*************************************************************
**** ****
**** Output from PHASE v2.0 ****
**** Code by M Stephens, with contributions from N Li ****
**** ****
*************************************************************
BEGIN COMMAND_LINE
/usr/local/genome/lib/phase/PHASE2 -d1 casp6.phase.inp casp6.phase.out
END COMMAND_LINE
BEGIN OUTFILE_LIST
casp6.phase.out_freqs : haplotype frequency estimates
casp6.phase.out_pairs : most likely haplotype pairs for each individual
casp6.phase.out_recom : estimates of recombination parameters
casp6.phase.out_monitor : file for monitoring convergence
END OUTFILE_LIST
BEGIN INPUT_SUMMARY
Number of Individuals: 90
Number of Loci: 24
Positions of loci: 838 2149 2849 2965 3604 3634 3941 5954 6227 6755 7617 9083 9250 9849 11411 11412 12104 13035 13225 14564 15676 15971 16284 16803
END INPUT_SUMMARY
List of haplotypes found in best reconstruction, with counts.
(See file casp6.phase.out_freqs for haplotype population frequency estimates)
BEGIN LIST_SUMMARY
1 CAGGGATCCAACTGTCTACATGCC 1.000000
2 CAGGGATTCGATCATCTGTCCACC 1.000000
3 CAGGGACCCAACTGTCTACATGCC 1.000000
4 CAGGGACTCGATCATCTGTCCACC 11.000000
5 CAGGGACTCGATCATCCATCCACT 2.000000
6 GAGGGATCCAACTGCTCATCCACT 6.000000
7 GAGGGATCCAACTGCTCGTCCGCT 2.000000
8 GAGGGATCCAACTGTCTGTCCACT 3.000000
9 GAGGGACCCAACTGTCTATCCACT 1.000000
10 GAGGGACCCAACTGTCCACATGCC 1.000000
11 GAGGGACCCAACTGTCCATCCACT 42.000000
12 GAGGGACCCAACTGTCCGTCCACC 1.000000
13 GAGGGACCCAACTGTCCGTCCACT 3.000000
14 GAGGGACCCAACTGTCCGTCCATT 12.000000
15 GAGGGACCCGACTGTCCATCCACT 1.000000
16 GAGCGACCAAACTGTCTGTCCACT 1.000000
17 GAGCGACCCAACTGTCTGTCCACT 6.000000
18 GAGCGACCCAACTGTCCACATGCC 2.000000
19 GAGCGACCCAACTGTCCGTCCATT 3.000000
20 GAGCGACCCGATCATCTGTCCACC 1.000000
21 GGAGAGTCAAACTGCTTACATGCC 41.000000
22 GGAGAGTCAAACTGCTTATCCACT 3.000000
23 GGAGAGTCAAACTGCTTGTCCACC 1.000000
24 GGAGAGTCAAACTGCTTGTCCATT 8.000000
25 GGAGAGTCAAACTGTCCGTCCATT 1.000000
26 GGAGAGTCAAATCATCTGTCCACC 1.000000
27 GGAGAGTCAAGCTGCTTACATGCC 8.000000
28 GGAGAGTCAAGCTGCTTATCCACT 2.000000
29 GGAGAGTCAGACTGCTTACATGCC 1.000000
30 GGAGAGTCAGACTGTCCGTCCATT 1.000000
31 GGGGAATCCAACTGCTTATCTGCC 3.000000
32 GGGGGATCCAACTGCTTATCCACT 1.000000
33 GGGGGATCCAACTGCTTATCCGCT 2.000000
34 GGGGGATCCAACTGCTTATCTGCC 2.000000
35 GGGGGATCCAACTGCTCACATGCC 1.000000
36 GGGGGATCCAACTGCTCATCCACT 2.000000
37 GGGGGATCCAACTGTCTGTCCACT 1.000000
END LIST_SUMMARY
Summary of best reconstruction
(numbers refer to the list of haplotypes given above)
BEGIN BESTPAIRS_SUMMARY
P001: (2,21)
P002: (11,16)
P003: (19,36)
P004: (3,4)
P005: (5,21)
P006: (14,21)
P007: (14,17)
P008: (21,24)
P009: (11,14)
P010: (20,21)
P011: (31,31)
P012: (14,30)
P013: (11,24)
P014: (10,18)
P015: (11,15)
P016: (11,27)
P017: (11,35)
P018: (7,11)
P019: (11,21)
P020: (18,21)
P021: (6,7)
P022: (11,22)
P023: (11,21)
P024: (11,28)
P025: (4,17)
P026: (17,19)
P027: (11,21)
P028: (5,29)
P029: (4,4)
P030: (12,21)
P031: (11,11)
P032: (14,21)
P033: (21,21)
P034: (11,11)
P035: (24,27)
P036: (11,21)
P037: (14,27)
P038: (6,8)
P039: (11,24)
P040: (11,21)
P041: (19,21)
P042: (8,21)
P043: (11,21)
P044: (11,24)
P045: (11,21)
P046: (11,22)
P047: (11,11)
P048: (4,14)
P049: (4,21)
P050: (8,21)
P051: (11,11)
P052: (4,21)
P053: (21,21)
P054: (13,27)
P055: (17,24)
P056: (13,34)
