************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 pank2.phase.inp pank2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST pank2.phase.out_freqs : haplotype frequency estimates pank2.phase.out_pairs : most likely haplotype pairs for each individual pank2.phase.out_recom : estimates of recombination parameters pank2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 17 Positions of loci: 243 438 654 836 2163 2208 2929 3016 20421 21208 28533 28623 29098 29651 31732 31835 37140 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file pank2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CAGCTCCCAACTCDAGC 13.000000 2 CAGCTCCCAACTCIAGC 24.000000 3 CAGCTCCCAACTCIAGT 2.000000 4 CAGCTCCCAACTADAGC 2.000000 5 CAGCTCCCAACTADGGC 3.000000 6 CAGCTCCCGGCTCIGGC 2.000000 7 CAGCTCCCGGTTADGAC 1.000000 8 CAGCTCCCGGTAADGAC 6.000000 9 CAGCTCCTGGTTCDGAC 2.000000 10 CAGCTCCTGGTTADGGC 2.000000 11 CAGCTCCTGGTTADGAC 1.000000 12 CAGCTCCTGGTACIGGC 1.000000 13 CAGCTCCTGGTACIGAC 5.000000 14 CAGCTCCTGGTAADGAC 35.000000 15 CAGCTGCCAACTCDAGC 26.000000 16 CAGCTGCCAACTCIAGC 1.000000 17 AAGTTCCCGGCTCDGGC 8.000000 18 AAGTTCCCGGCTCIGGC 3.000000 19 AAGTTCCCGGCTADGGT 1.000000 20 AAGTTCCTGGCTCDGGC 1.000000 21 AGGTTCCCAACTCDAGC 1.000000 22 AGGTTCCCAACTCIAGC 2.000000 23 AGGTTCCCAACTADAGC 1.000000 24 AGGTTCCCGGCTCIGGC 3.000000 25 AGGTTCCCGGTTCDGGC 4.000000 26 AGGTTCCCGGTTADGGT 1.000000 27 AGGTTCCTGGTTCIAGC 1.000000 28 AGGTTCCTGGTTADGGC 4.000000 29 AGGTTCCTGGTTADGGT 3.000000 30 AGGTTCTCAACTCIAGC 1.000000 31 AGGTTCTCGGCTCIGGC 1.000000 32 AGGTTCTCGGTTCDGGT 1.000000 33 AGGTTCTCGGTTADGGC 2.000000 34 AGGTTCTCGGTTADGGT 5.000000 35 AGGTTCTCGGTAADGAC 1.000000 36 AGATACCCGGTTCDGGC 2.000000 37 AGATACCCGGTTADGGC 18.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,15) D002: (9,13) D003: (4,31) D004: (15,32) D005: (2,15) D006: (12,36) D007: (22,36) D008: (1,17) D009: (2,27) D010: (5,23) D011: (15,24) D012: (3,37) D013: (24,30) D014: (10,15) D015: (1,25) DY01: (2,25) DY02: (17,24) DY03: (6,18) DY04: (1,5) DY05: (1,5) DY06: (1,9) DY07: (1,21) DY08: (1,26) DY09: (22,28) DY10: (1,25) DY11: (1,25) DY12: (1,2) E101: (13,20) E102: (8,18) E103: (17,18) E104: (13,14) E105: (14,15) E106: (6,14) E107: (14,15) E108: (14,35) E109: (2,15) E110: (10,14) E111: (8,14) E112: (2,13) E113: (13,14) E114: (8,14) E115: (14,15) E116: (2,2) E117: (2,2) E118: (14,17) E119: (2,37) E120: (14,15) E121: (4,19) E122: (1,15) H101: (14,29) H102: (14,14) H103: (2,14) H104: (8,14) H105: (2,15) H106: (8,37) H107: (14,14) H108: (14,17) H109: (7,15) H110: (14,28) H111: (2,29) H112: (37,37) H113: (14,37) H114: (11,14) H115: (2,14) H116: (2,17) H117: (8,14) H118: (29,37) H119: (2,15) H120: (17,37) H121: (2,14) H122: (14,37) X101: (28,37) X102: (2,15) X103: (16,37) X104: (15,37) X105: (3,14) X106: (14,15) X107: (15,28) X108: (2,15) X109: (15,34) X110: (15,17) X111: (2,33) X112: (14,34) X113: (2,15) X114: (37,37) X115: (14,33) X116: (15,34) X117: (14,37) X118: (2,15) X119: (14,34) X120: (14,14) X121: (37,37) X122: (15,15) X123: (2,37) X124: (1,34) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C A G C T [C] C C A A C T C D A G C C A G C T [G] C C A A C T C D A G C 0 D002 C A G C T C C T G G T T C D G A C C A G C T C C T G G T A C I G A C 0 D003 C A G C T C C C (A) (A) C T (A) (D) (A) G C A G G T T C T C (G) (G) C T (C) (I) (G) G C 0 D004 C A G C T [G] C C A A C T C