************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 slca6.phase.inp slca6.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST slca6.phase.out_freqs : haplotype frequency estimates slca6.phase.out_pairs : most likely haplotype pairs for each individual slca6.phase.out_recom : estimates of recombination parameters slca6.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 19 Positions of loci: 459 512 810 917 1441 2241 2504 2541 3419 3996 4120 4400 4810 6259 6481 8156 8200 10044 10580 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file slca6.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CAGACAGAAAGCCCTGCGA 3.000000 2 CAGACATGAAGCCCTGCGA 1.000000 3 CAGACATGACGCTCTGCGA 44.000000 4 CAGACATGACGCTCTGTGA 18.000000 5 CAGACATGACGCTCTACGA 1.000000 6 CAGACATGACGCTTAGCGA 1.000000 7 CAGACATGTCGCTCTGCGA 25.000000 8 CAGACGGAAAGCCCTGCGA 27.000000 9 CAGACGGAACGCCCTGCGA 3.000000 10 CAGACGGGACGCCCTGCGA 1.000000 11 CAGATGGAAAGCCTAGCGA 3.000000 12 CAGGTAGAAAGCCCTGCGA 2.000000 13 CAGGTAGAAAGCTCTGCGA 1.000000 14 CAGGTATAAAGCCTAGCGA 2.000000 15 CAGGTGGAAAGCCCTACGA 1.000000 16 CAGGTGGAAAGCCTAGCGA 2.000000 17 CAAACGTGAAGCTCTACGA 2.000000 18 CAAGCATGAAACTCTGCGA 5.000000 19 CAAGCGGAAAGCCCTGCGA 1.000000 20 CAAGCGGAACGCCCTACGA 4.000000 21 CAAGCGGGACGCCCTACGA 1.000000 22 CAAGTGGAAAGCCCTGCGA 16.000000 23 CAAGTGGAAAGCCTAGCGA 2.000000 24 CAAGTGGAAAGTCCTGCGA 13.000000 25 CAAGTGGAACGCCCTACGA 1.000000 26 GGGACATGACGCTCTGCAG 2.000000 27 GGGACATGTCGCCCTGCAG 2.000000 28 GGGGCATGAAACCCTGCAG 4.000000 29 GGGGCATGACGCCCTGCAG 1.000000 30 GGGGCATGTCGCCCTGCAG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,16) D002: (1,3) D003: (14,14) D004: (11,18) D005: (3,7) D006: (3,12) D007: (5,23) D008: (3,7) D009: (3,8) D010: (4,20) D011: (7,9) D012: (17,25) D013: (20,29) D014: (3,3) D015: (3,23) DY01: (3,20) DY02: (6,12) DY03: (3,3) DY04: (1,3) DY05: (13,27) DY06: (7,30) DY07: (1,17) DY08: (15,18) DY09: (3,19) DY10: (3,21) DY11: (3,20) DY12: (3,3) E101: (9,18) E102: (9,18) E103: (3,11) E104: (10,11) E105: (22,26) E106: (3,28) E107: (8,22) E108: (7,8) E109: (7,8) E110: (8,8) E111: (4,8) E112: (22,27) E113: (16,26) E114: (3,8) E115: (7,8) E116: (4,22) E117: (7,8) E118: (7,8) E119: (3,8) E120: (7,8) E121: (8,18) E122: (7,8) H101: (4,7) H102: (7,7) H103: (3,22) H104: (22,22) H105: (7,8) H106: (3,7) H107: (4,4) H108: (3,7) H109: (4,22) H110: (7,28) H111: (3,4) H112: (7,22) H113: (7,8) H114: (7,8) H115: (3,28) H116: (3,22) H117: (3,22) H118: (4,4) H119: (4,8) H120: (3,7) H121: (4,28) H122: (3,4) X101: (3,22) X102: (8,24) X103: (24,24) X104: (8,24) X105: (4,24) X106: (24,24) X107: (8,24) X108: (22,24) X109: (3,22) X110: (3,24) X111: (8,24) X112: (3,8) X113: (3,3) X114: (7,8) X115: (3,4) X116: (4,8) X117: (3,7) X118: (4,8) X119: (3,22) X120: (2,3) X121: (3,4) X122: (7,22) X123: (3,24) X124: (3,24) 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 A C A T G A C G C T C T G C G A C A G G T G G A A A G C C T A G C G A 0 D002 C A G A C A G A A A G C C C T G C G A C A G A C A T G A C G C T C T G C G A 0 D003 C A G G T A T A A A G C C T A G C G A C A G G T A T A A A G C C T A G C G A 0 D004 C A G A T G G A A A G C C T A G C G A C A A G C A T G A A A C T C T G C G A 0 D005 C A G A C A T G A C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 D006 C A G A C A T G A C G C T C T G C G A C A G G T A G A A A G C C C T G C G A 0 D007 C A G A C A T G A C G C T (C) (T) (A) C G A C A A G T G G A A A G C C (T) (A) (G) C G A 0 D008 C A G A C A T G A C G C T C T G C G A C A G A C A T G [T] C G C T C T G C G A 0 D009 C A G A C A T G A C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 D010 C A G A C A T G A C G C T C T G T G A C A A G C G G A A C G C C C T A C G A 0 D011 C A G A C A T G T C G C T C T G C G A C A G A C G G A A C G C C C T G C G A 0 D012 C A A A (C) G T G A A G C T C T A C G A C A A G (T) G G A A C G C C C T A C G A 0 D013 C A A G C G G A A C G C C C T A C G A G G G G C A T G A C G C C C T