************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /net/nickerson/lims/bin/phase/PHASE2 -d1 brafx.phase.inp brafx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST brafx.phase.out_freqs : haplotype frequency estimates brafx.phase.out_pairs : most likely haplotype pairs for each individual brafx.phase.out_recom : estimates of recombination parameters brafx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 26 Positions of loci: 730 822 1464 92302 117602 118632 126118 126434 139367 139490 143169 143338 144142 148315 148842 149563 149633 150099 150468 177419 177498 187240 191492 191724 192800 193421 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file brafx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TGAAATAGAGGTACATCAGGCCTAGI 1.000000 2 TGAAATAGAGGTACAACACGCCCAGI 4.000000 3 TGAAATAGAGGTGAATCACGCCCAGD 1.000000 4 TGAAATAGAGATACAACACGCCCAGI 1.000000 5 TGAAATAGGGGTACATCACAGCTAGI 3.000000 6 TGAACTAGAGGAACAACACGCCCAGI 2.000000 7 TGAACTAGGGGAACATCACAGCTAGI 6.000000 8 TGAGATAGAGATACATCAGGCCCAGI 1.000000 9 TGAGATAGAGATACAACACGCCTAGI 1.000000 10 TGAGATAGAGATACAACACGCCCAGI 2.000000 11 TGAGATAGAGATACGTCAGGCCCAGI 2.000000 12 TGAGATAGAGATACGACAGGCTCAAI 1.000000 13 TGAGATAGAGATACGACTGGCTCAAI 4.000000 14 TGAGATAGAGATAAATCACGCCCAGD 3.000000 15 TGAGATAGGGGTACATCACAGCTAGI 1.000000 16 TGAGATAGGGATACATCACACCTAGI 1.000000 17 TGAGATAGGGATACATCACAGCTAGI 93.000000 18 TGAGATAGGGATACATCACAGCCAGD 3.000000 19 TGAGATAGGGATAAATCACAGCTAGI 1.000000 20 TGAGATAGGAATACATCACAGCTAGI 1.000000 21 TGAGATTGGGATACATCACAGCTAGI 17.000000 22 TGGACTAGAGGAACGACTGGCTCAAI 4.000000 23 TGGACTAGAAGAACAATAGGCCCGGI 2.000000 24 TGGACAAAAAGTACAATAGGCCCAGI 4.000000 25 TGGGATAGAGATAAATCACGCCCAGD 2.000000 26 TAAACAAAGGGTACATCACAGCTAGI 1.000000 27 TAGACAAAAGGTACGACTGGCTCAAI 1.000000 28 TAGACAAAAAGTACAATAGGCCCGGI 8.000000 29 GGAAATAGAGGTGAATCACGCCCAGD 9.000000 30 GGAAATAGGGGTACATCACAGCTAGI 2.000000 31 GGAAATAGGGGTGCATCACAGCTAGI 4.000000 32 GGGAATAGAGGAACGACTGGCTCAAI 1.000000 33 GGGAATAGAGGTACGACTGGCTCAAI 2.000000 34 GGGAATAGAGGTGCATCAGGCCCAGI 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,7) D002: (17,22) D003: (17,29) D004: (7,25) D005: (9,17) D006: (6,17) D007: (6,29) D008: (17,17) D009: (3,19) D010: (10,22) D011: (13,31) D012: (17,29) D013: (17,33) D014: (5,17) D015: (31,33) DY01: (12,25) DY02: (2,13) DY03: (2,7) DY04: (8,13) DY05: (11,17) DY06: (14,17) DY07: (10,13) DY08: (14,27) DY09: (11,34) DY10: (5,32) DY11: (2,17) DY12: (4,22) E101: (7,17) E102: (17,31) E103: (7,30) E104: (7,31) E105: (5,23) E106: (17,17) E107: (17,17) E108: (17,28) E109: (17,17) E110: (17,17) E111: (17,17) E112: (26,30) E113: (17,23) E114: (17,17) E115: (17,28) E116: (17,17) E117: (20,28) E118: (17,17) E119: (17,28) E120: (17,28) E121: (14,28) E122: (17,17) H101: (17,21) H102: (17,17) H103: (17,21) H104: (17,17) H105: (17,17) H106: (17,21) H107: (17,17) H108: (17,17) H109: (18,21) H110: (17,21) H111: (17,17) H112: (17,21) H113: (17,17) H114: (2,29) H115: (16,28) H116: (17,18) H117: (17,18) H118: (17,21) H119: (21,22) H120: (15,17) H121: (17,28) H122: (17,17) X101: (17,24) X102: (29,29) X103: (17,24) X104: (21,24) X105: (17,17) X106: (17,29) X107: (17,17) X108: (17,21) X109: (17,21) X110: (17,17) X111: (17,29) X112: (21,24) X113: (17,17) X114: (17,21) X115: (17,17) X116: (17,21) X117: (17,29) X118: (17,17) X119: (17,17) X120: (17,21) X121: (17,17) X122: (17,21) X123: (17,17) X124: (17,21) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T G A A (A) T A G A G G (T) A C A T C A G G C C T A G I T G A A (C) T A G G G G (A) A C A T C A C A G C T A G I 0 D002 T G A G A T A G G G A T A C A T C A C A G C T A G I T G G A C T A G A G G A A C G A C T G G C T C A A I 0 D003 T G A G A T A G G G A T A C A T C A C A G C T A G I [G] G A A A T A G A G G T G A A T C A C G C C C A G D 0 D004 T G A (A) (C) T A G G G (G) (A) A C A T C A C A G C T A G I T G G (G) (A) T A G A G (A) (T) A A A T C A C G C C C A G D 0 D005 T G A G A T A G A G A T A C A A C A C G C C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 D006 T G A A C T