D A G C A G G T T C T C G G T T C D G G T 0 D005 C A G C T C C C A A C T C I A G C C A G C T [G] C C A A C T C D A G C 0 D006 C A G C T C C T G G T A C I G G C A G A T A C C C G G T T C D G G C 0 D007 A G (G) T T C C C A A C T C I A G C A G (A) T [A] C C C G G T T C D G G C 0 D008 C A G C T [C] C C A A C T C [D] A G C A A G T T C C C G G C T C [D] G G C 0 D009 C A G C T C C C A A C T C I A G C A G G T T C C T G G T T [C] I [A] G C 0 D010 C A G C T C C C A A C T A D (G) G C A [G] G T T C C C A A C T A D (A) G C 0 D011 C A G C T [G] C C A A C T C D A G C A G G T T C C C G G C T C I G G C 0 D012 C A G C T C C C A A C T C I A G (T) A G A T A C C C G G T T [A] D G G (C) 0 D013 A G G T T C (C) C G G C T C I G G C A G G T T C (T) C A A C T C I A G C 0 D014 C A G C T C C T G G T T A D G G C C A G C T [G] C C A A C T C D A G C 0 D015 C A G C T C C C A A C T C D A G C A G G T T C C C G G T T C D G G C 0 DY01 C A G C T C C C A A C T C I A G C A G G T T C C C G G T T C D G G C 0 DY02 A A G T T C C C G G C T C D G G C A G G T T C C C G G C T C I G G C 0 DY03 C A G C T C C C G G C T C I G G C A [A] G T T C C C G G C T C I G G C 0 DY04 C A G C T C C C A A C T C D A G C C A G C T C C C A A C T A D G G C 0 DY05 C A G C T C C C A A C T C D A G C C A G C T C C C A A C T A D G G C 0 DY06 C A G C T C C C A A C T C D A G C C A G C T C C T G G T T C D G A C 0 DY07 C A G C T C C C A A C T C D A G C A G G T T C C C A A C T [C] D A G C 0 DY08 C A G C T C C C A A C T (C) [D] A G (C) A G G T T C C C G G T T (A) D G G (T) 0 DY09 A G G T T C C C A A C T (C) (I) A G C A G G T T C C T G G T T (A) (D) G G C 0 DY10 C A G C T C C C A A C T C D A G C A G G T T C C C G G T T C D G G C 0 DY11 C A G C T C C C A A C T C D A G C A G G T T C C C G G T T C D G G C 0 DY12 C A G C T C C C A A C T C D A G C C A G C T C C C A A C T C I A G C 0 E101 C A G C T C C T G G T A C I G A C A A G T T C C T G G C T C D G G C 0 E102 C A G C T C C C G G T A A D G A C A A G T T C C C G G C T C I G G C 0 E103 A A G T T C C C G G C T C D G G C A A G T T C C C G G C T C I G G C 0 E104 C A G C T C C T G G T A C I G A C C A G C T C C T G G T A A D G A C 0 E105 C A G C T C C T G G T A A D G A C C A G C T G C C A A C T C D A G C 0 E106 C A G C T C C C G G C T C [I] G G C C A G C T C C T G G T A A D G A C 0 E107 C A G C T C C T G G T A A D G A C C A G C T G C C A A C T C D A G C 0 E108 C A G C T C C T G G T A A D G A C A G G T T C T C G G T A A D G A C 0 E109 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 E110 C A G C T C C T G G T T A D G [G] C C A G C T C C T G G T A A D G A C 0 E111 C A G C T C C C G G T A A D G A C C A G C T C C T G G T A A D G A C 0 E112 C A G C T C C C A A C T C [I] A G C C A G C T C C T G G T A C I G A C 0 E113 C A G C T C C T G G T A C I G A C C A G C T C C T G G T A A D G A C 0 E114 C A G C T C C C G G T A A D G A C C A G C T C C T G G T A A D G A C 0 E115 C A G C T C C T G G T A A D G A C C A G C T G C C A A C T C D A G C 0 E116 C A G C T C C C A A C T C I A G C C A G C T C C C A A C T C I A G C 0 E117 C A G C T C C C A A C T C I A G C C A G C T C C C A A C T C I A G C 0 E118 C A G C T C C T G G T A A D G A C A A G T T C C C G G C T C D G G C 0 E119 C A G C T C C C A A C T C I A G C A G A T A C C C G G T T A D G G C 0 E120 C A G C T C C T G G T A A D G A C C A G C T G C C A A C T C D A G C 0 E121 (C) A G C T C C C A A C T A D A G (C) (A) A G [T] T C C C G G C T A D G G (T) 0 E122 C A G C T C C C A A C T C D A G C C A G C T G C C A A C T C D A G C 0 H101 C A G C T C C T G G T A A D G A C A G G T T C C T G G T T A D G G T 0 H102 C A G C T C C T G G T A A D G A C C A G C T C C T G G T A A D G A C 0 H103 C A G C T C C C A A C T C I A G C C A G C T C C T G G T A A D G A C 0 H104 C A G C T C C C G G T A A D G A C C A G C T C C T G G T A A D G A C 0 H105 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 H106 C A G C T C C C G G T A A D G A C A G A T A C C C G G T T A D G G C 0 H107 C A G C T C C T G G T A A D G A C C A G C T C C T G G T A [A] D G A C 0 H108 C A G C T C C T G G T A A D G A C A A G T T C C C G G C T C D G G C 0 H109 C A G C T (C) C C G G T T A D G A C C A G C T (G) C C A A C T C D A G C 0 H110 C A G C T C C T G G T A A D G A C A G G T T C C T G G T T A D G G C 0 H111 C A G C T C C C A A C T C I A G (C) A G G T T C C T G G T T A D G G (T) 0 H112 A G A T A C C C G G T T A D G G C A G A T A C C C G G T T A D G G C 0 H113 C A G C T C C T G G T A A D G A C A G A T A C C C G G T T A D G G C 0 H114 C A G C T C C T G G T T A D G A C C A G C T C C T G G T A A D G A C 0 H115 C A G C T C C C A A C T C I A G C C A G C T C C T G G T A A D G A C 0 H116 C A G C T C C C A A C T C (I) A G C A A G T T C C C G G C T C (D) G G C 0 H117 C A G C T C C C G G T A A D G A C C A G C T C C T G G T A A D G A C 0 H118 A G G T T C C T G G T T A D G G T A G A T A C C C G G T T A D G G C 0 H119 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 H120 A A G T T C C C G G C T C D G G C A G A T A C C C G G T T A D G G C 0 H121 C A G C T C C C A A C T C I A G C C A G C T C C T G G T A A D G A C 0 H122 C A G C T C C [T] G G T A A D G A C A G A T A C C C G G T T A D G G C 0 X101 A G G T T C C T G G T T A D G G C A G A T A C C C G G T T [A] D G G C 0 X102 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 X103 C A G C T G C C A A C T C I A G C A G A T A C C C G G T T [A] D G G C 0 X104 C A G C T G C C A A C T C D A G C A G A T A C C C G G T T A D G G C 0 X105 C A G C T C C C A A C T (C) (I) A G (T) C A G C T C C T G G T A (A) (D) G A (C) 0 X106 C A G C T C C T G G T A A D G A C C A G C T G C C A A C T C D A G C 0 X107 C A G C T G C C A A C T C D A G C A G G T T C C T G G T T A D G G C 0 X108 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 X109 C A G C T G C C A A C T C D A G C A G G T T C T C G G T T A D G G T 0 X110 C A G C T G C C A A C T C D A G C A A G T T C C C G G C T C D G G C 0 X111 C A G C T C C C A A C T C I A G C A G G T T C T C G G T T A D G G C 0 X112 C A G C T C C T G G T A A D G A C A G G T T C T C G G T T A D G G T 0 X113 C A G C T C C C A A C T C I A G C C A G C T G C C A A C T C D A G C 0 X114 A G A T A C C C G G T T A D G G C A G A T A C C C G G T T [A] D G G C 0 X115 C A G C T C C T G G T A A D G A C A G G T T C T C G G T T A D G G C 0 X116 C A G C T G C C A A C T C D A G C A G G T T C T C G G T T A D G G T 0 X117 C A G C T C C T G G T A A D G A C A G A T A C C C G G T T A D G G C 0 X118 C A G C T C C C A A C T C [I] A G C C A G C T G C C A A C T C D A G C 0 X119 C A G C T C C T G G T A A D G A C A G G T T C T C G G T T A D G G T 0 X120 C A G C T C C T G G T A A D G A C C A G C T C C T G G T A A D G A C 0 X121 A G A T A C C C G G T T A D G G C A G A T A C C C G G T T A D G G C 0 X122 C A G C T G C C A A C T C D A G C C A G C T G