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      Summary:  Rate Classes is a result processing tool which displays information about rate classes for models with rate heterogeneity.

     Options/Output/Examples. There are several possible ways of showing rate variation information:

  • Class Assignment 1: display discrete distribution of the rate multiplier and most likely (in the sense of largest marginal likelihood) rates at each site.
    Sample mean = 1   (sample variance = 0.822552)
    
    Rate[0]=  0.11142890 (weight=0.2500000)
    Rate[1]=  0.43573211 (weight=0.2500000)
    Rate[2]=  0.97579352 (weight=0.2500000)
    Rate[3]=  2.47704547 (weight=0.2500000)
    
    Class Assignments:
    
    
    0   0   3   3   1   1   0   0   1   2   3   1   1   0   2   1   3   0   
    1   3   1   3   1   1   1   3   0   0   0   3   0   3   0   1   3   0   
    2   3   2   1   3   3   0   2   0   2   1   1   0   1 
    
  • Class Assignment 2: display discrete distribution of the rate multiplier and most likely (in the sense of largest marginal likelihood) rates at each site, with sites grouped by rate class, with site indices beginning at 1.
    Sample mean = 1   (sample variance = 0.822552)
    
    Rate[0]=  0.11142890 (weight=0.2500000)
    Rate[1]=  0.43573211 (weight=0.2500000)
    Rate[2]=  0.97579352 (weight=0.2500000)
    Rate[3]=  2.47704547 (weight=0.2500000)
    
    Rate Class 0
    	1    2    7    8   14   18   27   28   29   31   33   36   43   45   49
    
    Rate Class 1
    	5    6    9   12   13   16   19   21   23   24   25   34   40   47   48   50
    
    Rate Class 2
       10   15   37   39   44   46
    
    Rate Class 3
    
    	3    4   11   17   20   22   26   30   32   35   38   41   42
    		
  • Complete: Write 2 matrices to the file of user's choosing. The first matrix has dimension NxK, where N is the number of rate classes and K is the number of sites in the data file. The entry at position (i,j) is the conditional likelihood of site j, given that the rate class is i. The second matrix has dimension 1xK, and simply lists the most likely (max. conditional likelihood) rate class for that site. Both matrices can be imported as comma separated files, or manipulated by custom batch files.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002