A G A G G A A C A A C A C G C C C A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 D007 T G A A C T A G A G G A A C A A C A C G C C C A G I [G] G A A A T A G A G G T G A A T C A C G C C C A G D 0 D008 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 D009 T G A (A) A T A G A G G T [G] A A T C A C G C C C A G D T G A (G) A T A G G G [A] T A A A T C A C A G C T A G I 0 D010 T G A G A T A G A G A T A C A A C A C G C C C A G I T G G A C T A G A G G A A C G A C T G G C T C A A I 0 D011 (T) G A (G) A T A G A G (A) T (A) C G A C T G G C T C A A I (G) G A (A) A T A G G G (G) T (G) C A T C A C A G C T A G I 0 D012 T G A G A T A G G G A T A C A T C A C A G C T A G I G G A A A T A G A G G T G A A T C A C G C C C A G D 0 D013 (T) G (A) (G) A T A G G G (A) T A C A T C A C A G C T A G I (G) G (G) (A) A T A G A G (G) T A C G A C T G G C T C A A I 0 D014 T G A A A T A G G G G T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 D015 G G (A) A A T A G G G G T (G) C A T C A C A G C T A G I G G (G) A A T A G A G G T (A) C G A C T G G C T C A A I 0 DY01 T G (A) G A T A G A G A T A C G A C A G G C [T] C A [A] I T G (G) G A T A G A G A T A A A T C A C G C C C A G D 0 DY02 T G A A A T A G A G G T A C A A C A C G C C C A G I T G A G A T A G A G A T A C G A C T G G C T C A A I 0 DY03 T G A A (A) T A G A G G [T] A C A A C A C G C C C A G I T G A A (C) T A G G G G [A] A C A T C A C A G C T A G I 0 DY04 T G A G A T A G A G A T A C (A) T C A G G C C C A G I T G A G A T A G A G A T A C (G) A C T G G C T C A A I 0 DY05 T G A G A T A G A G A T A C (G) T C A G G C C C A G I T G A G A T A G G G A T A C (A) T C A C A G C T A G I 0 DY06 T G A G A T A G A G A T A A A T C A C G C C C A G D T G A G A T A G G G A T A C A T C A C A G C T A G I 0 DY07 T G A G A T A G A G A T A C A A C A C G C C C A G I T G A G A T A G A G A T A C G A C T G G C T C A A I 0 DY08 T (G) (A) (G) (A) (T) A (G) A G (A) T A A A T C A C G C C C A G D T (A) (G) (A) (C) (A) A (A) A G (G) T A C G A C T G G C T C A A I 0 DY09 T G (A) G A T A G A G A T A C (G) T C A G G C C C A G I [G] G (G) A A T A G A G G T G C (A) T C A G G C C C A G I 0 DY10 (T) G (A) A A T A G G G G (T) A C A T C A C A G C T A G I (G) G (G) A A T A G A G G (A) A C G A C T G G C T C A A I 0 DY11 T G A A A T A G A G G T A C A A C A C G C C C A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 DY12 T G A A (A) T A G A G (A) (T) A C A A C A C G C C C A G I T G G A (C) T A G A G (G) (A) A C G A C T G G C T C A A I 0 E101 T G A A C T A G G G G A A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E102 T G A G A T A G G G A T A C A T C A C A G C T A G I [G] G A A A T A G G G G T G C A T C A C A G C T A G I 0 E103 (T) G A A C T A G G G G A A C A T C A C A G C T A G I (G) G A A A T A G G G G T A C A T C A C A G C T A G I 0 E104 T G A A C T A G G G G A A C A T C A C A G C T A G I [G] G A A A T A G G G G T G C A T C A C A G C T A G I 0 E105 T G A A A T A G G G G T A C A T C A C A G C T A G I T G G A C T A G A A G A A C A A T A G G C C C G G I 0 E106 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E107 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E108 T G A G A T A G G G A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E109 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E110 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E111 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E112 T A A A C A A A G G G T [A] C A T C A C A G C T A G I G G A A A T A G G G G T [A] C A T C A C A G C T A G I 0 E113 T G A G A T A G G G A T A C A T C A C A G C T A G I T G G A C T A G A A G A A C A A T A G G C C C G G I 0 E114 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E115 T G A G A T A G G G A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E116 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E117 T G A G A T A G G A A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E118 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 E119 T G A G A T A G G G A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E120 T G A G A T A G G G