P057: (31,36)
P058: (11,17)
P059: (11,24)
P060: (21,21)
P061: (14,34)
P062: (11,11)
P063: (11,21)
P064: (17,21)
P065: (6,23)
P066: (21,28)
P067: (11,21)
P068: (21,27)
P069: (21,27)
P070: (21,27)
P071: (11,33)
P072: (11,11)
P073: (13,32)
P074: (22,33)
P075: (11,21)
P076: (21,21)
P077: (11,21)
P078: (1,6)
P079: (21,21)
P080: (6,6)
P081: (11,21)
P082: (11,25)
P083: (11,21)
P084: (4,4)
P085: (4,11)
P086: (14,14)
P087: (9,37)
P088: (4,26)
P089: (14,14)
P090: (24,27)
END BESTPAIRS_SUMMARY
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []:
BEGIN BESTPAIRS1
0 P001
C A G G G A T T C G A T C A T C T G T C C A C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P002
G A G G G A C C (C) A A C T G T C C A T C C A C T
G A G [C] G A [C] C (A) A A C T G T C T G T C C A C T
0 P003
G (A) G C G A C C C A A C T G T C C G T C C A T T
G (G) G G G A T C C A A C T G C T C A T C C A C T
0 P004
C A G G G A C C C A A C T G T C T A C A T G C C
C A G G G A C T C G A T C A T C T G T C C A C C
0 P005
C A G G G A C T C G A T C A T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P006
G A G G G A C C C A A C T G T C C G T C C A T T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P007
G A G G G A C C C A A C T G T C C G T C C A T T
G A G C G A C C C A A C T G T C T G T C C A C T
0 P008
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T G T C C A T T
0 P009
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C G T C C A T T
0 P010
G A G C G A C C C G A T C A T C T G T C C A C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P011
G G G G A A T C C A A C T G C T T A T C T G C C
G G G G A A T C C A A C T G C T T A T C T G C C
0 P012
G A G G G A C C C (A) A C T G T C C G T C C A T T
G G A G A G T C A (G) A C T G T C C G T C C A T T
0 P013
G A G G G A C C C A A C T G T C C (A) T C C A (C) T
G G A G A G T C A A A C T G C T T (G) T C C A (T) T
0 P014
G A G G G A C C C A A C T G T C C A C A T G C C
G A G [C] G A C C C A A C T G T C C A C A T G C C
0 P015
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C G A C T G T C C A T C C A C T
0 P016
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A G C T G C T T A C A T G C C
0 P017
G A G G G A C C C A A C T G T C C A T C C A C T
G G G G G A T C C A A C T G C T C A C A T G C C
0 P018
G A G G G A T C C A A C T G C T C G T C C G C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P019
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P020
G A G C G A C C C A A C T G T C C A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P021
G A G G G A T C C A A C T G C T C A T C C A C T
G A G G G A T C C A A C T G C T C G T C C G C T
0 P022
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A T C C A C T
0 P023
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P024
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A G C T G C T T A T C C A C T
0 P025
C A G G G A C T C G A T C A T C T G T C C A C C
G A G C G A C C C A A C T G T C T G T C C A C T
0 P026
G A G C G A C C C A A C T G T C T G T C C A C T
G A G C G A C C C A A C T G T C C G T C C A T T
0 P027
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P028
C A G G G A C T C G A T C A T C C A T C C A C T
G G A G A G T C A G A C T G C T T A C A T G C C
0 P029
C A G G G A C T C G A T C A T C T G T C C A C C
C A G G G A C T C G A T C A T C T G T C C A C C
