************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 tgm1x.phase.inp tgm1x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tgm1x.phase.out_freqs : haplotype frequency estimates tgm1x.phase.out_pairs : most likely haplotype pairs for each individual tgm1x.phase.out_recom : estimates of recombination parameters tgm1x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 20 Positions of loci: 277 626 2061 3854 4216 6022 8421 8760 9542 10239 10518 12631 12653 13945 14120 14778 15803 16527 16868 17649 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tgm1x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CICCTCCCAGGCAGTGTGAC 1.000000 2 CICCTCCCAGGCAGTGTAAC 1.000000 3 CICCTCCCATGCAGTGTGAC 1.000000 4 CICCTCCGAGACGGCGCGAC 6.000000 5 CICCTCCGAGGCGGCGCGAC 1.000000 6 TICCTCCCATGCAGTGTGAC 6.000000 7 TICCTCCCATGCAGTGTAAC 7.000000 8 TICCTCCCATGCGGCGCGGC 1.000000 9 TICCTCCCATGCGGTGTGAC 1.000000 10 TICCTCCCGGACGGTGCGAC 2.000000 11 TICCTCCGGGACAGTGTAAC 1.000000 12 TICCTCCGGGAGAGCGCGGG 1.000000 13 TICCTCCGGGAGGGCGCGGG 17.000000 14 TICCTCTCATGCAGTGTAAC 1.000000 15 TICCTCTCATGCGATCCGAC 1.000000 16 TICCTACCAGACGGTGTGAC 5.000000 17 TICCTACCATGCAGTGTGAC 4.000000 18 TICCTACCATGCAGTGTAAC 1.000000 19 TICCTACCATGCGGTGTGAC 2.000000 20 TICCGCCCAGACGGTGTAAC 1.000000 21 TICCGCCCATGCAGTGTGAC 3.000000 22 TICCGCCCATGCAGTGTAAC 3.000000 23 TICCGACCATGCGGTGTGAC 6.000000 24 TDCCTCCCAGGCGGCGCGGC 1.000000 25 TDCCTCCCATGCAGCGCGGG 2.000000 26 TDCCTCCCATGCAGTGTAAC 59.000000 27 TDCCTCCGGGAGGGCGCGGG 1.000000 28 TDCCTCTCATGCGATCCGAC 4.000000 29 TDCCTACCAGACGGTGCGAC 3.000000 30 TDCCTACCATGCAGTGTAAC 1.000000 31 TDCCTACCATGCGGTGTGAC 1.000000 32 TDCCGCTCATGCGATCCGAC 2.000000 33 TDCTTCCCAGACAGTGTAAC 1.000000 34 TDCTTCCCATGCAGTGTAAC 1.000000 35 TDCTTCCGGGAGGGCGCGGG 2.000000 36 TDCTTCTCATGCAGTGTAAC 1.000000 37 TDCTTCTCATGCGATCCGAC 8.000000 38 TDTCTCCCAGACGGTGTGAC 1.000000 39 TDTCTCCCAGGCGGCGCGGC 1.000000 40 TDTCTCCCATGCAGTGTGAC 8.000000 41 TDTCTCCCATGCAGTGTAAC 17.000000 42 TDTCTCCGGGACGGTGCGAC 1.000000 43 TDTCTCCGGGACGATCCGAC 1.000000 44 TDTCGCCCATGCAGTGTGAC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (5,38) D002: (8,26) D003: (7,33) D004: (37,44) D005: (26,40) D006: (19,26) D007: (21,26) D008: (4,7) D009: (26,42) D010: (24,37) D011: (41,41) D012: (1,17) D013: (3,39) D014: (26,41) D015: (26,26) DY01: (40,41) DY02: (17,18) DY03: (4,26) DY04: (4,17) DY05: (17,41) DY06: (4,19) DY07: (4,41) DY08: (16,34) DY09: (21,40) DY10: (10,41) DY11: (26,37) DY12: (2,20) E101: (32,41) E102: (26,28) E103: (26,41) E104: (26,26) E105: (30,41) E106: (26,37) E107: (26,28) E108: (26,28) E109: (26,26) E110: (26,37) E111: (16,26) E112: (23,26) E113: (26,41) E114: (7,41) E115: (26,26) E116: (26,26) E117: (23,26) E118: (26,32) E119: (26,43) E120: (26,26) E121: (16,41) E122: (31,37) H101: (7,7) H102: (4,26) H103: (27,40) H104: (26,40) H105: (15,16) H106: (23,23) H107: (7,26) H108: (26,26) H109: (26,26) H110: (40,41) H111: (16,26) H112: (26,41) H113: (23,35) H114: (9,10) H115: (22,26) H116: (23,26) H117: (22,29) H118: (7,26) H119: (26,26) H120: (22,41) H121: (26,26) H122: (26,35) X101: (13,25) X102: (26,26) X103: (6,29) X104: (13,40) X105: (14,26) X106: (13,28) X107: (6,13) X108: (25,26) X109: (13,13) X110: (13,37) X111: (13,21) X112: (13,36) X113: (37,40) X114: (11,13) X115: (12,13) X116: (13,13) X117: (6,13) X118: (13,26) X119: (6,26) X120: (13,26) X121: (13,26) X122: (26,41) X123: (6,6) X124: (26,29) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C I C C T C C G A G G C G G C G C G A C T D T C T C C C A G A C G G T G T G A C 0 D002 T (I) C C T C C C A T G C G G C G C G G C T (D) C C T C C C A T G C A G T G T A A C 0 D003 T (I) C (C) T C C C A T G C A G T G T A A C T (D) C (T) T C C C A G A C A G