************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 tnfp2.phase.inp tnfp2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tnfp2.phase.out_freqs : haplotype frequency estimates tnfp2.phase.out_pairs : most likely haplotype pairs for each individual tnfp2.phase.out_recom : estimates of recombination parameters tnfp2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 47 Positions of loci: 118 356 685 2766 3299 4584 4591 4914 5346 5837 5958 6388 6553 6874 6914 7798 8085 8289 8355 8660 8682 8948 9198 9289 9372 10489 11103 11629 11991 12008 12846 12847 12920 12921 13004 13045 13463 13573 13919 14045 14443 14465 14466 14526 15058 15158 15627 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tnfp2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACGDCACCCATCCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 2 ACGDCACCCAACCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTCT 1.000000 3 ACGDCACCCAACCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 4 ACGDCACCCGTCGAGGGCIAAGTTTCTAACGACTGTAGCGGGGGTCC 1.000000 5 ACGDCACCGGTCCAAACCDAAGCTCCCGGCGACTATGGCGAGGGCCC 1.000000 6 ACGDCACCGGTCCAGACCIGAGCCCCCAGCGACGGTAACGGGGGTCC 1.000000 7 ACGDCACCGGTCCAGACCIGAGCCCCCAGCGACGGTAACGGGAGTCC 2.000000 8 ACGDCACCGGTCCAGACCDGAGCCCCCAGCGACGGTAACGGGAGTCC 1.000000 9 ACGDGACCCATCCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 3.000000 10 ACGDGACCCAACCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 21.000000 11 ACGDGACCCAACCAAGGCIAAGCTCCCAGCGACGGTAACGGGAGTCC 2.000000 12 ACGDGACCCAACCAAGGCIAAACTCCCGGCATTGGTAGCGGGGGTTT 2.000000 13 ACGDGACCCAACCAAGGTIAAGCTCCCGGCATCGGTAGCGGGGGTTT 1.000000 14 ACGDGACCCAACCAAGGTIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 15 ACGDGACCCAACCAAAGCIAAGCTCCCGGCATTGGTAGCGGGGGTCT 1.000000 16 ACGDGACCCAATCAAAGCIAAGCTCCCAGCATTGGTAGCGGGGGTCT 2.000000 17 ACGDGACCGAACCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 3.000000 18 ACGDGACCGAACCAAGGCIAAGCTCCCGGCGTTGGTAGCGGCGGTTT 1.000000 19 ACGDGACCGAACCAAGGCIAAACTCCCGGCATTGGTAGCGGGGGTTT 2.000000 20 ACGDGACTGGTCCAAACCDAAGCTCCCAGCGACTATGGCGGCGGCCC 1.000000 21 ACGDGACTGGTCCAAACCDAAGCTCCCAGCGACTATGGCGAGGGCCC 1.000000 22 GCGICACTGGTCCAAGCCIGTGTTTCTAGCGATGGTAGTAGGGGTCC 2.000000 23 GCGICACTGGTCGAGGGTIAAGCTCCCGGCGACGGAAGCGGGGGTCT 1.000000 24 GCGDCACCGAACCAAGGTIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 25 GCGDCACCGGTCCAAGCCIGTGTTTCTAACGACTGTAGCGGGGGTCC 1.000000 26 GCGDCACCGGTCCAGGCCDAAGCTCTCAGCGATGGTAGCGGGGGTTT 1.000000 27 GCGDCACCGGTCCAGACCIGAGCCCCCGGCATTGGTAGCGGGGGTTT 1.000000 28 GCGDCACCGGTCCAGACCIGAGCCCCCAGCATTGGTAGCGGGGGTTT 2.000000 29 GCGDCACCGGTCCAGACCIGAGCCCCCAGCGACGGTAACGGGAGTCC 9.000000 30 GCGDCACTCAATCAAGGCIAAGCTCCCAGCATTGGTAGCGGGGATTT 2.000000 31 GCGDCACTGGTCCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 32 GCGDCACTGGTCCAAGCCIGTGTTTCTAGCGATGGTAGTAGGGGTCC 1.000000 33 GCGDCACTGGTCCAAGCCDAAGCTCCCGGTGATGGTAGCGGCGATTT 1.000000 34 GCGDCACTGGTCCAAGCCDAAGCTCTCGGTGATGGTAGCGGGGATTT 2.000000 35 GCGDCACTGGTCCAAGCCDAAGCTCTCGGTGATGGTAGCGAGGGCTT 1.000000 36 GCGDCACTGGTCCAAACCDAAGCTCCCAGCGACTATGGCGAGGGCCC 1.000000 37 GCGDCACTGGTCCAGGCCDAAGCTCTCAGCGATGGTAGCGGGGGTTT 1.000000 38 GCGDCACTGGTCGAGGGCIAAGCTCCCAGCGACGGAAGCGGGGGTTT 4.000000 39 GCGDGACCCAACCAAGGCIAAGCTCCCGGCATTGGTAGCGGGGGTTT 1.000000 40 GCGDGACTGGTCCAAACCDAAGCTCCCAACGACTATGGCGAGGGCCC 6.000000 41 GTADCACCGGTCCAGACCIGAGCCCCCGGCATTGGTAGCGGGGGTTT 1.000000 42 GTADCGTTGGTCCGAGCCDAAGCTCCCAGCGACGGTAGTAGGGGTCC 