** Mx startup successful **
  
   **MX-OSF version 1.49**
 ! Script to estimate haplotype frequencies
 
 
 The following MX script lines were read for group  1
 
 #NGROUPS 2
  Note: #NGroup set number of groups to           2
  
 TITLE ESTIMATE FREQS
 DATA NI=1
 BEGIN MATRICES;
 I UNIT 1 1
 T FULL 1 1
 W FULL 3 4
 O FULL 3 3 ! OBSERVED GENOTYPE FREQS
 H FULL 2 2 FREE ! HAPLOTYPE FREQS
 END MATRICES;
 MATRIX O ! OBSERVED FREQS
 10 15 5
 10 50 13
 3 13 10
 MATRIX T 2
 MATRIX W
 1 0 0 0
 0 1 1 0
 0 0 0 1
 BEGIN ALGEBRA;
 A = H@H;
 E = W&A;
 END ALGEBRA;
 MATRIX H .25 .25 .25 .25
 BOUND 0 1 H 1 1 TO H 2 2
 COMPUTE -T. \SUM(O.\LN(E));
 OPTION USER
 END GROUP
 
 
 The following MX script lines were read for group  2
 
 CONSTRAIN HAPLOTYPE FREQS TO SUM TO 1
 CONSTRAINT
 BEGIN MATRICES = GROUP 1;
 END MATRICES;
 CONSTRAIN I=\SUM(H);
 OPTION RS
  *** WARNING! ***
  End of input file but End statement missing!
  End statement automatically added... 
  
  
  PARAMETER SPECIFICATIONS
  
  GROUP NUMBER:           1
  
Title estimate freqs                                                                                                            
  
  MATRIX A
 This is a computed FULL matrix of order    4 by    4
  It has no free parameters specified
  
  MATRIX E
 This is a computed FULL matrix of order    3 by    3
  It has no free parameters specified
  
  MATRIX H
 This is a FULL matrix of order    2 by    2
    1 2
 1  1 2
 2  3 4
  
  MATRIX I
 This is a UNIT matrix of order    1 by    1
  
  MATRIX O
 This is a FULL matrix of order    3 by    3
  It has no free parameters specified
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
  It has no free parameters specified
  
  MATRIX W
 This is a FULL matrix of order    3 by    4
  It has no free parameters specified
  
  GROUP NUMBER:           2
  
Constrain haplotype freqs to sum to 1                                                                                           
  
  MATRIX A
 This is a computed FULL matrix of order    4 by    4
  It has no free parameters specified
  
  MATRIX E
 This is a computed FULL matrix of order    3 by    3
  It has no free parameters specified
  
  MATRIX H
 This is a FULL matrix of order    2 by    2
    1 2
 1  1 2
 2  3 4
  
  MATRIX I
 This is a UNIT matrix of order    1 by    1
  
  MATRIX O
 This is a FULL matrix of order    3 by    3
  It has no free parameters specified
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
  It has no free parameters specified
  
  MATRIX W
 This is a FULL matrix of order    3 by    4
  It has no free parameters specified
  
  
  
  
  MX PARAMETER ESTIMATES
  
  GROUP NUMBER:           1
  
Title estimate freqs                                                                                                            
  
  MATRIX A
 This is a computed FULL matrix of order    4 by    4
  [=H@H]
          1       2       3       4
 1   0.1074  0.0615  0.0615  0.0353
 2   0.0501  0.1087  0.0287  0.0623
 3   0.0501  0.0287  0.1087  0.0623
 4   0.0234  0.0507  0.0507  0.1099
  
  MATRIX E
 This is a computed FULL matrix of order    3 by    3
  [=W&A]
          1       2       3
 1   0.1074  0.1231  0.0353
 2   0.1002  0.2748  0.1245
 3   0.0234  0.1014  0.1099
  
  MATRIX H
 This is a FULL matrix of order    2 by    2
          1       2
 1   0.3277  0.1878
 2   0.1529  0.3316
  
  MATRIX I
 This is a UNIT matrix of order    1 by    1
  
  MATRIX O
 This is a FULL matrix of order    3 by    3
             1          2          3
 1     10.0000    15.0000     5.0000
 2     10.0000    50.0000    13.0000
 3      3.0000    13.0000    10.0000
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
             1
 1      2.0000
  
  MATRIX W
 This is a FULL matrix of order    3 by    4
          1       2       3       4
 1   1.0000  0.0000  0.0000  0.0000
 2   0.0000  1.0000  1.0000  0.0000
 3   0.0000  0.0000  0.0000  1.0000
  
  GROUP NUMBER:           2
  
Constrain haplotype freqs to sum to 1                                                                                           
  
  MATRIX A
 This is a computed FULL matrix of order    4 by    4
  [=H@H]
          1       2       3       4
 1   0.1074  0.0615  0.0615  0.0353
 2   0.0501  0.1087  0.0287  0.0623
 3   0.0501  0.0287  0.1087  0.0623
 4   0.0234  0.0507  0.0507  0.1099
  
  MATRIX E
 This is a computed FULL matrix of order    3 by    3
  [=W&A]
          1       2       3
 1   0.1074  0.1231  0.0353
 2   0.1002  0.2748  0.1245
 3   0.0234  0.1014  0.1099
  
  MATRIX H
 This is a FULL matrix of order    2 by    2
          1       2
 1   0.3277  0.1878
 2   0.1529  0.3316
  
  MATRIX I
 This is a UNIT matrix of order    1 by    1
  
  MATRIX O
 This is a FULL matrix of order    3 by    3
             1          2          3
 1     10.0000    15.0000     5.0000
 2     10.0000    50.0000    13.0000
 3      3.0000    13.0000    10.0000
  
  MATRIX T
 This is a FULL matrix of order    1 by    1
             1
 1      2.0000
  
  MATRIX W
 This is a FULL matrix of order    3 by    4
          1       2       3       4
 1   1.0000  0.0000  0.0000  0.0000
 2   0.0000  1.0000  1.0000  0.0000
 3   0.0000  0.0000  0.0000  1.0000
  
  CONSTRAINT VALUES (should be near zero)
               1
 1   -3.5226E-06
  
 Your model has    4 estimated parameters and      1 Observed statistics
 Observed statistics include   1 constraints.
  
 User defined function value =   496.469
 'Degrees of freedom' >>>>>>>>>>>>>>>>        -3
  
 This problem used  0.0% of my workspace
  
 Task                     Time elapsed (DD:HH:MM:SS)
 Reading script & data      0: 0: 0: 0.01
 Execution                  0: 0: 0: 0.02
 TOTAL                      0: 0: 0: 0.03
  
 Total number of warnings issued:           1
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