T G T A A C 0 D004 T D C T (T) C T C A T G C G A T C C G A C T D T C (G) C C C A T G C A G T G T G A C 0 D005 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T G A C 0 D006 T (I) C C T A C C A T G C G G T G T G A C T (D) C C T C C C A T G C A G T G T A A C 0 D007 T I C C G C C C A T G C A G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 D008 C I C C T C C G A G A C G G C G C G A C T I C C T C C C A T G C A G T G T A A C 0 D009 T D (C) C T C C C A T G C A G T G T A A C T D (T) C T C C G G G A C G G T G C G A C 0 D010 T D C C T C C C A G G C G G C G C G G C T D C T T C T C A T G C G A T C C G A C 0 D011 T D T C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 D012 C I C C T C C C A G G C A G T G T G A C T I C C T A C C A T G C A G T G T G A C 0 D013 (C) (I) (C) C T C C C A (T) G C A G T G T G A C (T) (D) (T) C T C C C A (G) G C G G C G C G G C 0 D014 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 D015 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 DY01 T D T C T C C C A T G C A G T G T G A C T D T C T C C C A T G C A G T G T A A C 0 DY02 T I C C T A C C A T G C A G T G T G A C T I C C T A C C A T G C A G T G T A A C 0 DY03 C I C C T C C G A G A C G G C G C G A C T D C C T C C C A T G C A G T G T A A C 0 DY04 C I C C T C C G A G A C G G C G C G A C T I C C T A C C A T G C A G T G T G A C 0 DY05 T I C C T A C C A T G C A G T G T (G) A C T D T C T C C C A T G C A G T G T (A) A C 0 DY06 C I C C T C C G A G A C G G C G C G A C T I C C T A C C A T G C G G T G T G A C 0 DY07 C I C C T C C G A G A C G G C G C G A C T D T C T C C C A T G C A G T G T A A C 0 DY08 T I C C T A C C A (G) (A) C G G T G T G A C T D C T T C C C A (T) (G) C A G T G T A A C 0 DY09 T I C C (G) C C C A T G C A G T G T G A C T D T C (T) C C C A T G C A G T G T G A C 0 DY10 T I C C T C C C G G A C G G T G C G A C T D T C T C C C A T G C A G T G T A A C 0 DY11 T D C C T C C C A T G C A G T G T A A C T D C T T C T C A T G C G A T C C G A C 0 DY12 C I C C T C C C A G G C (A) G T G T A A C T I C C G C C C A G A C (G) G T G T A A C 0 E101 T D (C) C G C T C A T G C G A T C C G A C T D (T) C T C C C A T G C A G T G T A A C 0 E102 T D C C T C C C A T G C A G T G T A A C T D C C T C T C A T G C G A T C C G A C 0 E103 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 E104 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 E105 T D (C) C T A C C A T G C A G T G T A A C T D (T) C T C C C A T G C A G T G T A A C 0 E106 T D C C T C C C A T G C A G T G T A A C T D C T T C T C A T G C G A T C C G A C 0 E107 T D C C T C C C A T G C A G T G T A A C T D C C T C T C A T G C G A T C C G A C 0 E108 T D C C T C C C A T G C A G T G T A A C T D C C T C T C A T G C G A T C C G A C 0 E109 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 E110 T D C C T C C C A T G C A G T G T A A C T D C T T C T C A T G C G A T C C G A C 0 E111 T I C C T A C C A G A C G G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 E112 T I C C G A C C A T G C G G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 E113 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 E114 T I C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 E115 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 E116 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 E117 T I C C G A C C A T G C G G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 E118 T D C C T C C C A T G C A G T G T A A C T D C C G C T C A T G C G A T C C G A C 0 E119 T D (C) C T C C C A T G C A G T G T A A C T D (T) C T C C G G G A C G A T C C G A C 0 E120 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 E121 T I C C T A C C A G A C G G T G T G A C T D T C T C C C A T G C A G T G T [A] A C 0 E122 T D C C T A C C A T G C G G T G T G A C T D