0 P030
G A G G G A C C C A A C T G T C C (G) (T) (C) (C) (A) C C
G G A G A G T C A A A C T G C T T (A) (C) (A) (T) (G) C C
0 P031
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P032
G A G G G A C C C A A C T G T C C G T C C A T T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P033
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P034
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P035
G G A G A G T C A A (A) C T G C T T G T C C A T T
G G A G A G T C A A (G) C T G C T T A C A T G C C
0 P036
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P037
G A G G G A C C C A A C T G T C C G T C C A T T
G G A G A G T C A A G C T G C T T A C A T G C C
0 P038
G A G G G A T C C A A C T G C T C A T C C A C T
G A G G G A T C C A A C T G T C T G T C C A C T
0 P039
G A G G G A C C C A A C T G T C C (A) T C C A (C) T
G G A G A G T C A A A C T G C T T (G) T C C A (T) T
0 P040
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P041
G A G C G A C C C A A C T G T C C (G) (T) (C) (C) (A) (T) (T)
G G A G A G T C A A A C T G C T T (A) (C) (A) (T) (G) (C) (C)
0 P042
G A G G G A T C C A A C T G T C T G T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P043
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P044
G A G G G A C C C A A C T G T C C (A) T C C A (C) T
G G A G A G T C A A A C T G C T T (G) T C C A (T) T
0 P045
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P046
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A T C C A C T
0 P047
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P048
C A G G G A C T C G A T C A T C T G T C C A C C
G A G G G A C C C A A C T G T C C G T C C A T T
0 P049
C A G G G A C T C G A T C A T C T G T C C A C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P050
G A G G G A T C C A A C T G T C T G T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P051
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P052
C A G G G A C T C G A T C A T C T G T C C A C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P053
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P054
G A G G G A C C C A A C T G T C C G T C C A C T
G G A G A G T C A A G C T G C T T A C A T G C C
0 P055
G A G C G A C C C A A C T G T C T G T C C A C T
G G A G A G T C A A A C T G C T T G T C C A T T
0 P056
G A G G G A C C C A A C T G T C C G T C C A C T
G G G G G A T C C A A C T G C T T A T C T G C C
0 P057
G G G G A A T C C A A C T G C T T A T C T G C C
G G G G G A T C C A A C T G C T [C] A T C C A C T
0 P058
G A G G G A C C C A A C T G T C C A T C C A C T
G A G C G A C C C A A C T G T C T G T C C A C T
0 P059
G A G G G A C C C A A C T G T C C (A) T C C A (C) T
G G A G A G T C A A A C T G C T T (G) T C C A (T) T
0 P060
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P061
G A G G G A C C C A A C T G T C C G T C C A T T
G G G G G A T C C A A C T G C T T A T C T G C C
0 P062
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P063
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P064
G A G C G A C C C A A C T G T C T G T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P065
G A G G G A T C C A A C T G C T C A T C C A C T
G G A G A G T C A A A C T G C T T G T C C A C C
0 P066
G G A G A G T C A A (A) C T G C T T A C A T G C C
G G A G A G T C A A (G) C T G C T T A T C C A C T
