************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 pltpt.phase.inp pltpt.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST pltpt.phase.out_freqs : haplotype frequency estimates pltpt.phase.out_pairs : most likely haplotype pairs for each individual pltpt.phase.out_recom : estimates of recombination parameters pltpt.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 37 Positions of loci: 244 1240 1278 1977 1979 3107 3231 3383 3511 3897 4317 4584 5592 5649 6239 6379 7144 7863 8293 9214 9425 10707 10966 10970 11592 11664 11821 12198 12301 12659 13238 13666 13717 15157 15283 17293 18177 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file pltpt.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GGGAIDIGGTDCCAACCIIACGTTCGTCGCCCCCCCT 1.000000 2 GGGAIDIGGTDCAGGCTIIATGATGGCTGACCCCCCC 1.000000 3 GGGAIDIGGCDGAGATCIIACGTTCGCTGCACCTCCC 1.000000 4 GGGAIDICCTDCCAACCIIACGAAGGTCTAATCCCCC 1.000000 5 GGGAIDICCTDCCAACCIIACGTTCGTCGAACCCTCC 1.000000 6 GGGAIDICCTDCCAACCIIACGTTCGTCGAACCTCCC 2.000000 7 GGGAIDICCTDCCAACCIIACGTTCGTCGCACCCCCC 1.000000 8 GGGAIDICCTDCCAACCIIACTTTGGTCGAACCCTCC 4.000000 9 GGGAIIIGGCDGAGATCIIACGATGGTCGCCCCCCCC 1.000000 10 GGGAIIIGGCDGAGATCIIACGTTGGTCGAACCCCCC 1.000000 11 GGGAIIIGGCDGAGATCIIACGTTGGTCGAACCTCCC 7.000000 12 GGGAIIIGGCDGAGATCIIACGTTGGTCGAACACCCC 4.000000 13 GGGAIIDGGCDGAGATCDIATGATGGTCGCCCCCCCT 8.000000 14 GGGADDIGGTDCCAACCIIACGTTGGCTGACCCCCCC 1.000000 15 GGGADDIGGTDCCAACCIIACGTTCGTCGAACCCTTC 1.000000 16 GGGADDIGGTDCCAACCIIACGTTCGTCGACCCCCCC 8.000000 17 GGGTIDIGGTDCAGGCCIIACGAAGGCCGACCCCCCC 2.000000 18 GGGTIDIGGTDCAGGCTIIATGATGGCTGAACCCTTC 1.000000 19 GGGTIDIGGTDCAGGCTIIATGATGGCTGACCCCCCC 6.000000 20 GGGTIDIGGTDGAGATCIDACGAAGGTCGAACCCTCC 1.000000 21 GGGTIDIGGTICAGACCIIGTGATGGTCTAATCCCCC 5.000000 22 GGGTIDIGGCDCAGACTIIATGATGGCTGACCCCCCC 1.000000 23 GGTAIDIGGCDGAGATCIDACGAAGGCCGAACCCCCC 1.000000 24 GGTAIDIGGCDGAGATCIDACGAAGGCCGACCCCCCC 2.000000 25 GGTAIDIGGCDGAGATCIDACGAAGGCCTCACCTCCC 1.000000 26 GGTAIDIGGCDGAGATCIDACGAAGGCTGAACCCCCC 2.000000 27 GGTAIDIGGCDGAGATCIDACGAAGGCTGAACCCTTC 20.000000 28 GGTAIDIGGCDGAGATCIDACGTTGGTCGAACCTCCC 1.000000 29 GAGADDIGGTDCCAACCIIACGTTCATTGAACCCTTC 3.000000 30 AGGAIDIGGCDGAGATCIIACGTTGGCCGCACCTCCC 1.000000 31 AGGAIDIGGCDGAGATCIIACGTTGGCTGAACCCTTC 2.000000 32 AGGAIDIGGCDGAGATCIIACGTTGGCTGACCCCCCC 1.000000 33 AGGAIDIGGCDGAGATCIIATGATGGTCGAACCCCCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (4,8) D002: (7,22) D003: (12,27) D004: (16,27) D005: (11,17) D006: (10,27) D007: (13,21) D008: (12,28) D009: (13,16) D010: (16,31) D011: (5,13) D012: (13,13) D013: (6,11) D014: (17,25) D015: (9,16) D016: (12,13) D033: (21,21) D034: (12,30) D035: (21,21) D036: (19,27) D037: (1,13) D038: (3,27) D039: (16,33) D040: (13,27) E001: (24,26) E002: (27,31) E003: (8,11) E004: (11,27) E005: (15,16) E006: (26,27) E007: (14,29) E008: (18,27) E009: (16,27) E010: (19,27) E011: (6,27) E012: (27,27) E013: (2,8) E014: (11,27) E015: (11,32) E016: (19,27) E017: (11,27) E018: (19,19) E019: (27,27) E020: (23,29) E021: (8,16) E022: (19,20) E023: (24,29) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 G G G A I D I [C] [C] T D C C A A C C I I A C G A A G G T C T A A T C C C C C G G G A I D I C C T D C C A A C C I I A C T T T G G T C G A A C C C T C C 0 D002 G G G A I D I [C] [C] (T) D C C A A C C I I A C G T T C G T C G C A C C C C C C G G G T I D I G G (C) D C A G A C T I I A T G A T G G C T G A C C C C C C C 0 D003 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C A C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 D004 