C T T C T C A T G C G A T C C G A C 0 H101 T I C C T C C C A T G C A G T G T A A C T I C C T C C C A T G C A G T G T A A C 0 H102 C I C C T C C G A G A C G G C G C G A C T D C C T C C C A T G C A G T G T A A C 0 H103 T D C C T C C G G G A G G G C G C G G G T D T C T C C C A T G C A G T G T G A C 0 H104 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T G A C 0 H105 T I C C T C T C A T G C G A T C C G A C T I C C T A C C A G A C G G T G T G A C 0 H106 T I C C G A C C A T G C G G T G T G A C T I C C G A C C A T G C G G T G T G A C 0 H107 T I C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H108 T D C C T C C C A T G C A G T G T A A C T [D] C C T C C C A T G C A G T G T A A C 0 H109 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H110 T D T C T C C C A T G C A G T G T G A C T D T C T C C C A T G C A G T G T A A C 0 H111 T I C C T A C C A G A C G G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 H112 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 H113 T I C C G A C C A T G C G G T G T G A C T D C T T C C G G G A G G G C G C G G G 0 H114 T I C C T C C C A T G C G G T G T G A C T I C C T C C C G G A C G G T G C G A C 0 H115 T I C C G C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H116 T I C C G A C C A T G C G G T G T G A C T D C C T C C C A T G C A G T G T A A C 0 H117 T (I) C C (G) C C C A T G C A G T G T A A C T (D) C C (T) A C C A G A C G G T G C G A C 0 H118 T I C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H119 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H120 T I C C G C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 H121 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 H122 T D C C T C C C A T G C A G T G T A A C T D C T T C C G G G A G G G C G C G G G 0 X101 T I C C T C C G G G A G G G C G C G G G T D C C T C C C A T G C A G C G C G G G 0 X102 T D C C T C C C A T G C A G T G T A A C T D C C T C C C A T G C A G T G T A A C 0 X103 T (I) C C T C C C A T G C A G T G T G A C T (D) C C T A C C A G A C G G T G C G A C 0 X104 T I C C T C C G G G A G G G C G C G G G T D T C T C C C A T G C A G T G T G A C 0 X105 T (I) C C T C T C A T G C A G T G T A A C T (D) C C T C C C A T G C A G T G T A A C 0 X106 T I C C T C C G G G A G G G C G C G G G T D C C [T] C T C A T G C G A T C C G A C 0 X107 T I C C T C C C A T G C A G T G T G A C T I C C T C C G G G A G G G C G C G G G 0 X108 T D C C T C C C A T G C A G C G C G G G T D C C T C C C A T G C A G T G T A A C 0 X109 T I C C T C C G G G A G G G C G C G G G T I C C T C C G G G A G G G C G C G G G 0 X110 T I C C T C C G G G A G G G C G C G G G T D C T T C T C A T G C G A T C C G A C 0 X111 T I C C T C C G G G A G G G C G C G G G T I C C G C C C A T G C A G T G T G A C 0 X112 T (I) C (C) T C C G G G A G G G C G C G G G T (D) C (T) T C T C A T G C A G T G T A A C 0 X113 T D C T T C T C A T G C G A T C C G A C T D T C T C C C A T G C A G T G T G A C 0 X114 T I C C T C C G G G A C A G T G T [A] A C T I C C T C C G G G A G G G C G C G G G 0 X115 T I C C T C C G G G A G A G C G C G G G T I C C T C C G G G A G G G C G C G G G 0 X116 T I C C T C C G G G A G G G C G C G G G T I C C T C C G G G A G G G C G C G G G 0 X117 T I C C T C C C A T G C A G T G T G A C T I C C T C C G G G A G G G C G C G G G 0 X118 T I C C T C C G G G A G G G C G C G G G T D C C T C C C A T G C A G T G T A A C 0 X119 T (I) C C T C C C A T G C A G T G T G A C T (D) C C T C C C A T G C A G T G T A A C 0 X120 T I C C T C C G G G A G G G C G C G G G T D C C T C C C A T G C A G T G T A A C 0 X121 T I C C T C C G G G A G G G C G C G G G T [D] C C T C C C A T G C A G T G T A A C 0 X122 T D C C T C C C A T G C A G T G T A A C T D T C T C C C A T G C A G T G T A A C 0 X123 T I C C T C C C A T G C A G T