  ==========================================================
    Example: sequence data set wit two loci [simulated data]
  ==========================================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  ==========================================================
  Version debug 2.5.1

  Program started at Fri Jul  4 17:34:40 2008
                                                   


Options in use:
---------------

Analysis strategy is                          Maximum likelihood



Datatype: DNA sequence data

Pseudo-random number generator: Mersenne-Twister                                
Random number seed (with internal timer)            307248403

Start parameters:
   First genealogy was started using a UPGMA-tree
   Theta values were generated  from an FST-calculation
   M values were generated from the FST-calculation

Migration model:
   Migration matrix model with variable Theta  

Mutation rate is constant for all loci

Markov chain settings:
   Short chains (short-chains):                           10
      Trees sampled (short-inc*samples):               10000
      Trees recorded (short-sample):                     500
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):               100000
      Trees recorded (long-sample):                     5000
   Averaging over long chains
   Number of discard trees per chain:                  10000
   Parameter-likelihood epsilon:                   100.00000

Print options:
   Data file:                                         infile
   Output file (ASCII text):                         outfile
   Output file (PDF):                            outfile.pdf
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No                                            
   Profile likelihood: Yes, tables and summary             
             Fast method
             with df=1 and for Theta and M=m/mu




Summary of data:
Title:   Example: sequence data set wit two loci [simulated data]
Datatype:                                       Sequence data
Number of loci:                                             2

Population                                    Locus  Gene copies
----------------------------------------------------------------
  1 Africa_                                      1     25
                                                 2     25
  2 Americas_                                    1     25
                                                 2     25
  3 Pacific_                                     1     25
                                                 2     25
  4 Asia_                                        1     25
                                                 2     25
Total of all populations                         1    100
                                                 2    100