G C A G 0 D014 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G C G A 0 D015 C A G A C A T G A C G C T (C) (T) G C G A C A A G T G G A A A G C C (T) (A) G C G A 0 DY01 C A G A C A T G A C G C T C T G C G A C A A G C G G A A C G C C C T A C G A 0 DY02 C A G A C A T G A C G C T (T) (A) G C G A C A G G T A G A A A G C C (C) (T) G C G A 0 DY03 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G C G A 0 DY04 C A G A C A G A A A G C C C T G C G A C A G A C A T G A C G C T C T G C G A 0 DY05 C A G G T A G A (A) A G C (T) C T G C G A G G G A C A T G (T) C G C (C) C T G C A G 0 DY06 C A G (A) C A T G T C G C T C T G C G A G G G (G) C A T G T C G C C C T G C A G 0 DY07 C A G A C (A) G A A A G C C C T G C G A C A A A C (G) T G A A G C T C T A C G A 0 DY08 C A (G) G T G G A A A G C C C T (A) C G A C A (A) G C A T G A A A C T C T (G) C G A 0 DY09 C A (G) (A) C A T G A C G C T C T G C G A C A (A) (G) C G G A A A G C C C T G C G A 0 DY10 C A G A C A T G A C G C T C T G C G A C A A G C G G G A C G C C C T A C G A 0 DY11 C A G A C A T G A C G C T C T G C G A C A A G C G G A A C G C C C T A C G A 0 DY12 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G C G A 0 E101 C A G A C (G) (G) (A) A C G C (C) C T G C G A C A A G C (A) (T) (G) A A A C (T) C T G C G A 0 E102 C A (G) (A) C G G A A (C) (G) C C C T G C G A C A (A) (G) C A T G A (A) (A) C T C T G C G A 0 E103 C A G A C A T G A C G C T C T G C G A C A G A T G G A A A G C C T A G C G A 0 E104 C A G A C G G G A C G C C C T G C G A C A G A T G G A A A G C C T A G C G A 0 E105 C A A G T G G A A A G C C C T G C G A G G G A C A T G A C G C T C T G C A G 0 E106 C A G A C A T G [A] C G C T C T G C G A G G G G C A T G A A A C C C T G C A G 0 E107 C A G A C G G A A A G C C C T G C G A C A A G T G G A A A G C C C T G C G A 0 E108 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E109 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E110 C A G A C G G A A A G C C C T G C G A C A G A C G G A A A G C C C T G C G A 0 E111 C A G A C A T G A C G C T C T G T G A C A G A C G G A A A G C C C T G C G A 0 E112 C A A (G) T G G A A A G C C C T G C G A G G G (A) C A T G T C G C C C T G C A G 0 E113 C A G G T G G A A A G C C T A G C G A G G G A C A T G A C G C T C T G C A G 0 E114 C A G A C A T G A C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E115 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E116 C A G A C A T G A C G C T C T G T G A C A A G T G G A A A G C C C T G C G A 0 E117 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E118 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E119 C A G A C A T G A C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E120 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 E121 C A G A C G G A A A G C C C T G C G A C A A G C A T G A A A C T C T G C G A 0 E122 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 H101 C A G A C A T G A C G C T C T G T G A C A G A C A T G T C G C T C T G C G A 0 H102 C A G A C A T G T C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 H103 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 H104 C A A G T G G A A A G C C C T G C G A C A A G T G G A A A G C C C T G C G A 0 H105 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 H106 C A G A C A T G A C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 H107 C A G A C A T G A C G C T C T G T G A C A G A C A T G A C G C T C T G T G A 0 H108 C A G A C A T G A C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 H109 C A G A C A T G A C G C T C T G T G A C A A G T G G A A A G C C C T G C G A 0 H110 C A G A C A T G T C G C T C T G C G A G G G G C A T G A A A C C C T G C A G 0 H111 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G T G A 0 H112 C A G A C A T G T C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 H113 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 H114 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 H115 C A G A C A T G A C G C T C T G C G A G G G G C A T