G T G A C T I C C T C C C A T G C A G T G T G A C 0 X124 T [D] C C T C C C A T G C A G T G T A A C T [D] C C T A C C A G A C G G T G C G A 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 C I C = = = = G = = G ? ? = C = C = = = T D T = = = = C = = A ? ? = T = T = = = 0 D002 = (I) = = = = = = = = = = G = C = C G G = = (D) = = = = = = = = = = A = T = T A A = 0 D003 = (I) = (C) = = = = = T G = = = = = = = = = = (D) = (T) = = = = = G A = = = = = = = = = 0 D004 = = C T (T) = T = = = = = G A = C C = = = = = T C (G) = C = = = = = A G = G T = = = 0 D005 = = C = ? = = = = = ? = = = = = = A = = = = T = ? = = = = = ? = = = = = = G = = 0 D006 = (I) = = = A = = = = = = G = = = = G = = = (D) = = = C = = = = = = A = = = = A = = 0 D007 = I = = G = = = = = = = = = = = = G = = = D = = T = = = = = = = = = = = = A = = 0 D008 C = = = = = = G = G A = G = C = C G = = T = = = = = = C = T G = A = T = T A = = 0 D009 = = (C) = = = = C A T G = A = = = T A = ? = = (T) = = = = G G G A = G = = = C G = ? 0 D010 = = = C = = C = = G = ? ? G C G = = G = = = = T = = T = = T = ? ? A T C = = A = 0 D011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D012 C = = = = C = = = G = = = = = = = = = = T = = = = A = = = T = = = = = = = = = = 0 D013 (C) (I) (C) = = = = = = (T) = = A = T = T = A = (T) (D) (T) = = = = = = (G) = = G = C = C = G = 0 D014 = = C = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = 0 D015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY01 = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = A = = 0 DY02 = = = = = = = = = = = = = = = ? = G = ? = = = = = = = = = = = = = = = ? = A = ? 0 DY03 C I = = = = = G = G A = G = C = C G = = T D = = = = = C = T G = A = T = T A = = 0 DY04 C = = = = C = G = G A = G = C = C = = = T = = = = A = C = T G = A = T = T = = = 0 DY05 = I C = = A = = = = = = = = = = = (G) = = = D T = = C = = = = = = = = = = = (A) = = 0 DY06 C = = = = C = G = G A = = = C = C = = = T = = = = A = C = T G = = = T = T = = = 0 DY07 C I C = = = = G = G A = G = C = C G = = T D T = = = = C = T G = A = T = T A = = 0 DY08 = I = C = A = = = (G) (A) = G = = = = G = = = D = T = C = = = (T) (G) = A = = = = A = = 0 DY09 = I C = (G) = = = = = = = = = = = = = = = = D T = (T) = = = = = = = = = = = = = = = 0 DY10 = I C = = = ? = G G A = G = = = C G = = = D T = = = ? = A T G = A = = = T A = = 0 DY11 = = = C = = C = = = = = A G = G T A = = = = = T = = T = = = = = G A = C C G = = 0 DY12 C = = = T = = = = = G = (A) = = = = = = = T = = = G = = = = = A = (G) = = = = = = = 0 E101 = = (C) = G = T = = = = = G A = C C G = = = = (T) = T = C = = = = = A G = G T A = = 0 E102 = = = = = = C = = = = = A G = ? T A = = = = = = = = T = = = = = G A = ? C G = = 0 E103 = = C = ? = = = = = = = = = = = = = = = = = T = ? = = = = = = = = = = = = = = = 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 = = (C) = = A = = = = = = = = = = = = = = = = (T) = = C = = = = = = = = = = = = = = 0 E106 = = = C = = C = = = = = A G = G T A = = = = = T = = T = = = = = G A = C C G = = 0 E107 = = = = = = C = = = = = A G = G T A = = = = = = = = T = = = = = G A = C C G = = 0 E108 = = = = = = C = = = = = A G = G T A = = = = = = = = T = = = = = G A = C C G = = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = = = C = = C = = = = = A G = G T A = = = = = T = = T = = = = = G A = C C G = = 0 E111 = I = = ? A = = = G A = G = = = = G = = = D = = ? C = = = T G = A = = = = A = = 0 E112 = I = = G A = = = = = = G = = = = G = = = D = = T C = = = = = = A = = = = A = = 0 E113 = = C = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = 0 E114 = I C = = = = = = = = = = = = = = = = = = D T = = = = = = = = = = = = = = = = = 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = 0 E117 = I = = G A = = = = = = G = = = = G = = = D = = T C = = = = = = A = = = = A = = 0 E118 = = = = T = C = = = = = A G = G T A = = = = = = G = T = = = = = G A = C C G = = 0 E119 = = (C) = ? = = C A T G = A G = G T A = = = = (T) = ? = = G G G A = G A = C C G = = 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 = I C = = A = = = G A ? ? = = ? = ? ? ? = D T = = C = = = T G ? ? = = ? = ? ? ? 