0 P067
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P068
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A G C T G C T T A C A T G C C
0 P069
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A G C T G C T T A C A T G C C
0 P070
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A G C T G C T T A C A T G C C
0 P071
G A G G G A C C C A A C T G T C C A T C C A C T
G G G G G A T C C A A C T G C T T A T C C G C T
0 P072
G A G G G A C C C A A C T G T C C A T C C A C T
G A G G G A C C C A A C T G T C C A T C C A C T
0 P073
G (A) G G G A C C C A A C T G T C (C) (G) T C C A C T
G (G) G G G A T C C A A C T G C T (T) (A) T C C A C T
0 P074
G G A G A G T C A A A C T G C T T A T C C A C T
G G G G G A T C C A A C T G C T T A T C C G C T
0 P075
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P076
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P077
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P078
(C) A G G G A T C C A A C T G T C T A C A T G C C
(G) A G G G A T C C A A C T G C T C A T C C A C T
0 P079
G G A G A G T C A A A C T G C T T A C A T G C C
G G A G A G T C A A A C T G C T T A C A T G C C
0 P080
G A G G G A T C C A A C T G C T C A T C C A C T
G A G G G A T C C A A C T G C T C A T C C A C T
0 P081
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P082
G A G G G A C C C A A C T G T C C (A) T C C A (C) T
G G A G A G T C A A A C T G T C C (G) T C C A (T) T
0 P083
G A G G G A C C C A A C T G T C C A T C C A C T
G G A G A G T C A A A C T G C T T A C A T G C C
0 P084
C A G G G A C T C G A T C A T C T G T C C A C C
C A G G G A C T C G A T C A T C T G T C C A C C
0 P085
C A G G G A C T C G A T C A T C T G T C C A C C
G A G G G A C C C A A C T G T C C A T C C A C T
0 P086
G A G G G A C C C A A C T G T C C G T C C A T T
G A G G G A C C C A A C T G T C C G T C C A T T
0 P087
G (A) G G G A (C) C C A A C T G T C T A T C C A C T
G (G) G G G A (T) C C A A C T G T C T G T C C A C T
0 P088
C A G G G A C T C G A T C A T C T G T C C A C C
G G A G A G T C A [A] A T C A T C T G T C C A C C
0 P089
G A G G G A C C C A A C T G T C C G T C C A T T
G A G G G A C C C A A C T G T C C G T C C A T T
0 P090
G G A G A G T C A A (A) C T G C T T G T C C A T T
G G A G A G T C A A (G) C T G C T T A C A T G C C
END BESTPAIRS1
Haplotype estimates for each individual, with uncertain phases enclosed in ()
and uncertain genotypes enclosed in []
with phase known positions indicated by =
BEGIN BESTPAIRS2
0 P001
C ? G = G A = ? C G = T C ? T C = G T ? C A = =
G ? A = A G = ? A A = C T ? C T = A C ? T G = =
0 P002
= ? ? ? = ? ? = (C) = = = ? ? = = C A = = = = = =
= ? ? ? = ? ? = (A) = = = ? ? = = T G = = = = = =
0 P003
= (A) = C = = C ? = = = = = = T C = G = = = = T =
= (G) = G = = T ? = = = = = = C T = A = = = = C =
0 P004
= = = = = = = C = A = C T G = = = A C A T G = =
= = = = = = = T = G = T C A = = = G T C C A = =
0 P005
C A G = G A C T C G = T C A T C C = T C C A = T
G G A = A G T C A A = C T G C T T = C A T G = C
0 P006
= A G = G A C = C = = = = = T C C G T C C A T T
= G A = A G T = A = = = = = C T T A C A T G C C
0 P007
= = = G = = = = = = = = = = = = C = = = = = T =
= = = C = = = = = = = = = = = = T = = = = = C =
0 P008
? = = = = = = = = = = = = = = = = A C A T G C C
? = = = = = = = = = = = = = = = = G T C C A T T
0 P009