C C A A C T C D A G C 0 X123 C A G C T C C C A A C T C I A G C A G A T A C C C G G T T A D G G C 0 X124 C A G C T [C] C C A A C T C [D] A G C A G G T T C [T] [C] G G T T A D G G T 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 = = = = ? ? = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = 0 D002 = ? = = ? ? = = = = = T = D = = = = ? = = ? ? = = = = = A = I = = = 0 D003 C A = C = = C = (A) (A) = = (A) (D) (A) = = A G = T = = T = (G) (G) = = (C) (I) (G) = = 0 D004 C A = C ? ? C = A A C = = = A = C A G = T ? ? T = G G T = = = G = T 0 D005 = = = = ? ? = = = = = = = I = = = = = = = ? ? = = = = = = = D = = = 0 D006 C A G C ? ? = T = = = A = I = = = A G A T ? ? = C = = = T = D = = = 0 D007 ? = (G) = ? ? = = A A C = = I A = = ? = (A) = ? ? = = G G T = = D G = = 0 D008 C = = ? ? ? = = A A = = ? ? A = = A = = ? ? ? = = G G = = ? ? G = = 0 D009 C A = C ? ? = C A A C = ? = ? = = A G = T ? ? = T G G T = ? = ? = = 0 D010 C ? = C ? ? = = = = = = = = (G) = = A ? = T ? ? = = = = = = = = (A) = = 0 D011 C A = C ? ? = = A A = = = D A = = A G = T ? ? = = G G = = = I G = = 0 D012 C A G C ? ? = = A A C = ? I A = (T) A G A T ? ? = = G G T = ? D G = (C) 0 D013 = = = = ? ? (C) = G G = = = = G = = = = = = ? ? (T) = A A = = = = A = = 0 D014 = = = = ? ? = T G G T = A = G = = = = = = ? ? = C A A C = C = A = = 0 D015 C A = C = = = = A A C = = = A = = A G = T = = = = G G T = = = G = = 0 DY01 C A = C = = = = A A C = = I ? ? = A G = T = = = = G G T = = D ? ? = 0 DY02 = A = = = = = = = = = = = D = = = = G = = = = = = = = = = = I = = = 0 DY03 C ? = C = = = = = = = = = = ? ? = A ? = T = = = = = = = = = = ? ? = 0 DY04 = = = = = = = = = = = = C = A = = = = = = = = = = = = = = A = G = = 0 DY05 = = = = = = = = = = = = C = A = = = = = = = = = = = = = = A = G = = 0 DY06 = = = = = = = C A A C = = = A G = = = = = = = = T G G T = = = G A = 0 DY07 C A = C = = = = = = = = ? = = = = A G = T = = = = = = = = ? = = = = 0 DY08 C A = C = = = = A A C = (C) ? A = (C) A G = T = = = = G G T = (A) ? G = (T) 0 DY09 = = = = = = = C A A C = (C) (I) A = = = = = = = = = T G G T = (A) (D) G = = 0 DY10 ? A = C = = = = A A C = = = A = = ? G = T = = = = G G T = = = G = = 0 DY11 C ? = C = = = = A A C = = = A = = A ? = T = = = = G G T = = = G = = 0 DY12 = = = ? = = = = = = = = = D = = = = = = ? = = = = = = = = = I = = = 0 E101 C = = C = = = = = = T A = I = A = A = = T = = = = = = C T = D = G = 0 E102 C = = ? = = = = ? = T A A D = ? = A = = ? = = = = ? = C T C I = ? = 0 E103 = = = ? = = = = = = = = = D = = = = = = ? = = = = = = = = = I = = = 0 E104 = = = = = = = = = = = = C I = = = = = = = = = = = = = = = A D = = = 0 E105 = = = = = C = T G G T A ? = G A = = = = = = G = C A A C T ? = A G = 0 E106 = = = = = = = C = = C T C ? = G = = = = = = = = T = = T A A ? = A = 0 E107 = ? = = = C = T G G T A A = G A = = ? = = = G = C A A C T C = A G = 0 E108 C A = C = = C T = = = = = = = = = A G = T = = T C = = = = = = = = = 0 E109 = = = = = C = = = = = = = I = = = = = = = = G = = = = = = = D = = = 0 E110 = = = = = = = = = = = T = = = ? = = = = = = = = = = = = A = = = ? = 0 E111 = = = = = = = C = = = = = = = ? = = = = = = = = T = = = = = = = ? = 0 E112 = = = = = = = C A A C T = ? A G = = = = = = = = T G G T A = ? G A = 0 E113 ? = = = = = = = = = = = C I = = = ? = = = = = = = = = = = A D = = = 0 E114 = = = = = = = C = = = = = = = = = = = = = = = = T = = = = = = = = = 0 E115 = ? = = = C = T G G T A A = G A = = ? = = = G = C A A C T C = A G = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 C = = ? = = = T = = T A A = = A = A = = ? = = = C = = C T C = = G = 0 E119 C A G C T = = = A A C = C I A = = A G A T A = = = G G T = A D G = = 0 E120 = = = = = C = T G G T A A ? G A = = = = = = G = C A A C T C ? A G = 0 E121 (C) = = ? = = = = A A = = = = A = (C) (A) = = ? = = = = G G = = = = G = (T) 0 E122 = = = = = C = = = = = = = = = = = = = = = = G = = = = = = = = = = = 0 H101 C ? = C ? ? = = = = = A = = = A C A ? = T ? ? = = = = = T = = = G T 0 H102 = = = = ? ? = = = = = = = = ? ? = = = = = ? ? = = = = = = = = ? ? = 0 H103 = = = = = = = C A A C T C I A G = = = = = = = = T G G T A A D G A = 0 H104 = = = = ? ? = C = = = = = = = = = = = = = ? ? = T = = = = = = = = = 0 H105 = = = = ? C = = = = = = = I = = = = = = = ? G = = = = = = = D = = = 0 H106 C A G C T = = = = = = A = ? = A = A G A T A = = = = = = T = ? = G = 0 H107 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = ? ? = = = 0 H108 C = = C = = = T = = T A A = = A = A = = T = = = C = = C T C = = G = 0 H109 = ? = = = (C) = = G G T = A = G A = = ? = = = (G) = = A A C = C = A G = 0 H110 C A = ? = = = = = = = A = = ? ? = A G = ? = = = = = = = T = = ? ? = 0 H111 C A = C = = = C A A C = C I A = (C) A G = T = = = T G G T = A D G = (T) 0 H112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H113 C A G C T = = T = = = A = = = A = A G A T A = = C = = = T = = = G = 0 H114 = = = = = = = = = = = T = = = = = = = = = = = = = = = = A = = = = = 0 H115 = = = = = = = C A A C T ? I A G = = = = = = = = T G G T A ? D G A = 0 H116 C = = C = = = = A A = = = (I) A = = A = = T = = = = G G = = = (D) G = = 0 H117 = ? = = = = = C = = = = = = = = = = ? = = = = = T = = = = = = = = = 0 H118 = = G = T = = T = = = = = = = = T = = A = A = = C = = = = = = = = C 0 H119 = = = = = C = = = = = = = I = = = = = = = = G = = = = = = = D = = = 0 H120 = A G ? T = ? ? = = C = C = = = = = G A ? A = ? ? = = T = A = = = = 0 H121 = = = = = = = C A A C T C I A G = = = = = = = = T G G T A A D G A = 0 H122 C A G ? T = ? ? = = = A = ? = A = A G A ? A = ? ? = = = T = ? = G = 0 X101 = = G = T = = T = = = = ? = = = = = = A = A = = C = = = = ? = = = = 0 X102 = = = ? = C = = = = = = = I = = = = = = ? = G = = = = = = = D = = = 0 X103 C ? G C T G = = A A C = ? I A = = A ? A T A C = = G G T = ? D G = = 0 X104 C A G C T G = = A A C = C = A = = A G A T A C = = G G T = A = G = = 0 X105 = = = = = = = C A A ? ? (C) (I) A G (T) = = = = = = = T G G ? ? (A) (D) G A (C) 0 X106 = = = = = C = T G G T A A = G A = = = = = = G = C A A C T C = A G = 0 X107 C A = C = G = C A A C = C = A = = A G = T = C = T G G T = A = G = = 0 X108 = = = ? = C ? ? = = = = = I = = = = = = ? = G ? ? = = = = = D = = = 0 X109 C A = C = G C = A A C = C = A = C A G = T = C T = G G T = A = G = T 0 X110 C = = ? = G = = A A = = = = A = = A = = ? = C = = G G = = = = G = = 0 X111 C ? = C = = C = A A C = C I A = = A ? = T = = T = G G T = A D G = = 0 X112 C A = C = = C T = = = A = = = A C A G = T = = T C = = = T = = = G T 0 X113 = = = = = C = = = = = = = I = = = = = = = = G = = = = = = = D = = = 0 X114 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = 0 X115 C A = C = = C T = = = A = = = A = A G = T = = T C = = = T = = = G = 0 X116 C A = C = G C = A A C = C = A = C A G = T = C T = G G T = A = G = T 0 X117 C A G C T = = T = = = A = = = A = A G A T A = = C = = = T = = = G = 0 X118 = = = = = C = = = = = = = ? = = = = = = = = G = = = = = = = ? = = = 0 X119 C ? = C = = C T = = = A = = = A C A ? = T = = T C = = = T = = = G T 0 X120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X121 = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 0 X122 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = ? ? = = = = = 0 X123 C A G C T ? = = A A C = C I A = = A G A T A ? = = G G T = A D G = = 0 X124 C A = ? = ? ? ? A A ? ? C ? A = C A G = ? = ? ? ? G G ? ? A ? G = 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 = = = 0.94 0.94 = 0.94 = = 0.95 = 0.90 0.90 = = 0.65 0.65 0.80 = = 1.00 1.00 = 1.00 ? ? 1.00 = 1.00 1.00 1.00 = = = 1.00 = 0.98 = = = = ? ? = = = = = = = 0.97 = = = 1.00 1.00 1.00 1.00 ? ? = 1.00 = = = 1.00 = 0.94 = = = ? = 0.71 = ? ? = = 1.00 1.00 1.00 = = 0.97 1.00 = = 1.00 = = ? ? ? = = 1.00 1.00 = = ? ? 1.00 = = 0.94 0.94 = 0.94 ? ? = 0.99 1.00 1.00 1.00 = ? = ? = = 1.00 ? = 1.00 ? ? = = = = = = = = 0.78 = = 1.00 1.00 = 1.00 ? ? = = 0.99 0.99 = = = 0.98 0.99 = = 1.00 1.00 1.00 1.00 ? ? = = 1.00 1.00 1.00 = ? 1.00 1.00 = 0.69 = = = = ? ? 0.55 = 1.00 1.00 = = = = 0.99 = = = = = = ? ? = 1.00 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 ? ? = = 0.98 = = = = = = = = = = = 1.00 = = = 1.00 ? = 1.00 = = = = = = = = = = ? ? = = = = = = = = = = = = = 0.99 = 1.00 = = = = = = = = = = = = = = 0.99 = 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = = = = = = = ? = = = = 0.92 0.92 = 0.92 = = = = 1.00 1.00 1.00 = 0.74 ? 1.00 = 0.76 = = = = = = = 1.00 1.00 1.00 1.00 = 0.87 0.84 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 = = = 0.99 = = 0.99 = = = = = = 1.00 1.00 = 0.99 = 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 = = = = = = = = 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 = = = = = = = = = = = = = = 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 = = ? = = = 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 = 0.86 = = ? = = = = 0.96 0.96 = = = = 0.92 = 0.72 = = = = = 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 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 = = 1.00 = = = 0.96 = = 1.00 1.00 1.00 = = 1.00 = = ? = = = 0.83 = = 1.00 1.00 1.00 = 0.98 = 1.00 0.98 = 1.00 1.00 = ? = = = = = = = 1.00 = = ? ? = 0.99 0.99 = 0.99 = = = 0.99 1.00 1.00 1.00 = 1.00 0.99 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 ? 0.90 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 1.00 = = = 0.80 1.00 = = = ? = = = = = 1.00 = = = = = = = = = = = 1.00 = 1.00 = = 1.00 = = = = = = = = 0.93 = = = = = 0.95 = = = = = = = 1.00 = = = = 1.00 1.00 ? 1.00 = ? ? = = 1.00 = 0.99 = = = = = = = = = = = 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 = = = = ? = = = = = = = ? = 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 ? ? 0.90 0.90 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 1.00 1.00 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 = 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 1.00 = = = 1.00 = = = 1.00 0.99 = = = = = 0.95 = = = = = = = 1.00 = = = = = = = = = = = = = = = ? = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 0.95 = = = 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 = = = = = = 0.97 = = = = = = = ? = = = 1.00 ? = 1.00 = = 1.00 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 1.00 ? ? 1.00 ? 1.00 = 1.00 END PHASEPROBS