A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E121 T G A G A T A G A G A T A A A T C A C G C C C A G D T A G A C A A A A A G T A C A A T A G G C C C G G I 0 E122 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H101 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H102 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H103 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H104 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H105 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H106 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H107 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H108 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H109 T G A G A T A G G G A T A C A T C A C A G C C A G D T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H110 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H111 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H112 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H113 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H114 T G A A A T A G A G G T A C A A C A C G C C C A G I G G A A A T A G A G G T G A A T C A C G C C C A G D 0 H115 T G A G A T A G G G A T A C A T C A C A C C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 H116 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C C A G D 0 H117 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C C A G D 0 H118 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 H119 T G A G A T T G G G A T A C A T C A C A G C T A G I T G G A C T A G A G G A A C G A C T G G C T C A A I 0 H120 T G A G A T A G G G G T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 H121 T G A G A T A G G G A T A C A T C A C A G C T A G I T A G A C A A A A A G T A C A A T A G G C C C G G I 0 H122 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X101 T G A G A T A G G G A T A C A T C A C A G C T A G I T G G A C A A A A A G T A C A A T A G G C C C A G I 0 X102 G G A A A T A G A G G T G A A T C A C G C C C A G D G G A A A T A G A G G T G A A T C A C G C C C A G D 0 X103 T G A G A T A G G G A T A C A T C A C A G C T A G I T G G A C A A A A A G T A C A A T A G G C C C A G I 0 X104 T G A G A T T G G G A T A C A T C A C A G C T A G I T G G A C A A A A A G T A C A A T A G G C C C A G I 0 X105 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X106 T G A G A T A G G G A T A C A T C A C A G C T A G I [G] G A A A T A G A G G T G A A T C A C G C C C A G D 0 X107 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X108 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X109 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X110 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X111 T G A G A T A G G G A T A C A T C A C A G C T A G I G G A A A T A G A G G T G A A T C A C G C C C A G D 0 X112 T G A G A T T G G G A T A C A T C A C A G C T A G I T G G A C A A A A A G T A C A A T A G G C C C A G I 0 X113 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X114 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X115 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X116 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X117 T G A G A T A G G G A T A C A T C A C A G C T A G I G G A A A T A G A G G T G A A T C A C G C C C A G D 0 X118 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X119 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X120 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X121 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X122 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 0 X123 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T A G G G A T A C A T C A C A G C T A G I 0 X124 T G A G A T A G G G A T A C A T C A C A G C T A G I T G A G A T T G G G A T A C A T C A C A G C T A G I 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) = = = A = = (T) = = = = = = G G C = = = = = ? ? = = (C) = = = G = = (A) = = = = = = C A G = = = = = 0 D002 = = A G A = = = G = A T = = A T = A C A G C ? = G = = = G A C = = = A = G A = = G A = T G G C T ? = A = 0 D003 ? ? = G = = = = G = A = A C = = = = = A G = T = = I ? ? = A = = = = A = G = G A = = = = = G C = C = = D 0 D004 = = A (A) (C) = = = G = (G) (A) = C = = = = = A G = ? ? = I = = G (G) (A) = = = A = (A) (T) = A = = = = = G C = ? ? = D 0 D005 = = = = = = = = A ? = = = = = A = = = G C = = = = = = = = = = = = = G ? = = = = = T = = = A G = = = = = 0 D006 = = = A C = = = A = G A = = = A = = = G C = C = = = = = = G A = = = G = A T = = = T = = = A G = T = = = 0 D007 ? ? = = C = = = = = = A A C = A = = = = = = = = = I ? ? = = A = = = = = = T G A = T = = = = = = = = = D 0 D008 ? ? = ? ? ? ? ? = ? ? ? ? = = = = = = = = = = = = = ? ? = ? ? ? ? ? = ? ? ? ? = = = = = = = = = = = = = 0 D009 = = = (A) = = = = A = ? ? ? = = = = = = G C = C = = D = = = (G) = = = = G = ? ? ? = = = = = = A G = T = = I 0 D010 = = A G A = = = = = A T = = A = = A C = = C = = G = = = G A C = = = = = G A = = G = = T G = = T = = A = 0 D011 (T) = = (G) = = = = A = (A) = (A) = G A = T G G C T C = A = (G) = = (A) = = = = G = (G) = (G) = A T = A C A G C T = G = 0 D012 T = = G = = = = G = A = A C = = = = = A G = T = = I G = = A = = = = A = G = G A = = = = = G C = C = = D 0 D013 (T) = (A) (G) = = = = G = (A) = = = A T = A C A G C T = G = (G) = (G) (A) = = = = A = (G) = = = G A = T G G C T C = A = 0 D014 = = = A = = = = = = G = = = = = = = = = = = = = ? = = = = G = = = = = = A = = = = = = = = = = = = = ? = 0 D015 = = (A) = = = = = G = = = (G) = A T = A C A G C T = G = = = (G) = = = = = A = = = (A) = G A = T G G C T C = A = 0 DY01 = = (A) = = = = = = = = = = C G A = = G = = ? ? ? ? I = = (G) = = = = = = = = = = A A T = = C = = ? ? ? ? D 0 DY02 = = = A = = = = = = G = = = A = = A C = = C = = G = = = = G = = = = = = A = = = G = = T G = = T = = A = 0 DY03 ? ? = = (A) = = = A = ? ? = = = A = = = G C = C = = = ? ? = = (C) = = = G = ? ? = = = T = = = A G = T = = = 0 DY04 = = = = = = = = = = = = = = (A) T = A = = = C = = ? ? = = = = = = = = = = = = = = (G) A = T = = = T = = ? ? 0 DY05 = = = = = = = = A = = = = = (G) = = = G G C = C = = = = = = = = = = = G = = = = = (A) = = = C A G = T = = = 0 DY06 = = = = = = = = A = = = = A = = = = = G C = C = = D = = = = = = = = G = = = = C = = = = = A G = T = = I 0 DY07 = = = = = = = = = = = = = = A = = A C = = C = = G = = = = = = = = = = = = = = = G = = T G = = T = = A = 0 DY08 = (G) (A) (G) (A) (T) = (G) = = (A) = = A A T = A C = = C = = G D = (A) (G) (A) (C) (A) = (A) = = (G) = = C G A = T G = = T = = A I 0 DY09 ? ? (A) G = = = = = = A = A = (G) = = = = = = = = = = = ? ? (G) A = = = = = = G = G = (A) = = = = = = = = = = = 0 DY10 (T) = (A) = = = = = G = = (T) = = A T = A C A G C T = G = (G) = (G) = = = = = A = = (A) = = G A = T G G C T C = A = 0 DY11 ? ? = A = = = = A = G = = = = A = = = G C = C = = = ? ? = G = = = = G = A = = = = T = = = A G = T = = = 0 DY12 = = A = (A) = = = = = (A) (T) = = A = = A C = ? C = = G = = = G = (C) = = = = = (G) (A) = = G = = T G = ? T = = A = 0 E101 = = = A C = = = = = G A = = = = = = ? = = = = = = = = = = G A = = = = = A T = = = = = = ? = = = = = = = 0 E102 ? ? = G = = = = = = A = A = = = = = = = = = = = = = ? ? = A = = = = = = G = G = = = = = = = = = = = = = 0 E103 (T) = = = C = = = = ? = A = = = = = = = = = = = = = = (G) = = = A = = = = ? = T = = = = = = = = = = = = = = 0 E104 ? ? = = C = = = = = = A A = = = = = = = = = = = = = ? ? = = A = = = = = = T G = = = = = = = = = = = = = 0 E105 = = A = A = = = G G = T = = = T C = C A G = T A = = = = G = C = = = A A = A = = = A T = G G C = C G = = 0 E106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0 E108 = G A G A T = G G G A = = = = T C = C A G = T A = = = A G A C A = A A A G = = = = A T = G G C = C G = = 0 E109 = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = ? 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 = = = = = = = = = = = = = = = = = = ? = = = ? ? ? ? = = = = = = = = = = = = = = = = = = ? = = = ? ? ? ? 