= = = = = = = = = = = = = = = = = A = = = = C =
= = = = = = = = = = = = = = = = = G = = = = T =
0 P010
= ? G C G A C = C G ? T C A T C = G T ? C A = =
= ? A G A G T = A A ? C T G C T = A C ? T G = =
0 P011
= = = = = = = = = = = = = = = = ? = = = = = = =
= = = = = = = = = = = = = = = = ? = = = = = = =
0 P012
= ? G = G A C = C (A) = = = = = = = = = = = = = =
= ? A = A G T = A (G) = = = = = = = = = = = = = =
0 P013
= A G = G A C = C = = = = = T C C (A) = = = = (C) =
= G A = A G T = A = = = = = C T T (G) = = = = (T) =
0 P014
= = ? ? = = = = = ? = = = = = = = = = ? = = = =
= = ? ? = = = = = ? = = = = = = = = = ? = = = =
0 P015
= = = = = = = = = A = ? = = = = = = = = = = = =
= = = = = = = = = G = ? = = = = = = = = = = = =
0 P016
= A G = G A C = C = A ? = = T C C = T C C A = T
= G A = A G T = A = G ? = = C T T = C A T G = C
0 P017
= A ? ? = = C ? = = = = = ? T C = = T C C A = T
= G ? ? = = T ? = = = = = ? C T = = C A T G = C
0 P018
= = = = = = T = = = = = = = C T = G = = = G = =
= = = = = = C = = = = = = = T C = A = = = A = =
0 P019
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P020
= A G C G A C = C = = = = = ? ? C = = = ? = = =
= G A G A G T = A = = = = = ? ? T = = = ? = = =
0 P021
= = = = = = = = = = = = = = = = ? A = = = A = =
= = = = = = = = = = = = = = = = ? G = = = G = =
0 P022
= A G = G A C = C = = = = = T C C = = = = = = =
= G A = A G T = A = = = = = C T T = = = = = = =
0 P023
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P024
= A G = G A C = C = A ? = = T C C = = = = = = =
= G A = A G T = A = G ? = = C T T = = = = = = =
0 P025
? = = G = = = ? = G = T C A = = = = = = = = = C
? = = C = = = ? = A = C T G = = = = = = = = = T
0 P026
= = = = = = = = = = = ? = = = = T = = = = = C =
= = = = = = = = = = = ? = = = = C = = = = = T =
0 P027
= A G = G A C = C = = = = = ? ? C = T C C A = T
= G A = A G T = A = = = = = ? ? T = C A T G = C
0 P028
C A G = G A C T C = = T C A T C C = T C C A = T
G G A = A G T C A = = C T G C T T = C A T G = C
0 P029
= = ? ? = = = ? = ? = = = = = = = = = = = = = =
= = ? ? = = = ? = ? = = = = = = = = = = = = = =
0 P030
= A G = G A C = C = = = = = T C C (G) (T) (C) (C) (A) = =
= G A = A G T = A = = = = = C T T (A) (C) (A) (T) (G) = =
0 P031
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P032
= A G = G A C = C = = = = = T C C G T C C A T T
= G A = A G T = A = = = = = C T T A C A T G C C
0 P033
= = = = = = = = = ? = = = = = = = = = = = = = =
= = = = = = = = = ? = = = = = = = = = = = = = =
0 P034
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P035
= = = = = = = = = = (A) = = = = = = G T C C A T T
= = = = = = = = = = (G) = = = = = = A C A T G C C
0 P036
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P037
= ? G ? G A C = C ? A = = = ? ? C G T C C A T T
= ? A ? A G T = A ? G = = = ? ? T A C A T G C C
0 P038
= = = = = = = = = = = = = = C T C A = = = = = =
= = = = = = = = = = = = = = T C T G = = = = = =
0 P039
= A G = G A C = C = = = = = T C C (A) = = = = (C) =
= G A = A G T = A = = = = = C T T (G) = = = = (T) =
0 P040
? A G = G A C = C = = = = = T C C = T C C A = T
? G A = A G T = A = = = = = C T T = C A T G = C
0 P041
= A G C G A C = C = = = = = T C C (G) (T) (C) (C) (A) (T) (T)
= G A G A G T = A = = = = = C T T (A) (C) (A) (T) (G) (C) (C)
0 P042
? ? ? ? G A = = C = = = = = T C = G T C C A = T