1.000000 43 GTADCGTTGGTCCGAGCCDAAGCTCCCAGCGATGGTAGTAGGGGTCC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (9,23) D002: (13,42) D003: (24,30) D004: (10,43) D005: (16,37) D006: (16,38) D007: (28,29) D008: (10,40) D009: (10,25) D010: (21,40) D011: (14,20) D012: (10,34) D013: (4,40) D014: (26,34) D015: (22,22) D016: (3,7) D033: (35,40) D034: (10,43) D035: (15,38) D036: (2,12) D037: (39,40) D038: (10,32) D039: (12,19) D040: (40,43) E001: (10,17) E002: (11,17) E003: (10,30) E004: (10,29) E005: (10,29) E006: (9,28) E007: (10,10) E008: (8,36) E009: (10,29) E010: (10,10) E011: (6,10) E012: (7,41) E013: (27,29) E014: (10,29) E015: (10,10) E016: (10,29) E017: (1,33) E018: (18,19) E019: (9,31) E020: (11,38) E021: (10,38) E022: (5,17) E023: (29,29) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A C G D [G] A C C C A T C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G I C A C T G G T C G A G G G T I A A G C T C C C G G C G A C G G A A G C G G G G G T C T 0 D002 A C G D G A C C C A A C C A A G G T I A A G C T C C C G G C A T C G G T A G C G G G G G T T T G T A D C G T T G G T C C G A G C C D A A G C T C C C A G C G A C G G T A G T A G G G G T C C 0 D003 G C G D [C] A C C G A A C C A A G G (T) I A A G C T C C C G G C A T T G G T A G C G G G G (G) T T T G C G D C A C T C A A T C A A G G (C) I A A G C T C C C A G C A T T G G T A G C G G G G (A) T T T 0 D004 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G T A D C G T T G G T C C G A G C C D A A G C T C C C A G C G A T G G T A G T A G G G G T C C 0 D005 A C G D G A C C C A A T C A A A G C I A A G C T C C C A G C A T T G G T A G C G G G G G T C T [G] C G D C A C T G G T C C A [G] G C C D A A G C T C T C A G C G A T G G T A G C G G G G G T T T 0 D006 A C G D G A C C C A A T C A A A G C I A A G C T C C C A G C A T T G G T A G C G G G G G T C T G C G D C A C T G G T C G A G G G C I A A G C T C C C A G C G A C G G A A G C G G G G G T T T 0 D007 G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 D008 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D [G] A C T G G T C C A A A C C D A A G C T C C C A [A] C G A C T A T G G C G A G G G C C C 0 D009 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T [G] C G D C A C C G G T C C A A G C C I G T G T T T C T A A C G A C T G T A G C G G G G G T C C 0 D010 (A) C G D G A C T G G T C C A A A C C D A A G C T C C C A G C G A C T A T G G C G A G G G C C C (G) C G D G A C T G G T C C A A A C C D A A G C T C C C A A C G A C T A T G G C G A G G G C C C 0 D011 A C G D G A C C C A A C C A A G G (T) I A A G C T C C C G G C A T T G G T A G C G G (G) G G T T T [A] C G D G A C T G G T C C A A A C (C) D A A G C T C C C A G C G A C T A T G G C G G (C) G G C C C 0 D012 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C T G G T C C A A G C C D A A G C T C T C G G T G A T G G T A G C G G G G A T T T 0 D013 A C G D C A C C C G T C G A G G G C I A A G T T T C T A A C G A C T G T A G C G G G G G T C C [G] C G D G A C T G G T C C A A A C C D A A G C T C C C A [A] C G A C T A T G G C G A G G G C C C 0 D014 G C G D C A C (C) G G T C C A (G) G C C D A A G C T C T C A G C G A T G G T A G C G G G G G T T T G C G D C A C (T) G G T C C A (A) G C C D A A G C T C T C G G T G A T G G T A G C G G G G [A] T T T 0 D015 G C G I C A C T G G T C C A A G C C I G T G T T T C T A G C G A T G G T A G T A G G G G T C C G C G I C A C T G G T C C A A G C C I G T G T