G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 D005 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C G G G T I D I G G T D C A G G C C I I A C G A A G G C C G A [C] C C C C C C 0 D006 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C C (C) (C) C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C (T) (T) C 0 D007 G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T G G G T I D I G G T I C A G A C C I I G T G A T G G T C T A A T C C C C C 0 D008 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C A C C C C G G T A I D I G G C D G A G A T C I [D] A C G [T] [T] G G T C G A A C C [T] [C] C C 0 D009 G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C 0 D010 G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A (C) C C C (C) (C) C A G G A I D I G G C D G A G A T C I I A C G T T G G C T G A (A) C C C (T) (T) C 0 D011 G G G A I D I C C T D C C A A C C I I A C G T T C G T C G A A C C C T C C G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T 0 D012 G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T 0 D013 G G G A I D I C C T D C C A A C C I I A C G T T C G T C G A A C C T C C C G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C 0 D014 G G G T I D I G G T D C A G G C C I I A C G A A G G C C (G) (A) (C) C C (C) C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C C (T) (C) (A) C C (T) C C C 0 D015 G G G A I I I G G C D G A G A T C I I A C G A T G G T C G C C C C C C C C G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C 0 D016 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C A C C C C G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T 0 D033 G G G T I D I G G T I C A G A C C I I G T G A T G G T C T A A T C C C C C G G G T I D I G G T I C A G A C C I I G T G A T G G T C T A A T C C C C C 0 D034 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C A C C C C A G G A I D I G G C D G A G A T C I I A C G [T] [T] G G C C G C A C C T C C C 0 D035 G G G T I D I G G T I C A G A C C I I G T G A T G G T C T A A T C C C C C G G G T I D I G G T I C A G A C C I I G T G A T G G T C T A A T C C C C C 0 D036 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 D037 G G G A I D I G G T D C C A A C C I I A C G T T [C] G T C G C C C C C C C T G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T 0 D038 G G (G) A I D I G G C D G A G A T C I (I) A C G (T) (T) (C) G C T G (C) A C C (T) (C) (C) C G G (T) A I D I G G C D G A G A T C I (D) A C G (A) (A) (G) G C T G (A) A C C (C) (T) (T) C 0 D039 G G G A D D I G G T D C C A A C C I I A (C) G T T C G T C G A C C C C C C C A G G A I D I G G C D G A G A T C I I A (T) G [A] T G G T C G A A C C C C C C 0 D040 G G G A I I D G G C D G A G A T C D I A T G A T G G T C G C C C C C C C T G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E001 G G T A I D I G G C D G A G A T C I D A C G A A G G C (C) G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C (T) G A A C C C C C C 0 E002 G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C A G G A I D I G G C D G A G A T C I I A C G T T G G C T G A A C C C T T C 0 E003 G G G A I D I C C T D C C A A C C I I A C T T T G G T C G A A C C C T C C G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C 0 E004 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E005 G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A A C C C T T C G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C 0 E006 G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A [A] C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E007 G G G A D D I G G T D C C A A C C I I A C G T T G G C T G A C C C C C C C G