Legofit
infers population history from nucleotide site patterns.

Compare two sets of site-pattern counts or frequencies

diverg.py: compare two sets of site-pattern counts or frequencies

This program compares two sets of site-pattern counts or frequencies and summarizes the difference between them using the Kullback-Leibler divergence.

usage: diverg.py inputfile1 [inputfile2]
       Input file name "-" means standard input.
       At most one input may be "-".

Each input file should look like:

# SitePat           Count
      x:y          227852
      x:n             663
      y:n           17410

Here, the first line is an optional comment, which is used to label the columns. The first column contains site-pattern labels, which consist of population labels separated by colons. The second column contains the contribution of each site pattern. These need not be integers. They will be normalized in the output so that they sum to unity.

This input format is also the output format of the program legosim. This makes it possible to pipe legosim output into diverg.py. For example, suppose we have a file called "input.lgo" in lgo format, and a file called "sitepat.txt" containing observed site-pattern counts such as those above. Then the command

legosim -i 1000 input.lgo | diverg.py sitepat.txt -

would compare the data in sitepat.txt to the output of the legosim command. This would produce something like the following:

SitePat sitepat.txt         -     KL
    x:y     0.92651   0.87006 -0.055 *
    x:n     0.00270   0.00671  0.006
    y:n     0.07079   0.12323  0.068 *
                               0.019732

The "sitepat.txt" column contains the data from file sitepat.txt, re-expressed as relative frequencies. The "-" column summarizes the legosim output in the same fashion. The KL column lists contributions to the Kulback-Leiebler (KL) divergence. When these contributions are small, they are approximately equal to the difference between columns 3 and 2. Large KL contributions are marked with an asterisk. The bottom entry in this column is the KL divergence, a measure of the discrepancy between the two frequency distributions.