T T C T A G C G A T G G T A G T A G G G G T C C 0 D016 A C G D C A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T A C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 D033 G C G D C A C T G G T C C A A G C C D A A G C T C T C G G T G A T G G T A G C G A G G G C (T) (T) G C G D G A C T G G T C C A A A C C D A A G C T C C C A A C G A C T A T G G C G A G G G C (C) (C) 0 D034 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G T A D C G T T G G T C C G A G C C D A A G C T C C C A G C G A T G G T A G T A G G G G T C C 0 D035 A C G D G A C C C A A C C A A (A) G C I A A G C T C C C G G C A T T G G T A G C G G G G G T (C) T G C G D C A C T G G T C G A G (G) G C I A A G C T C C C A G C G A C G G A A G C G G G G G T (T) T 0 D036 A C G D (C) A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T (C) T A C G D (G) A C C C A A C C A A G G C I A A A C T C C C G G C A T T G G T A G C G G G G G T (T) T 0 D037 G C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D G A C T G G T C C A A A C C D A A G C T C C C A A C G A C T A T G G C G A G G G C C C 0 D038 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C T G G T C C A A G C C I G T G T T T C T A G C G A T G G T A G T A G G G G T C C 0 D039 A C G D G A C C C A A C C A A G G C I A A A C T C C C G G C A T T G G T A G C G G G G G T T T A C G D G A C C G A A C C A A G G C I A A A C T C C C G G C A T T G G T A G C G G G G G T T T 0 D040 [G] C G D G A C T G G T C C A A A C C D A A G C T C C C A A C G A C T A T G G C G A G G G C C C G T A D C G T T G G T C C G A G C C D A A G C T C C C A G C G A T G G T A G T A G G G G T C C 0 E001 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T A C G D G A C C G A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E002 A C G D G A C C (C) A A C C A A G G C I A A G C T C C C A G C G A C G G T A A C G G G A G T C C A C G D G A C C (G) A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E003 A C G D (G) A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D (C) A C T C A A T C A A G G C I A A G C T C C C A G C A [T] [T] G G [T] A G C G G G G [A] T T T 0 E004 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E005 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E006 A C G D G A C C C A T C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C A T T G G T A G C G G G G G T T T 0 E007 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E008 (A) C G D C A C C G G T C C A G A C C D G A G C C C C C A G C G A C G G T A A C G G G A G T C C (G) C G D C A C T G G T C C A A A C C D A A G C T C C C A G C G A C T A T G G C G A G G G C C C 0 E009 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E010 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E011 A C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G G G T C C A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E012 (A) (C) (G) D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C (G) (T) (A) D C A C C G G T C C A G A C C I G A G C C C C C G G C A T T G G T A G C G G G G G T T T 0 E013 G C G D C A C C G G T C C A G A C C I G A G C C C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E014 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E015 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E016 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C 0 E017 (A) C G D C A C C C A T C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T (G) C G D C A C [T] G G T C C A A [G] C C