations. Sampling either occurs as a certain number of samples per population or by randomly-sampling populations (a single population could be sampled multiple times). Input Required parameters Base output file name, including the path Nm (population size = 1000 times the migration rate) The number of demes The number of populations to sample Optional parameters Whether random sampling is turned on or off. (Default: random sampling turned on) If you want to run it with overdominance, and the overdominance selection coefficient (default: no overdominance) If you want to run it with directional selection, and the selection coefficient (default: no directional selection) Arguments -o base file name (include path). Example: N1000s10 -p Population size (N). This number is set to 1000 if not specified and is constant among all populations. -n Nm -d number of demes -r random sample? In interactive mode, use Y to turn on and N to turn off. In command-line mode, use 1 to turn on. -s number of populations to sample -v Overdominance? Follow -v with the selection coefficient (s) -ds Directional Selection? Follow -ds with the selection coefficient (s) -h Prints the arguments list no arguments: interactive mode Output Average Allele frequencies, Fsts, etc. for each generation (*.freqs.txt). Heterozygosities, Fsts, and average allele frequency for all demes (not the sampled populations) for each locus at the end of the 5000 generations (*.output.txt). Heterozygosities, Fsts, and average allele frequency calculated from the sampled populations (whether populations were randomly sampled or not) for each locus (*.sampledpops.txt). Genepop file for the sampled output, ready to be input to LOSITAN. Installation and Usage Windows Put the executable (numerical_analysis.exe) in a useful folder. It is easiest (the path you must provide is shortest) if you put it in your desired output directory. Ubuntu Put the executable in a useful folder. It is easiest (the path you must provide is shortest) if you put it in your desired output directory. **You may need to alter file permissions for it to run: chmod u+x numerical_analysis To run the file in interactive mode: ./numerical_analysis To run the file with arguments: ./numerical_analysis -o file_namebase -n 0.1 -d 100 -s 10 -r y For help: ./numerical_analysis -h Other operating systems Compile the source code using the g++ compiler. For example: g++ numerical_analysis.cpp -o numerical_analysis -std=c++0x Note: This program has not been tested on any platforms other than Windows and Ubuntu. fdist2 This is the fdist2 program from Beaumont & Nichols (1996). It is not mine and belongs to them, but I provide the version I used here so that all of my scripts can be used.