G A A A C C C T G C A G 0 H116 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 H117 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 H118 C A G A C A T G A C G C T C T G T G A C A G A C A T G A C G C T C T G T G A 0 H119 C A G A C A T G A C G C T C T G T G A C A G A C G G A A A G C C C T G C G A 0 H120 C A G A C A T G A C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 H121 C A G A C A T G A C G C T C T G T G A G G G G C A T G A A A C C C T G C A G 0 H122 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G T G A 0 X101 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 X102 C A G A C G G A A A G C C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X103 C A A G T G G A A A G T C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X104 C A G A C G G A A A G C C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X105 C A G A C A T G A C G C T C T G T G A C A A G T G G A A A G T C C T G C G A 0 X106 C A A G T G G A A A G T C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X107 C A G A C G G A A A G C C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X108 C A A G T G G A A A G C C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X109 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 X110 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G T C C T G C G A 0 X111 C A G A C G G A A A G C C C T G C G A C A A G T G G A A A G T C C T G C G A 0 X112 C A G A C A T G A C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 X113 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G C G A 0 X114 C A G A C A T G T C G C T C T G C G A C A G A C G G A A A G C C C T G C G A 0 X115 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G T G A 0 X116 C A G A C A T G A C G C T C T G T G A C A G A C G G A A A G C C C T G C G A 0 X117 C A G A C A T G A C G C T C T G C G A C A G A C A T G T C G C T C T G C G A 0 X118 C A G A C A T G A C G C T C T G T G A C A G A C G G A A A G C C C T G C G A 0 X119 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 X120 C A G A C A T G A A G C C C T G C G A C A G A C A T G A C G C T C T G C G A 0 X121 C A G A C A T G A C G C T C T G C G A C A G A C A T G A C G C T C T G T G A 0 X122 C A G A C A T G T C G C T C T G C G A C A A G T G G A A A G C C C T G C G A 0 X123 C A G A C A T G A C G C T C T G C G A C A A G T G G A A A G T C C T G C G A 0 X124 C A G A C A T G [A] C G C T C T G C G A C A A G T G G A A A G T C C T G C G A 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 = = = A C A T G = C = = T C T = = = = = = = G T G G A = A = = C T A = = = = 0 D002 = = = = = = G A = A = = C = = = = = = = = = = = = T G = C = = T = = = = = = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 = = G A T G G A = = G = C T A = = = = = = A G C A T G = = A = T C T = = = = 0 D005 = = = = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 D006 = = = A C = T G = C = = T = = = = = = = = = G T = G A = A = = C = = = = = = 0 D007 = = G A C A T G = C = = T (C) (T) (A) = = = = = A G T G G A = A = = C (T) (A) (G) = = = 0 D008 = = = = ? = = = ? ? ? = = ? ? = = = = = = = = ? = = = ? ? ? = = ? ? = = = = 0 D009 = = = = = A T G = C = = T = = = = = = = = = = = G G A = A = = C = = = = = = 0 D010 = = G A = A T G = = = = T = = G T = = = = A G = G G A = = = = C = = A C = = 0 D011 = = = = = A T G T = = = T = = = = = = = = = = = G G A A = = = C = = = = = = 0 D012 = = = A (C) = T G = A = = T = = = = = = = = = G (T) = G A = C = = C = = = = = = 0 D013 C A A = = G G A = = = = = = = A = G A G G G = = A T G = = = = = = = G = A G 0 D014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D015 = = G A C A T G = C = = T (C) (T) = = = = = = A G T G G A = A = = C (T) (A) = = = = 0 DY01 = = G A = A T G = = = = T = = G = = = = = A G = G G A = = = = C = = A = = = 0 DY02 = = ? A C = T G = C = = T (T) (A) = = = = = = ? G T = G A = A = = C (C) (T) = = = = 0 DY03 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY04 = = = = = = G A = A = = C = = = = = = = = = = = = T