List of haplotypes found in best reconstruction,
with frequencies in parentheses.

1: C A A G T G C G G A G G C C (11)
2: C G T G G A A G C A G T T C (13)
3: C A A G G G C G G A G G C C (11)
4: C A A G T G C G G A T G C C (3)
5: C G A G G A A G G A G T T C (4)
6: C G T G G A A G G A G T T C (2)
7: C G A G G A C G G A G G C C (1)
8: C G T G G A A G C A G G T C (1)


Summary of best reconstruction
(numbers refer to the list of haplotypes given above)

E001: (1,1)
E002: (2,2)
E003: (2,2)
E004: (1,1)
E005: (3,3)
E006: (3,3)
E007: (3,3)
E008: (1,1)
E009: (4,4)
E010: (2,2)
E011: (1,1)
E012: (2,2)
E013: (2,5)
E014: (6,2)
E015: (5,7)
E016: (1,1)
E017: (3,3)
E018: (6,2)
E019: (5,3)
E020: (8,1)
E021: (4,5)
E022: (2,3)
E023: (2,3)


Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:

E001
C A A G T G C G G A G G C C 
C A A G T G C G G A G G C C 
E002
C G T G G A A G C A G T T C 
C G T G G A A G C A G T T C 
E003
C G T G G A A G C A G T T C 
C G T G G A A G C A G T T C 
E004
C A A G T G C G G A G G C C 
C A A G T G C G G A G G C C 
E005
C A A G G G C G G A G G C C 
C A A G G G C G G A G G C C 
E006
C A A G G G C G G A G G C C 
C A A G G G C G G A G G C C 
E007
C A A G G G C G G A G G C C 
C A A G G G C G G A G G C C 
E008
C A A G T G C G G A G G C C 
C A A G T G C G G A G G C C 
E009
C A A G T G C G G A T G C C 
C A A G T G C G G A T G C C 
E010
C G T G G A A G C A G T T C 
C G T G G A A G C A G T T C 
E011
C A A G T G C G G A G G C C 
C A A G T G C G G A G G C C 
E012
C G T G G A A G C A G T T C 
C G T G G A A G C A G T T C 
E013
C G T G G A A G C A G T T C 
C G A G G A A G G A G T T C 
E014
C G T G G A A G G A G T T C 
C G T G G A A G C A G T T C 
E015
C G A G G A A G G A G T T C 
C G A G G A C G G A G G C C 
E016
C A A G T G C G G A G G C C 
C A A G T G C G G A G G C C 
E017
C A A G G G C G G A G G C C 
C A A G G G C G G A G G C C 
E018
C G T G G A A G G A G T T C 
C G T G G A A G C A G T T C 
E019
C G A G G A A G G A G T T C 
C A A G G G C G G A G G C C 
E020
C G T G G A A G C A G G T C 
C A A G T G C G G A G G C C 
E021
C A A G T G C G G A T G C C 
C G A G G A A G G A G T T C 
E022
C G T G G A A G C A G T T C 
C A A G G G C G G A G G C C 
E023
C G T G G A A G C A G T T C 
C A A G G G C G G A G G C C 



Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []
with phase known positions indicated by =

E001
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E002
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E003
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E004
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E005
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E006
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E007
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E008
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E009
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E010
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E011
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E012
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E013
= = T = = = = = C = = = = = 
= = A = = = = = G = = = = = 
E014
= = = = = = = = G = = = = ? 
= = = = = = = = C = = = = ? 
E015
= = = = = = A = = = = T T = 
= = = = = = C = = = = G C = 
E016
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E017
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
E018
= = = = = = = = G = = = = = 
= = = = = = = = C = = = = = 
E019
= G = = = A A = = = = T T = 
= A = = = G C = = = = G C = 
E020
= G T = G A A = C = = = T = 
= A A = T G C = G = = = C = 
E021
= A = = T G C = = = T G C = 
= G = = G A A = = = G T T = 
E022
? G ? = = A A = C = = T ? ? 
? A ? = = G C = G = = G ? ? 
E023
= G T = = A A = C = = T T = 
= A A = = G C = G = = G C = 



Phase probabilities at each site
with phase known positions indicated by =
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = 0.99 = = = = = 1 = = = = = 
= = = = = = = = 1 = = = = = 
= = = = = = 1 = = = = 1 1 = 
= = = = = = = = = = = = = = 
= = = = = = = = = = = = = = 
= = = = = = = = 1 = = = = = 
= 1 = = = 1 1 = = = = 1 1 = 
= 1 1 = 0.99 1 1 = 1 = = = 1 = 
= 1 = = 1 1 1 = = = 0.97 1 1 = 
= 1 = = = 1 1 = 0.99 = = 1 = = 
= 1 1 = = 1 1 = 1 = = 1 1 =