? ? ? ? A G = = A = = = = = C T = A C A T G = C
0 P043
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P044
= A G = G A C = C = = = = = T C C (A) = = = = (C) =
= G A = A G T = A = = = = = C T T (G) = = = = (T) =
0 P045
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P046
= ? G = G A C = C = = = = = T C C = = = = = = =
= ? A = A G T = A = = = = = C T T = = = = = = =
0 P047
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P048
C = = ? = = = T = G = T C A = = T = = = = = C C
G = = ? = = = C = A = C T G = = C = = = = = T T
0 P049
C ? G ? G A C T C G = T C A T C = G T C C A = ?
G ? A ? A G T C A A = C T G C T = A C A T G = ?
0 P050
= A G = G A = = C = = = = = T C = G T C C A = T
= G A = A G = = A = = = = = C T = A C A T G = C
0 P051
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P052
C A G = G A C T C G = T C A T C = G T C C A = =
G G A = A G T C A A = C T G C T = A C A T G = =
0 P053
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P054
= A ? ? G A C = C = A = = = T C C G T C C A = T
= G ? ? A G T = A = G = = = C T T A C A T G = C
0 P055
= A G C G A C = C = = = = = T C = = = = = = C =
= G A G A G T = A = = = = = C T = = = = = = T =
0 P056
= A = = = = ? ? = = = = = = T C C G = = C A = T
= G = = = = ? ? = = = = = = C T T A = = T G = C
0 P057
= = = = A = = ? = = = = = = = = ? = = = T G = C
= = = = G = = ? = = = = = = = = ? = = = C A = T
0 P058
= = = G = = = = = = = = = = = = C A = = = = = =
= = = C = = = = = = = = = = = = T G = = = = = =
0 P059
= A G = G A C = C = = = = = T C C (A) = ? = = (C) =
= G A = A G T = A = = = = = C T T (G) = ? = = (T) =
0 P060
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P061
= A = = = = C ? = = = = = = T C C ? ? = C A T T
= G = = = = T ? = = = = = = C T T ? ? = T G C C
0 P062
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P063
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P064
= A G C G A C = C = = = = = T C = G T C C A = T
= G A G A G T = A = = = = = C T = A C A T G = C
0 P065
= A G = G A = = C = = = = = = = C A = = = = = T
= G A = A G = = A = = = = = = = T G = = = = = C
0 P066
= = = = = = = = = = (A) = = = = = = = C A T G = C
= = = = = = = = = = (G) = = = = = = = T C C A = T
0 P067
= A G = G A C = C = ? = = = T C C = T C C A = T
= G A = A G T = A = ? = = = C T T = C A T G = C
0 P068
= = = = = = = = = = A = = = = = = = = = = = = =
= = = = = = = = = = G = = = = = = = = = = = = =
0 P069
= = = = = = = = = = A = = = = = = = = = = = = =
= = = = = = = = = = G = = = = = = = = = = = = =
0 P070
= = = = = = = = = = A = = = = = = = = = = = = =
= = = = = = = = = = G = = = = = = = = = = = = =
0 P071
= A = = = = C = = = = ? = = T C C = = = = A = =
= G = = = = T = = = = ? = = C T T = = = = G = =
0 P072
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P073
= (A) = = = = C = = = = = = = T C (C) (G) = = = = = =
= (G) = = = = T = = = = = = = C T (T) (A) = = = = = =
0 P074
= = A = A G = ? A = = = = = = = = = = = = A = =
= = G = G A = ? C = = = = = = = = = = = = G = =
0 P075
= A G = G A C = C = = = = = T C C = T C C A = T
= G A = A G T = A = = = = = C T T = C A T G = C
0 P076
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P077
= A G = G A C = C = = = = ? T C C = T C C A = T
= G A = A G T = A = = = = ? C T T = C A T G = C
0 P078
