spflanagan/fst_outliers: fhetboot v1.0

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_1.0.zip fhetboot_1.0.tar.gz fhetboot-manual.pdf

Please see the vignette for instructions on how to use fhetboot.

scripts.tar.gz All of these scripts run the other programs.

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).

• 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

• 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)

-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

• 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.

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.

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

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.

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.