0 E122 = = = C = A C = = = = = = G = G T = = = = = = T = C T = = = = = = A = C C = = = 0 H101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H102 C I = = = = = ? = G A = G = C = C G = = T D = = = = = ? = T G = A = T = T A = = 0 H103 = = C = ? = = G G G A G G = C = C = G G = = T = ? = = C A T G C A = T = T = A C 0 H104 = = C = = = = = = = = = = = = = = A = = = = T = = = = = = = = = = = = = = G = = 0 H105 = = = = = C T = = T G = = A = C C = = = = = = = = A C = = G A = = G = G T = = = 0 H106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H107 = I = = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = 0 H108 ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = 0 H109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H110 = ? = = = = = = = = = = = = = = = G = = = ? = = = = = = = = = = = = = = = A = = 0 H111 = I = = = A = = = G A = G = = = = G = = = D = = = C = = = T G = A = = = = A = = 0 H112 = = C = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = 0 H113 = I = C G A = C A T G C = = T = T = A C = D = T T C = G G G A G = = C = C = G G 0 H114 = = = = = = = ? A T G = = = = = T = = = = = = = = = = ? G G A = = = = = C = = = 0 H115 = I = = G = = = = = = = = = = = = = = = = D = = T = = = = = = = = = = = = = = = 0 H116 = I = = G A = = = = = = G = = = = G = = = D = = T C = = = = = = A = = = = A = = 0 H117 = (I) = = (G) C = = = T G = A = = = T A = = = (D) = = (T) A = = = G A = G = = = C G = = 0 H118 = I = = = = ? = = = = = = = = = = = = = = D = = = = ? = = = = = = = = = = = = = 0 H119 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H120 = I C = G = = = = = = = = = = = = = = = = D T = T = = = = = = = = = = = = = = = 0 H121 = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 0 H122 = = = C = = = C A T G ? A = T = T A A C = = = T = = = G G G A ? G = C = C G G G 0 X101 = I = = = = = G G G A G G = = ? = = = = = D = = = = = C A T G C A = = ? = = = = 0 X102 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = 0 X103 = (I) = = ? C = = = T ? = A = = = T = = = = (D) = = ? A = = = G ? = G = = = C = = = 0 X104 = I C = ? = = G G G A G G = C = C = G G = D T = ? = = C A T G C A = T = T = A C 0 X105 = (I) = = = = T = = = = = = = = = = = = = = (D) = = = = C = = = = = = = = = = = = = 0 X106 = I = = ? = C G G G A ? ? G C G = = G G = D = = ? = T C A T G ? ? A T C = = A C 0 X107 = = = = = = = C A T G C A = T = T = A C = = = = = = = G G G A G G = C = C = G G 0 X108 = = = = = = = = = = = = = = C = C G G G = = = = = = = = = = = = = = T = T A A C 0 X109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X110 = I = C = = C G G G A G = G C G = = G G = D = T = = T C A T G C = A T C = = A C 0 X111 = = = = T = = G G G A G G = C = C = G G = = = = G = = C A T G C A = T = T = A C 0 X112 = (I) = (C) = = C G G G A G G = C = C G G G = (D) = (T) = = T C A T G C A = T = T A A C 0 X113 = = C T = = T = = = = = G A = C C = = = = = T C = = C = = = = = A G = G T = = = 0 X114 = = = = = = = = = = = C A = T = T ? A C = = = = = = = = = = = G G = C = C ? G G 0 X115 = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = G = = = = = = = 0 X116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X117 = = = = = = ? C A T G C A = T = T = A C = = = = = = ? G G G A G G = C = C = G G 0 X118 = I = = = ? = G G G A G G = C = C G G G = D = = = ? = C A T G C A = T = T A A C 0 X119 = (I) ? = = = = = = = = = = = = = = G = = = (D) ? = = = = = = = = = = = = = = A = = 0 X120 = I = = = = = G G G A G G = C ? C G G G = D = = = = = C A T G C A = T ? T A A C 0 X121 = ? = = = = = G G G A G G = C = C G G G = ? = = = = = C A T G C A = T = T A A C 0 X122 = = C = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = 0 X123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X124 = ? = = ? C = ? = T G = A = = = T A = = = ? = = ? A = ? = G A = G = = = C G = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.99 0.99 0.99 = = = = 0.97 = = 0.91 ? ? = 0.91 = 0.91 = = = = 0.68 = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = 0.67 = 0.73 = = = = = 1.00 1.00 = = = = = = = = = = = 0.96 0.91 0.66 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = = = = = 0.93 = ? = = = = = ? = = = = = = 1.00 = = = 0.86 = = = 0.98 = = = = = = 1.00 = = = = 1.00 = = = 0.99 = = 0.98 = = = = = = = = = = = = 0.93 = = 1.00 = = = = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = 0.54 = = = = 0.96 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 = ? = = = 0.92 = = 1.00 = = 1.00 = ? ? 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 0.99 = = = 0.98 = = = = = = = = = = 0.55 0.55 0.53 = = = = = = 0.50 = = 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 = = = = 0.99 0.99 = = 0.96 = = = = = = = = = = = 0.81 = = 1.00 = = = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = 0.93 = 0.92 = 0.99 = = = 0.70 0.70 = 0.99 = = = = 0.99 = = = 1.00 1.00 = 0.77 = = = = = = = = = = = = = = = = 0.92 0.91 = = = ? = 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 = = 0.94 = = = 0.95 = = = = = 0.97 = 0.57 = = = = = = = = = 0.89 = 0.92 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = 1.00 = = = = = 1.00 1.00 = ? 1.00 1.00 = = = = 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.59 = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = 0.98 = = ? 1.00 = = = 0.99 0.99 = 1.00 = = = = 1.00 = = = 0.98 = = 0.98 1.00 = = = = = = 1.00 = = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = 0.98 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0.98 = = 0.98 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = 0.91 = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = 0.54 = ? = = 0.93 0.93 0.93 0.93 = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = 0.97 = = = 0.99 0.99 ? ? = = ? = ? ? ? = = = 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 = = = = 0.92 = ? = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = 0.92 = = = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = 0.99 = 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 = = = = 0.97 = = 1.00 = = = = = = = = = = = = = = = = 0.98 = = 0.98 1.00 = = = = = = 1.00 = = = = 1.00 = = = 0.69 = = 0.67 1.00 = = = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = = 1.00 = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 0.99 = 0.94 = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = 0.95 = = = 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 = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = 0.79 = = ? 0.98 = = = 1.00 ? = 1.00 = = = 0.97 = = = = 0.98 0.98 = ? = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = 0.73 = = = = 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 0.98 = 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 0.97 = 0.96 = = 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 = 0.70 = 0.70 = = 0.97 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 = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 1.00 1.00 1.00 1.00 1.00 0.99 = 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 = 0.78 ? = = = = = = = = = = = = = = 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 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? 1.00 = ? = 1.00 1.00 = 1.00 = = = 1.00 1.00 = = END PHASEPROBS