D A A G C T C C C G G T G A T G G T A G C G G C G A T T T 0 E018 A C G D G A C C G A A C C A A G G C I A A (G) C T C C C G G C G [T] [T] G G [T] A G C G G C G G T T T A C G D G A C C G A A C C A A G G C I A A (A) C T C C C G G C A T T G G T A G C G G G G G T T T 0 E019 A C G D G A C C C A T C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G [D] C A C [T] G G T C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E020 A C G D G A C C C A A C C A A G G C I A A G C T C C C A G C G A C G G T A A C G G G A G T C C G C G D C A C T G G T C G A G G G C I A A G C T C C C A G C G A C G G A A G C G G G G G T T T 0 E021 A C G D G A C C C A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T G C G D C A C T G G T C G A G G G C I A A G C T C C C A G C G A C G G A A G C G G G G G T T T 0 E022 A C G D (C) A C C G G T C C A A A C C D A A G C T C C C G G C [G] A C T A T G G C G A G G G C C C A C G D (G) A C C G A A C C A A G G C I A A G C T C C C G G C A T T G G T A G C G G G G G T T T 0 E023 G C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T C C [G] C G D C A C C G G T C C A G A C C I G A G C C C C C A G C G A C G G T A A C G G G A G T 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 D001 ? ? = D ? = = ? C A = = C ? ? = = C = = = = = ? ? = = = = = A T T = = T = = = = = = = = = T = ? ? = I ? = = ? G G = = G ? ? = = T = = = = = ? ? = = = = = G A C = = A = = = = = = = = = C = 0 D002 A C G = ? A C C C A A = = A = = G T I = = = = = = = = G ? ? A T = = = = = = C G = = = = = T T G T A = ? G T T G G T = = G = = C C D = = = = = = = = A ? ? G A = = = = = = T A = = = = = C C 0 D003 = = = = ? = = C G = = C = = = = = (T) = = = = = = = = = G = = = = = = = = = = = = = = = (G) = = = = = = = ? = = T C = = T = = = = = (C) = = = = = = = = = A = = = = = = = = = = = = = = = (A) = = = 0 D004 A C G = ? A C C C A A = = A = = G = I = = = = = = = = G = = A T = = = = = = C G = = = = = T T G T A = ? G T T G G T = = G = = C = D = = = = = = = = A = = G A = = = = = = T A = = = = = C C 0 D005 ? ? = = ? = = C C A A T = ? ? A G = I = = = = = = C = = = = A T = = = = = = = = = = = = = C = ? ? = = ? = = T G G T C = ? ? G C = D = = = = = = T = = = = G A = = = = = = = = = = = = = T = 0 D006 A = = = ? = = C C A A T C = A A = = = = = ? ? ? ? = = = = = A T T = = T = = = = = = = = = C = G = = = ? = = T G G T C G = G G = = = = = ? ? ? ? = = = = = G A C = = A = = = = = = = = = T = 0 D007 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T T = = = = G = = = = G = = T T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G A C = = = = A = = = = A = = C C 0 D008 A = = = ? = = C ? A A = = = = ? G = I = = = = = = = = G ? ? A T T G G = A = = ? ? ? ? ? ? T T G = = = ? = = T ? G T = = = = ? C = D = = = = = = = = A ? ? G A C T A = G = = ? ? ? ? ? ? C C 0 D009 ? = = ? G = = = C A A = = = = ? G = = A A = C = C = C ? G = A T T G = = ? = = = = = = = = T T ? = = ? C = = = G G T = = = = ? C = = G T = T = T = T ? A = G A C T = = ? = = = = = = = = C C 0 D010 (A) = = ? = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = ? ? = = = = = = = = = = = (G) = = ? = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = ? ? = = = = = = = = = = = 0 D011 ? = = = = = = C C A A = = = = G G (T) I = = = = = = = = G = = A T T G G = A = = ? = (G) = = T T T ? = = = = = = T G G T = = = = A C (C) D = = = = = = = = A = = G A C T A = G = = ? = (C) = = C C C 0 D012 A = = ? G = = C C A A = = = = = G = I = = = = = = C = = = C A T = = = = = = = = = = = G ? = = G = = ? C = = T G G T = = = = = C = D = = = = = = T = = = T G A = = = = = = = = = = = A ? = = 0 D013 ? ? = = C = = C C = = = G ? ? G G = I = = = T = T = T = ? ? = = = = G = A = = ? ? ? ? ? T = = ? ? = = G = = T G = = = C ? ? A C = D = = = C = C = C = ? ? = = = = A = G = = ? ? ? ? ? C = = 0 D014 = = = = = = = (C) = = = = = = (G) = = = ? = = = = = = = = A = C = = = = = = = = = ? ? ? ? ? = = = = = = = = = = (T) = = = = = = (A) = = = ? = = = = = = = = G = T = = = = = = = = = ? ? ? ? ? = = = 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 = = = ? = = = = C A A = = = A G G = = A = = = T = = = G = = A T T = = = = G = = = = G = = T T = = = ? = = = = G G T = = = G A C = = G = = = C = = = A = = G A C = = = = A = = = = A = = C C 0 D033 = = = = C = = = = = = = = = = ? = = = = = = = = = T = ? G T = = T G G = A = = ? = = = = = (T) (T) = = = = G = = = = = = = = = = ? = = = = = = = = = C = ? A C = = C T A = G = = ? = = = = = (C) (C) 0 D034 A C G = G A C ? C A A = = A = = G = I = = = = = = = = G = = A T = = = = = = C G = = = = = T T G T A = C G T ? G G T = = G = = C = D = = = = = = = = A = = G A = = = = = = T A = = = = = C C 0 D035 A = = = G = = C C A A = C = A (A) = = = = = = = = = = = G = = A T T = = T = = = ? ? ? ? ? = (C) = G = = = C = = T G G T = G = G (G) = = = = = = = = = = = A = = G A C = = A = = = ? ? ? ? ? = (T) = 0 D036 = = = = (C) = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = (G) = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = (T) = 0 D037 = = = = = = = C C A A = = = = G G = I = = = = = = ? = ? G = A T ? ? ? ? A = = ? ? ? ? ? T T T = = = = = = = T G G T = = = = A C = D = = = = = = ? = ? A = G A ? ? ? ? G = = ? ? ? ? ? C C C 0 D038 A = = = G = = C C A A = = = = = G = = A A = C = C ? C G = = A T = = = = = = C G = = = = = T T G = = = C = = T G G T = = = = = C = = G T = T = T ? T A = = G A = = = = = = T A = = = = = C C 0 D039 = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D040 ? ? G = ? A C = = = = = = A = A = = = = = = = = = = = = A = = = C T A = G = C G A = = = C = = ? ? A = ? G T = = = = = = G = G = = = = = = = = = = = = G = = = T G G = A = T A G = = = T = = 0 E001 ? ? = = = = = = C = = = = = = ? = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = = = ? ? = = = = = = G = = = = = = ? = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = = = 0 E002 = = = = = = = = (C) = = = = = = = = = = = = = = = = = = A = = G A C = = = = A = ? ? ? ? ? = C C = = = = = = = = (G) = = = = = = = = = = = = = = = = = = G = = A T T = = = = G = ? ? ? ? ? = T T 0 E003 A = = = (G) = = C = = = C = = = = = = = = = = = = = = = G = = ? ? ? ? ? ? = = ? ? ? ? ? ? = = = G = = = (C) = = T = = = T = = = = = = = = = = = = = = = A = = ? ? ? ? ? ? = = ? ? ? ? ? ? = = = 0 E004 A = = = G = = = C A A = = = A G G = = A = = = T = = = G = = A T T = = = = G = = = = G = ? T T G = = = C = = = G G T = = = G A C = = G = = = C = = = A = = G A C = = = = A = = = = A = ? C C 0 E005 A = = = G = = = C A A = = = A G G = = A = = = T = = = G = = A T T = = = = G = ? ? ? ? ? = T T G = = = C = = = G G T = = = G A C = = G = = = C = = = A = = G A C = = = = A = ? ? ? ? ? = C C 0 E006 A = = = G = = = ? A = = = = A G G = = A = = = T = = = G = = = = = = = = = = = = = = = = = = = G = = = C = = = ? G = = = = G A C = = G = = = C = = = A = = = = = = = = = = = = = = = = = = = 0 E007 = = = = = ? ? = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? ? ? ? = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? ? ? ? = = = 0 E008 (A) = = = = ? ? C = = = = = = G = = = = G = = = C = = = = = = ? ? ? ? ? ? A A = = G = A = ? = = (G) = = = = ? ? T = = = = = = A = = = = A = = = T = = = = = = ? ? ? ? ? ? G G = = A = G = ? = = 0 E009 A = = = G = = ? C A A ? ? = A ? G = = A = = = T = = = G = = A T T = = = = G = = = = G = = T T G = = = C = = ? G G T ? ? = G ? C = = G = = = C = = = A = = G A C = = = = A = = = = A = = C C 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 = = = = C = = = G G T = = = G A C = = G = = = C = = = A = = G A C = = = = A = = = = = = = C C = = = = G = = = C A A = = = A G G = = A = = = T = = = G = = A T T = = = = G = = = = = = = T T 0 E012 (A) (C) (G) = = = = = ? ? = = = = = = = = = = = = = = = = = A = = G A C = = = = A = = = = A = = C C (G) (T) (A) = = = = = ? ? = = = = = = = = = = = = = = = = = G = = A T T = = = = G = = = = G = = T T 0 E013 = = = = = = = ? = = = ? ? = = = = = = = = = = = = = = G = = A T T = = = = G = = = = G = = T T = = = = = = = ? = = = ? ? = = = = = = = = = = = = = = A = = G A C = = = = A = = = = A = = C C 0 E014 A = = = G = = = C A A = = = A G G = = ? ? = = T = ? = G = = A T T = = = = G = = = = G = = T T G = = = C = = = G G T = = = G A C = = ? ? = = C = ? = A = = G A C = = = = A = = = = A = = C C 0 E015 = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E016 A = = = G = = = C A A = = = A G G = = A = = = T = = = G = = A T T = = = = G = = = = G = = T T G = = = C = = = G G T = = = G A C = = G = = = C = = = A = = G A C = = = = A = = = = A = = C C 0 E017 (A) = = ? = = = ? C A = ? ? = = ? G = ? = = = = = = = = ? = C A T = = = = = = = = = G = G = = = (G) = = ? = = = ? G G = ? ? = = ? C = ? = = = = = = = = ? = T G A = = = = = = = = = C = A = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = G ? ? ? ? ? = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = A ? ? ? ? ? = = = = = G = = = = = 0 E019 A = = ? G ? ? ? C A = ? ? = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = G = = ? C ? ? ? G G = ? ? = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = 0 E020 A = = = G = = C C A A = C = A = = = = = = = = = = = = = = = ? ? ? ? ? ? = A = = = = A = = C C G = = = C = = T G G T = G = G = = = = = = = = = = = = = = = ? ? ? ? ? ? = G = = = = G = = T T 0 E021 A = = = G = = C C A A = C = A = = = = = = = = = = = = G = = A T T = = T = = = = = = = = = = = G = = = C = = T G G T = G = G = = = = = = = = = = = = A = = G A C = = A = = = = = = = = = = = 0 E022 = = = = (C) = = = = G T = = = = A C = D = = = = = = = = = = = ? ? ? ? ? = G = = = A = = = C C C = = = = (G) = = = = A A = = = = G G = I = = = = = = = = = = = ? ? ? ? ? = A = = = G = = = T T T 0 E023 ? = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = ? ? = = = = = 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 0.95 = = 1.00 = = = = = 0.65 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = 0.88 = = = 1.00 1.00 1.00 = ? 1.00 1.00 1.00 1.00 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 1.00 1.00 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 1.00 = 1.00 1.00 = = = = = ? ? ? ? = = = = = 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 = = = ? = = 1.00 ? 1.00 1.00 = = = = ? 1.00 = 1.00 = = = = = = = = 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 = 1.00 = = ? ? ? ? ? ? 1.00 1.00 ? = = ? 0.94 = = = 1.00 1.00 1.00 = = = = ? 1.00 = = 1.00 1.00 = 1.00 = 1.00 = 1.00 ? 