distribution-file

NAME

     distribution-file - letter frequency distribution file  for-
     mat used for gamma and p-value computation.

DESCRIPTION

     The frequency distribution file format is as follows:

          length
          A          a-prob
          C          c-prob
          G          g-prob
          T          t-prob
     Where length is the desired length of the simulated segment;
     a-prob is the probability of letter "A" occurring, c-prob is
     the probability of letter "C" occurring, and so forth.

     To give equal probability to  all  letters  occurring,  with
     sequence  lengths of 100 by 100, both files would be as fol-
     lows:
          100
          A        0.25
          C        0.25
          G        0.25
          T        0.25
     Of course, the probabilities should sum to 1.

SEE ALSO

     seqaln-intro(1), pvlocalS(1), mpvlocalS(1).