G = C = = T = = = = = = 0 DY05 C A = G T = G A (A) A = = (T) = = = = G A G G = A C = T G (T) C = = (C) = = = = A G 0 DY06 C A = (A) = = = = = = = = T = = = = G A G G = (G) = = = = = = = = C = = = = A G 0 DY07 = = G = = (A) G A = = = = C = = G = = = = = A = = (G) T G = = = = T = = A = = = 0 DY08 = = (G) = T G G A = = G = C = = (A) = = = = = (A) = C A T G = = A = T = = (G) = = = 0 DY09 = = (G) (A) = A T G = C = = T = = = = = = = = (A) (G) = G G A = A = = C = = = = = = 0 DY10 = = G A = A T = = = = = T = = G = = = = = A G = G G = = = = = C = = A = = = 0 DY11 = = G A = A T G = = = = T = = G = = = = = A G = G G A = = = = C = = A = = = 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E101 = = ? A = (G) (G) (A) = C G = (C) = = = = = = = = ? G = (A) (T) (G) = A A = (T) = = = = = = 0 E102 = = (G) (A) = G G A = (C) (G) = C = = = = = = = = (A) (G) = A T G = (A) (A) = T = = = = = = 0 E103 = = = = C ? T G = C = = T C T = = = = = = = = T ? G A = A = = C T A = = = = 0 E104 = = = = C = = G = C = = = C T = = = = = = = = T = = A = A = = = T A = = = = 0 E105 C A A G T G G A = A ? = C = = = = G A G G G A C A T G = C ? = T = = = = A G 0 E106 C A = A = = = = ? ? G = T = ? = = G A G G = G = = = = ? ? A = C = ? = = A G 0 E107 = = G A ? = = = = = = = = = = = = = = = = A G ? = = = = = = = = = = = = = = 0 E108 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E109 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 = = = = = A T G = C = = T = = = T = = = = = = = G G A = A = = C = = = C = = 0 E112 C A A (G) T G G A A A = = = = = = = G A G G G (A) C A T G T C = = = = = = = A G 0 E113 C A = G T G G A = A = = C T A = = G A G G = A C A T G = C = = T C T = = A G 0 E114 = = = = = A T G = C = = T = = = = ? = = = = = = G G A = A = = C = = = = ? = 0 E115 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E116 = = G A C A T G = C = = T = = = T = = = = A G T G G A = A = = C = = = C = = 0 E117 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E118 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E119 = = = = = A T G = C = = T = = = = = = = = = = = G G A = A = = C = = = = = = 0 E120 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 E121 = = G A = G G A = = G = C = = = = = = = = A G = A T G = = A = T = = = = = = 0 E122 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 H101 = = = = = = = = A = = = = = = = T = = = = = = = = = = T = = = = = = = C = = 0 H102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H103 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 H104 = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0 H105 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 H106 = = = = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 H107 = = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = ? = = ? ? = = = = 0 H108 = = = = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 H109 = = G A C A T G = C = = T = = = T = = = = A G T G G A = A = = C = = = C = = 0 H110 C A = A = = = = T C G = T = = = = G A G G = G = = = = A A A = C = = = = A G 0 H111 = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = T = = 0 H112 = = G A C A T G T C = = T = = = = = = = = A G T G G A A A = = C = = = = = = 0 H113 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 H114 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 H115 C A = A = = = = = C G = T = = ? = G A G G = G = = = = = A A = C = = ? = A G 0 H116 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 H117 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 H118 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H119 = = = = = A T G = C ? = T = = = T = = = = = = = G G A = A ? = C = = = C = = 0 H120 = = = = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 H121 C A = A = = = = = C G = T = = = T G A G G = G = = = = = A A = C = = = C A G 0 H122 = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = T = = 0 X101 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 X102 = = G A C = = = = = = C = = = = = = = = = A G T = = = = = = T = = = = = = = 0 X103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X104 = = G A C = = = = = = C = = = = = = = = = A G T = = = = = = T = = = = = = = 0 X105 = = G A C A T G = C = C T = = = T = = = = A G T G G A = A = T C = = = C = = 0 X106 = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 0 X107 = = G A C = = = = = = C = = = = = = = = = A G T = = = = = = T = = = = = = = 0 X108 = = = = ? = = = = = = C = = = = = = = = = = = ? = = = = = = T = = = = = = = 0 X109 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 X110 = = G A C A T G = C = C T = = = = = = = = A G T G G A = A = T C = = = = = = 0 X111 = = G A C = = = = = = C = = = = = = = = = A G T = = = = = = T = = = = = = = 0 X112 = = = = = A T G = C = = T = = = = = = = = = = = G G A = A = = C = = = = = = 0 X113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X114 = = = = = A T G T C = = T = = = = = = = = = = = G G A A A = = C = = = = = = 0 X115 = = = = ? = = = = = = = = = = = C = = = = = = ? = = = = = = = = = = = T = = 0 X116 = = = = = A T G = C = = T = = = T = = = = = = = G G A = A = = C = = = C = = 0 X117 = = = = = = = = A = = = = = = = = = = = = = = = = = = T = = = = = = = = = = 0 X118 = = = = = A T G = C = = T = = = T = = = = = = = G G A = A = = C = = = C = = 0 X119 = = G A C A T G = C = = T = = = = = = = = A G T G G A = A = = C = = = = = = 0 X120 = = = = = = = = = A = = C = = = = = = = = = = = = = = = C = = T = = = = = = 0 X121 = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = T = = 0 X122 = = G A C A T G T C = = T = = = = = = = = A G T G G A A A = = C = = = = = = 0 X123 = = G A C A T G = C = C T = = = = = = = = A G T G G A = A = T C = = = = = = 0 X124 = = G A ? A T G ? C ? C T = = = = = = = = A G ? G G A ? A ? T C = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = 0.98 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 0.98 0.98 = = = = = = = = = = 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 = = = = = = = = = = = = = 0.98 0.98 = 1.00 1.00 = 1.00 = = 0.95 = = = = = = = = 0.93 0.93 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 0.59 0.59 0.51 = = = = = = = ? = = = ? ? ? = = ? ? = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = = = = = = 1.00 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 0.85 = 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 = = = = = = = = = = = = = = = = = = = = = 0.91 0.92 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 0.57 0.57 = = = = = = 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 0.50 0.50 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 = = = = = = 0.97 0.97 = 0.97 0.99 = 1.00 1.00 0.83 1.00 = = 0.50 = = = = 0.96 0.96 0.99 0.99 = 0.68 = = = = = = = = 1.00 = = = = 1.00 1.00 = = 0.95 = = 0.89 1.00 1.00 = = = = 1.00 = = 1.00 = = = = = 0.71 = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = 0.83 = = = = = 0.59 0.59 = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = = = = = = 0.94 0.94 = 1.00 1.00 = = = = = 1.00 = = 0.94 = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? 0.99 = 0.83 0.83 0.83 = 0.91 1.00 = 0.83 = = = = = = = = 0.82 0.83 = 1.00 1.00 1.00 = 0.74 0.83 = 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 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 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 0.83 0.99 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 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 = 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 1.00 1.00 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 = 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 = = = 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 = = = = = = 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = 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 1.00 = 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 = = = 0.98 = = = = = = = = = = 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 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