1.00 = 1.00 1.00 1.00 1.00 = = ? = = = = = = = = 1.00 1.00 0.84 = = ? = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? ? = = = = = = = = = = = ? = = = = = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 0.54 1.00 = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = ? = 0.59 = = 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 = = = = = = = = = = = 0.94 ? = = ? ? = = 1.00 = = 1.00 1.00 = = = 1.00 ? ? 1.00 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 = ? ? = = = = 1.00 = 1.00 = = ? ? ? ? ? 1.00 = = = = = = = = = 0.76 = = = = = = 0.82 = = = ? = = = = = = = = 1.00 = 1.00 = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0.96 0.96 0.96 = = = 0.96 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 1.00 1.00 = 1.00 = = ? = = = = = 0.53 0.53 1.00 1.00 1.00 = 1.00 1.00 1.00 ? 1.00 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 = = = 0.98 = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 0.54 = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = = ? ? ? ? ? = 0.68 = = = = = 0.85 = = = = = = = = = = = = = = = = 0.91 = = = = = = = = = = = = = = = = = = = = = = = 0.65 = = = = = = = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = ? = ? 1.00 = 1.00 1.00 ? ? ? ? 1.00 = = ? ? ? ? ? 1.00 1.00 1.00 0.94 = = = 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 = = = = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? 1.00 = ? 1.00 1.00 = = = = = = 1.00 = 1.00 = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 = = ? ? = = = = = = 1.00 = = = = = = ? = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 0.80 = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = = = = 1.00 = ? ? ? ? ? = 1.00 1.00 0.99 = = = 0.87 = = 1.00 = = = 1.00 = = = = = = = = = = = = = = = 1.00 = = ? ? ? ? ? ? = = ? ? ? ? ? ? = = = 0.95 = = = 1.00 = = = 1.00 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 0.98 0.95 = = = 1.00 = = = 1.00 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 0.98 = = = 0.98 = = = ? 1.00 = = = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = 0.99 = = = = = = = = = = = = = = = = = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? ? ? ? = = = 0.50 = = = = ? ? 0.99 = = = = = = 1.00 = = = = 1.00 = = = 1.00 = = = = = = ? ? ? ? ? ? 1.00 1.00 = = 1.00 = 1.00 = ? = = 0.96 = = = 1.00 = = ? 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 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = 0.94 = = 0.94 0.94 0.94 = = = = 0.94 = = = = = = = 0.92 0.92 0.65 0.64 0.64 = = = = = ? ? = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = = = = 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 = = = 1.00 = = = 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 0.98 = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = = 1.00 = = = 1.00 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 0.98 0.77 = = ? = = = ? 1.00 1.00 = ? ? = = ? 1.00 = ? = = = = = = = = ? = 1.00 1.00 1.00 = = = = = = = = = 0.98 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 0.52 = = = = = = = = 1.00 ? ? ? ? ? = = = = = 1.00 = = = = = 0.98 = = ? 0.99 ? ? ? 1.00 1.00 = ? ? = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = 0.99 = = = 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 = = = = = = = = = = = = = = = 0.87 = = = = 0.91 0.91 = = = = 0.91 0.91 = 0.91 = = = = = = = = = = = ? ? ? ? ? = 0.98 = = = 0.98 = = = 0.98 0.98 0.98 ? = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS