Legofit
infers population history from nucleotide site patterns.

Read a list of .raf files and write derived allele frequencies.

Rafdaf: read .raf files and write derived allele frequencies

Rafdaf reads multiple .raf files, the last of which must be an outgroup, which is used to call ancestral alleles. It writes several columns to standard output. The first output column is "chr", a character string representing the chromosome; the second is "pos", an integer representing the nucleotide position along the chromosome. The remaining columns give derived allele frequencies of the files listed on the command line. The outgroup (which must appear last on the command line) is not included in the output.

Usage

Usage: rafdaf [options] <x>=<in_1> <y>=<in_2> ... outgroup=<in_K>
   where <x> and <y> are arbitrary labels, and <in_i> are input
   files in raf format. Labels may not include the character ":".
   Final label must be "outgroup". Writes to standard output.

   If input file name ends with .gz, input is decompressed using
   gunzip.

Options may include:
   --version
      Print version and exit
   -h or --help
      Print this message