A G A D D I G G T D C C A A C C I I A C G T T C A T T G A A C C C T T C 0 E008 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A A C C C T T C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E009 G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E010 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E011 G G G A I D I C C T D C C A A C C I I A C G T T C G T C G A A C C T C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E012 G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E013 G G G A I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G G A I D I C C T D C C A A C C I I A C T T T G G T C G A A C C C T C C 0 E014 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E015 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C A G G A I D I G G C D G A G A T C I I A C G T T G G C T G A C C C C C C C 0 E016 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E017 G G G A I I I G G C D G A G A T C I I A C G T T G G T C G A A C C T C C C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E018 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C 0 E019 G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C G G T A I D I G G C D G A G A T C I D A C G A A G G C T G A A C C C T T C 0 E020 G G T A I D I G G C D G A G A T C I D A C G A A G G C (C) G A A C C C (C) (C) C G A G A D D I G G T D C C A A C C I I A C G T T C A T (T) G A A C C C (T) (T) C 0 E021 G G G A I D I C C T D C C A A C C I I A C T T T G G T C G A A C C C T C C G G G A D D I G G T D C C A A C C I I A C G T T C G T C G A C C C C C C C 0 E022 G G G T I D I G G T D C A G G C T I I A T G A T G G C T G A C C C C C C C G G G T I D I G G T D G A G A T C I D A C G A A G G T C G A A C C C T C C 0 E023 G G T A I D I G G C D G A G A T C I D A C G A A G G [C] (C) G A C C C C C C C G A G A D D I G G T D C C A A C C I I A C G T T C A T (T) G A A C C C T T 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 D001 = = = = = = = ? ? = = = = ? = = = = = = ? G A A = = = = T ? = ? ? = C = = = = = = = = = ? ? = = = = ? = = = = = = ? T T T = = = = G ? = ? ? = T = = 0 D002 = = = A = = = ? ? (T) = = C A = = C = = = C = T = C = T C = C A = = = = = = = = = T = = = ? ? (C) = = A G = = T = = = T = A = G = C T = A C = = = = = = 0 D003 = = G = = I ? ? = = = = = = = = = = I = = = T T = = T C = = = = A = C C = = = T = = D ? ? = = = = = = = = = = D = = = A A = = C T = = = = C = T T = 0 D004 = = G = D ? = = = T = C C A = C = = I = = = ? ? C = T C = = C = = = C C = = = T = I ? = = = C = G A G = T = = D = = = ? ? G = C T = = A = = = T T = 0 D005 = = = A = I = = = C = G = = A T = = = = = ? T T = = T = = = ? = = T = = = = = = T = D = = = T = C = = G C = = = = = ? A A = = C = = = ? = = C = = = 0 D006 = = G = = I = = = = = = = = = = = = I = = = T T = = T C = = = = = = (C) (C) = = = T = = D = = = = = = = = = = = = D = = = A A = = C T = = = = = = (T) (T) = 0 D007 = = = A = ? ? = = C D G = = = T = D = A = = = = ? ? = = G C C C = = = = T = = = T = ? ? = = T I C = = = C = I = G = = = = ? ? = = T A A T = = = = C 0 D008 = = G = = I ? = = = = = = = = = = ? ? ? ? ? ? ? = = = = = = = = A ? ? = = = = T = = D ? = = = = = = = = = = ? ? ? ? ? ? ? = = = = = = = = C ? ? = = 0 D009 = = = = I I D = = C = G A G = T = D = = T = A = G = = = = C = = = = = = T = = = = D D I = = T = C C A = C = I = = C = T = C = = = = A = = = = = = C 0 D010 G = = = D = = = = T = C C A = C = = = = = = = = C = T C = = (C) = = = (C) (C) = A = = = I = = = = C = G A G = T = = = = = = = = G = C T = = (A) = = = (T) (T) = 0 D011 = = = = = D I C C T = C C A = C = I ? = C = T = C = = = = A A = = = T = C = = = = = I D G G C = G A G = T = D ? = T = A = G = = = = C C = = = C = T 0 D012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D013 = = = = = D = C C T = C C A = C = = = = = = = = C = = = = = = = = = = = = = = = = = I = G G C = G A G = T = = = = = = = = G = = = = = = = = = = = = 0 D014 = = G T = = = = = T = C = = G C = = I = = ? = = = = = = (G) (A) (C) = = (C) = = = = = T A = = = = = C = G = = A T = = D = = ? = = = = = = (T) (C) (A) = = (T) = = = 0 D015 = = = = I I ? = = C = G A G = T = = = = = = A = G = = = = C = = = = = = = = = = = D D ? = = T = C C A = C = = = = = = T = C = = = = A = = = = = = = 0 D016 = = = = = = I = = = = = = = = = = I ? = C = T = = = = = = A A = A ? ? = C = = = = = = D = = = = = = = = = = D ? = T = A = = = = = = C C = C ? ? = T 0 D033 = ? ? ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? ? = = = ? ? ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? ? = = 0 D034 G ? ? ? ? I = = = = = = = = = = = = = = = = ? ? ? ? T = = A = = A C = = = A ? ? ? ? D = = = = = = = = = = = = = = = = ? ? ? ? C = = C = = C T = = = 0 D035 = = = = = = = = = = = = = = = = = = ? = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? ? ? ? ? = = = = = = = = = = = 0 D036 = = G T = = = = = T = C = = G C T = I = T = ? ? ? ? = = = = C = = = C C = = = T A = = = = = C = G = = A T C = D = C = ? ? ? ? = = = = A = = = T T = 0 D037 = = = = = D I = = T = C C A = C = I = = C = T = ? ? = = = = = = = = = = = = = = = = I D = = C = G A G = T = D = = T = A = ? ? = = = = = = = = = = = 0 D038 = = (G) = = = = = = = = = = = = = = = (I) = = = (T) (T) (C) = = = = (C) = = = (T) (C) (C) = = = (T) = = = = = = = = = = = = = = = (D) = = = (A) (A) (G) = = = = (A) = = = (C) (T) (T) = 0 D039 G = = = D = = = = T = C C A = C = = = = (C) = ? ? C = = = = = C = = = = = = A = = = I = = = = C = G A G = T = = = = (T) = ? ? G = = = = = A = = = = = = 0 D040 = = G = = I D = = = = = ? = = = = D ? = T = ? ? ? ? T C = C C = = = C C T = = T = = D I = = = = = ? = = = = I ? = C = ? ? ? ? C T = A A = = = T T C 0 E001 = ? ? = = = = = = = = = = = = = = = = = = = = = = = = (C) = = C = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = (T) = = A = = = = = = 0 E002 G = T = = = = = = = = = = = = = = = D = = = A A = = = = = = = = = = = = = A = G = = = = = = = = = = = = = = = I = = = T T = = = = = = = = = = = = = 0 E003 = = = = = D = C C T = C C A = C = = ? = = T = = = = = = = = = = = C T = = = = = = = I = G G C = G A G = T = = ? = = G = = = = = = = = = = = T C = = 0 E004 = = G = = I = = = = = = = = = = = = I = = = T T = = T C = = = = = T C C = = = T = = D = = = = = = = = = = = = D = = = A A = = C T = = = = = C T T = 0 E005 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = C C = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = C C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = T T = 0 E007 = G = = = = = = = = = = = = = = = = = = = = = = G G C = = = C = = = C C = = A = = = = = = = = = = = = = = = = = = = = = = C A T = = = A = = = T T = 0 E008 = = G T = = = = = T = C = = G ? T = ? = T ? = T = = = = = = = = = = = = = = = T A = = = = = C = G = = A ? C = ? = C ? = A = = = = = = = = = = = = = 0 E009 = = G = D = = = = T = C C A = C = = I = = = T T C = T C = = C = = = C C = = = T = I = = = = C = G A G = T = = D = = = A A G = C T = = A = = = T T = 0 E010 = = G T = = = = = T = C = = G C T = I = T = = T = = = = = = ? = = = C C = = = T A = = = = = C = G = = A T C = D = C = = A = = = = = = ? = = = T T = 0 E011 = = G = = = = C C T = C C A = C = = I = = = T T C = T C = = = = = T C C = = = T = = = = G G C = G A G = T = = D = = = A A G = C T = = = = = C T T = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = = = G G = = = A G G = T = = = T G A = = = C T = = C = = = C = = = = = = = = = C C = = = C A A = C = = = C T T = = = T C = = A = = = T = = 0 E014 = = G = = I = = = = = = = = = = = = I = = = T T = = T C = = = = = T C C = = = T = = D = = = = = = = = = = = = D = = = A A = = C T = = = = = C T T = 0 E015 G = = = = I = = = = = = = = = = = = = = = = = = = = T C = = A = = T = = = A = = = = D = = = = = = = = = = = = = = = = = = = = C T = = C = = C = = = 0 E016 = = G T = = = = = T = C = = G C T = ? = T ? = T = = = = = ? C = = ? ? C = = = T A = = = = = C = G = = A T C = ? = C ? = A = = = = = ? A = = ? ? T = 0 E017 = = G = = I = = = = = = = = = = = = I = = = T T = = T C = = = = = T C C = = = T = = D = = = = = = = = = = = = D = = = A A = = C T = = = = = C T T = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E020 = G T = I = = = = C = G A G = T = = D = = = A A G G C (C) = = = = = = (C) (C) = = A G = D = = = = T = C C A = C = = I = = = T T C A T (T) = = = = = = (T) (T) = 0 E021 = = = = I = = C C = = = = = = = = = = = = T = = G ? ? = = ? A = = = T = = = = = = D = = G G = = = = = = = = = = = = G = = C ? ? = = ? C = = = C = = 0 E022 = = = = = = = = = = = C = = G C T = I = T = = T = = C T = = C = = = C = = = = = = = = = = = = = G = = A T C = D = C = = A = = T C = = A = = = T = = 0 E023 = G T = I = = = = C = G A G = T = = D = = ? A A G G ? (C) = = C = = = C C = = A G = D = = = = T = C C A = C = = I = = ? T T C A ? (T) = = A = = = T T = 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 = = = ? ? 0.55 = = 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 = = 0.99 = = = 0.99 0.99 = = = = 1.00 = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 = = = = = ? 1.00 1.00 = = 1.00 = = = ? = = 0.97 = = = = = 1.00 = = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 1.00 = = 0.99 0.99 = = = = = = 0.87 0.87 = = = = 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 = = 0.86 = = = 0.86 0.86 = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = ? = = = = = = 0.56 0.81 0.81 = = 0.81 = = = = = = = 1.00 1.00 ? = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = 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 = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = ? = = ? ? ? ? ? = = = = = = = = = = = = = 1.00 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = ? ? ? ? = = = = 0.98 = = = 0.98 0.98 = = = = = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 = ? ? = = = = = = = = = = = = = 0.85 = = = = = = = = = = = = = = = 0.87 = = = 0.87 0.87 0.74 = = = = 0.85 = = = 0.85 0.85 0.85 = 1.00 = = = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = 0.80 = ? ? 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 = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0.70 = = 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 = = 0.99 = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = 0.91 = = = 0.91 0.91 = = = 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 = = = 1.00 1.00 = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = ? = = = 0.96 0.96 = = = 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 = 0.99 = = = = 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 = = = = = ? 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 = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 0.97 0.60 = = = = = = 0.77 0.77 = = = = = 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 = = = 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 ? 0.86 = = 0.98 = = = 0.96 0.96 = END PHASEPROBS