(C) = = = = = = = = = = = = = T C T = C A T G = C
(G) = = = = = = = = = = = = = C T C = T C C A = T
0 P079
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
0 P080
= = = = ? ? = = = = = = = = = = = = = = = = = =
= = = = ? ? = = = = = = = = = = = = = = = = = =
0 P081
? A G = G A C = C = = = = = T C C = T C C A = T
? G A = A G T = A = = = = = C T T = C A T G = C
0 P082
= A G = G A C = C = = = = = = = = (A) = = = = (C) =
= G A = A G T = A = = = = = = = = (G) = = = = (T) =
0 P083
= A G = G A ? = C = = = = = T C C = T C C A = T
= G A = A G ? = A = = = = = C T T = C A T G = C
0 P084
= = = = = = = ? = = = = = = = = = = = = = = = =
= = = = = = = ? = = = = = = = = = = = = = = = =
0 P085
C = = = = = = T = G = T C A = = T G = = = = = C
G = = = = = = C = A = C T G = = C A = = = = = T
0 P086
= = = = = = = = = = = = = = = = = = = ? = = = =
= = = = = = = = = = = = = = = = = = = ? = = = =
0 P087
= (A) = = = = (C) ? = = = = = = = = = A = = = = = =
= (G) = = = = (T) ? = = = = = = = = = G = = = = = =
0 P088
? A G = G A C T C ? = = = = = = = = = = = = = =
? G A = A G T C A ? = = = = = = = = = = = = = =
0 P089
? = = = = = = = = = = = = = = = = = = = = = = =
? = = = = = = = = = = = = = = = = = = = = = = =
0 P090
? = = = = = = = = = (A) = = = = = = G T C C A T T
? = = = = = = = = = (G) = = = = = = A C A T G C C
END BESTPAIRS2
Phase probabilities at each site
with phase known positions indicated by =
and missing data positions indicated by ?
BEGIN PHASEPROBS
1.00 ? 1.00 = 1.00 1.00 = ? 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 = =
= ? ? ? = ? ? = 0.52 = = = ? ? = = 1.00 1.00 = = = = = =
= 0.85 = 0.95 = = 1.00 ? = = = = = = 1.00 1.00 = 0.97 = = = = 0.97 =
= = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 = =
1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.96 0.96 0.96 0.96 0.96 0.96 0.96
= = = 0.97 = = = = = = = = = = = = 1.00 = = = = = 1.00 =
? = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00
= = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 =
= ? 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 1.00 = =
= = = = = = = = = = = = = = = = ? = = = = = = =
= ? 1.00 = 1.00 1.00 1.00 = 1.00 0.73 = = = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.78 = = = = 0.78 =
= = ? ? = = = = = ? = = = = = = = = = ? = = = =
= = = = = = = = = 1.00 = ? = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 0.99 ? = = 1.00 1.00 1.00 = 0.98 0.98 0.98 0.98 = 0.98
= 0.92 ? ? = = 0.99 ? = = = = = ? 0.99 0.99 = = 1.00 1.00 1.00 1.00 = 1.00
= = = = = = 1.00 = = = = = = = 1.00 1.00 = 0.99 = = = 0.99 = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = ? ? 1.00 = = = ? = = =
= = = = = = = = = = = = = = = = ? 1.00 = = = 1.00 = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 0.98 ? = = 1.00 1.00 1.00 = = = = = = =
? = = 0.99 = = = ? = 1.00 = 1.00 1.00 1.00 = = = = = = = = = 1.00
= = = = = = = = = = = ? = = = = 1.00 = = = = = 1.00 =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = ? ? 1.00 = 0.99 0.99 0.99 0.99 = 0.99
1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00
= = ? ? = = = ? = ? = = = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.77 0.77 0.77 0.77 0.77 = =
= = = = = = = = = = = = = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.96 0.96 0.96 0.96 0.96 0.96 0.96
= = = = = = = = = ? = = = = = = = = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = = = = = = = 0.83 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= ? 1.00 ? 1.00 1.00 1.00 = 1.00 ? 1.00 = = = ? ? 1.00 0.98 0.98 0.98 0.98 0.98 0.98 0.98
= = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.78 = = = = 0.78 =
? 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 0.99 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.89 0.89 0.89 0.89 0.89 0.89 0.89
? ? ? ? 1.00 1.00 = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.78 = = = = 0.78 =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= ? 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = = = = = = =
= = = = = = = = = = = = = = = = = = = = = = = =
1.00 = = ? = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = = 1.00 1.00
1.00 ? 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = ?
= 1.00 1.00 = 1.00 1.00 = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00
= = = = = = = = = = = = = = = = = = = = = = = =
1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = =
= = = = = = = = = = = = = = = = = = = = = = = =
= 1.00 ? ? 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 0.95 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = = = = = 1.00 =
= 0.98 = = = = ? ? = = = = = = 0.99 0.99 0.96 0.99 = = 0.99 0.99 = 0.99
= = = = 0.95 = = ? = = = = = = = = ? = = = 1.00 1.00 = 1.00
= = = 1.00 = = = = = = = = = = = = 1.00 1.00 = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 0.78 = ? = = 0.78 =
= = = = = = = = = = = = = = = = = = = = = = = =
= 1.00 = = = = 1.00 ? = = = = = = 1.00 1.00 1.00 ? ? = 1.00 1.00 1.00 1.00
= = = = = = = = = = = = = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00
= 1.00 1.00 = 1.00 1.00 = = 1.00 = = = = = = = 1.00 0.90 = = = = = 0.90
= = = = = = = = = = 0.54 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = ? = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= = = = = = = = = = 1.00 = = = = = = = = = = = = =
= = = = = = = = = = 1.00 = = = = = = = = = = = = =
= = = = = = = = = = 1.00 = = = = = = = = = = = = =
= 1.00 = = = = 1.00 = = = = ? = = 1.00 1.00 1.00 = = = = 1.00 = =
= = = = = = = = = = = = = = = = = = = = = = = =
= 0.85 = = = = 1.00 = = = = = = = 0.96 0.96 0.65 0.63 = = = = = =
= = 1.00 = 1.00 1.00 = ? 1.00 = = = = = = = = = = = = 1.00 = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= = = = = = = = = = = = = = = = = = = = = = = =
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = ? 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
0.84 = = = = = = = = = = = = = 0.92 0.92 0.95 = 1.00 1.00 1.00 1.00 = 1.00
= = = = = = = = = = = = = = = = = = = = = = = =
= = = = ? ? = = = = = = = = = = = = = = = = = =
? 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = 0.62 = = = = 0.62 =
= 1.00 1.00 = 1.00 1.00 ? = 1.00 = = = = = 1.00 1.00 1.00 = 0.99 0.99 0.99 0.99 = 0.99
= = = = = = = ? = = = = = = = = = = = = = = = =
1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = = = = = 1.00
= = = = = = = = = = = = = = = = = = = ? = = = =
= 0.70 = = = = 0.86 ? = = = = = = = = = 0.90 = = = = = =
? 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? = = = = = = = = = = = = = =
? = = = = = = = = = = = = = = = = = = = = = = =
? = = = = = = = = = 0.83 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00
END PHASEPROBS