0 E112 T A = = C A = A = = = = ? = = = = = = = = = = = = = G G = = A T = G = = = = ? = = = = = = = = = = = = = 0 E113 = = A G A = = = G G A T = ? ? T C = C A G = T A ? = = = G A C = = = A A G A = ? ? A T = G G C = C G ? = 0 E114 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0 E115 = G A G A T = ? G G A = ? = = T C = C A G = T A = = = A G A C A = ? A A G = ? = = A T = G G C = C G = = 0 E116 ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = G A G A T = G G = A = = = = T C = C A G = T A = = = A G A C A = A A = G = = = = A T = G G C = C G = = 0 E118 = = = = = = = = = = = = = = = = = = ? = ? = ? = = = = = = = = = = = = = = = = = = = = = ? = ? = ? = = = 0 E119 = G A G A T = G G G A = = = = T C = ? A G = T A = = = A G A C A = A A A G = = = = A T = ? G C = C G = = 0 E120 = G A G A T = G G ? A = = = = T C = C A G = T A = = = A G A C A = A A ? G = = = = A T = G G C = C G = = 0 E121 = G A G A T = G = G A = = A = T C = C = = = = A ? ? = A G A C A = A = A G = = C = A T = G = = = = G ? ? 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H101 = = = = = = A = = = ? ? = = = = = = = = = = = = = = = = = = = = T = = = ? ? = = = = = = = = = = = = = = 0 H102 = = = = = ? = = = = = = = ? = = = = = = ? = = = = = = = = = = ? = = = = = = = ? = = = = = = ? = = = = = 0 H103 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 H104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H106 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 H107 = = = = = = = = = = ? ? ? = = = = = = = = = ? ? = = = = = = = = = = = = ? ? ? = = = = = = = = = ? ? = = 0 H108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H109 = = = = = = A = = = = = = = = = = = = = = = C = = D = = = = = = T = = = = = = = = = = = = = = = T = = I 0 H110 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 H111 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 H112 ? ? = = = = A = = = = = = = = = = = = = = = = = = = ? ? = = = = T = = = = = = = = = = = = = = = = = = = 0 H113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H114 T = = = = = = = = = = = A C = A = = = = = = = = = I G = = = = = = = = = = = G A = T = = = = = = = = = D 0 H115 = G A G A T = G G G A = ? = = T C = C A = = T A ? ? = A G A C A = A A A G = ? = = A T = G G = = C G ? ? 0 H116 = = = = = = = = = = = = = = = = = = = = = = T = = I = = = = = = = = = = = = = = = = = = = = = = C = = D 0 H117 = = = = = = = = = = = = = = = = = = = = = = T = = I = = = = = = = = = = = = = = = = = = = = = = C = = D 0 H118 = = = = = = A = = = = = = = = = = = = = = ? ? ? = = = = = = = = T = = = = = = = = = = = = = = ? ? ? = = 0 H119 = = A G A = T = G = A T = = A T = A C A G C T = G = = = G A C = A = A = G A = = G A = T G G C T C = A = 0 H120 ? ? = = = = = = = = G = = = = = = = = = = = ? ? = = ? ? = = = = = = = = A = = = = = = = = = = = ? ? = = 0 H121 = G A G A T = G G G A = = = = T C = C A G = T A = = = A G A C A = A A A G = = = = A T = G G C = C G = = 0 H122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X101 = = A G A T = G G G A = = = = T C = C A G = T = = = = = G A C A = A A A G = = = = A T = G G C = C = = = 0 X102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X103 = = A G A T = G G G A = = = = T C = C A G ? ? ? = = = = G A C A = A A A G = = = = A T = G G C ? ? ? = = 0 X104 = = A G A T T G G G A = = = = T C = C A G = T = = = = = G A C A A A A A G = = = = A T = G G C = C = = = 0 X105 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0 X106 ? ? = G = = = = G = A = A C = = = = = A G = T = = I ? ? = A = = = = A = G = G A = = = = = G C = C = = D 0 X107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X108 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 X109 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 X110 ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 X111 T = = G = = = = G = A = A C = = = = = A G = T = = I G = = A = = = = A = G = G A = = = = = G C = C = = D 0 X112 = = A G A T T G G G A = = = = T C = C A G = T = = = = = G A C A A A A A G = = = = A T = G G C = C = = = 0 X113 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 X114 = = = = = = A = = = = = = = = = = = = = = = ? ? = = = = = = = = T = = = = = = = = = = = = = = = ? ? = = 0 X115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X116 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 X117 T = = G = = = = G = A = A C = = = = = A G = ? ? = I G = = A = = = = A = G = G A = = = = = G C = ? ? = D 0 X118 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 X119 ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 X120 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 X121 ? ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0 X122 = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = 0 X123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X124 = = = ? = ? A = = = ? ? = = = = = = = = = = = = = = = = = ? = ? T = = = ? ? = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? ? = = 0.61 = = = 1.00 = = 0.61 = = = = = = 1.00 1.00 1.00 = = = = = = = 1.00 1.00 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 = 0.98 = 0.98 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = = 0.96 0.53 0.53 = = = 1.00 = 0.53 0.53 = 1.00 = = = = = 1.00 1.00 = ? ? = 1.00 = = = = = = = = 1.00 ? = = = = = 1.00 = = = 1.00 1.00 = = = = = = = = 0.93 0.93 = = = 1.00 = 0.93 0.93 = = = 1.00 = = = 1.00 1.00 = 1.00 = = = ? ? = = 1.00 = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = 1.00 ? ? = ? ? ? ? ? = ? ? ? ? = = = = = = = = = = = = = = = = 0.81 = = = = 1.00 = ? ? ? = = = = = = 1.00 1.00 = 1.00 = = 1.00 = = 0.98 0.95 0.95 = = = = = 0.95 0.95 = = 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 = 0.61 = = 0.61 = = = = 1.00 = 0.61 = 0.61 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 0.98 = = 0.98 = = = = 1.00 = 0.98 = 0.98 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 0.74 = 0.76 0.74 = = = = 1.00 = 0.74 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = ? = = = 0.74 = = = = = 1.00 = = = 0.71 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 0.59 = = = = = = = = = = 1.00 1.00 1.00 = = 1.00 = = ? ? ? ? 1.00 = = = 0.98 = = = = = = 0.97 = = = 1.00 = = 1.00 1.00 = = 1.00 = = 1.00 = ? ? = = 0.56 = = = 1.00 = ? ? = = = 1.00 = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = 0.81 1.00 = 1.00 = = = 1.00 = = ? ? = = = = = = = = 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 = = 0.80 0.77 0.80 0.80 0.80 = 0.80 = = 0.82 = = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = 1.00 1.00 ? ? 0.60 1.00 = = = = = = 1.00 = 1.00 = 0.55 = = = = = = = = = = = 0.67 = 0.86 = = = = = 1.00 = = 0.50 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? ? = 0.96 = = = = 1.00 = 0.96 = = = = 1.00 = = = 1.00 1.00 = 1.00 = = = = = 0.98 = 0.84 = = = = = 0.86 0.86 = = 1.00 = = 1.00 1.00 = ? 1.00 = = 1.00 = = = = 1.00 1.00 = = = = = 1.00 1.00 = = = = = = ? = = = = = = = ? ? = 1.00 = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = 0.82 = = = 1.00 = = = = ? = 1.00 = = = = = = = = = = = = = = ? ? = = 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? ? ? ? 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = ? = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = ? ? 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 1.00 1.00 1.00 1.00 1.00 = ? 1.00 1.00 1.00 = ? = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = ? = ? = ? = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = ? 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 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 = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? ? = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = ? = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = ? ? ? = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? ? = = = = = = = = 1.00 = = = = = = = = = = = ? ? = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 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 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? = 0.99 = = = = 1.00 = 0.99 = 0.99 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = 0.98 = = = = 1.00 = 0.98 = 0.98 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 0.95 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 0.98 = = 0.98 = = = = 1.00 = 0.98 = 0.98 1.00 = = = = = 1.00 1.00 = ? ? = 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = ? 1.00 = = = ? ? = = = = = = = = = = = = = = END PHASEPROBS