************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mmp12.phase.inp mmp12.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mmp12.phase.out_freqs : haplotype frequency estimates mmp12.phase.out_pairs : most likely haplotype pairs for each individual mmp12.phase.out_recom : estimates of recombination parameters mmp12.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 20 Positions of loci: 832 2150 2493 3536 5656 5678 6996 8305 9126 9680 10983 11206 12488 12525 12598 13418 14162 14395 14466 14716 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mmp12.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DICATGTCGIAAC 2 GTDGAC 1.000000 2 DICGTGTCGIAAC 2 GTDGAC 1.000000 3 DICGTGTCGIAAC 4 GTDGAC 45.000000 4 DICGTGTCGDAAC 2 GTDGAC 14.000000 5 DICGTGTCGDAAC 2 GTDGGC 15.000000 6 DICGTGTCAIAAC 2 GTDGAC 1.000000 7 DICGTCTCGDAAC 2 GTDGAC 31.000000 8 DICGTCTCGDAAC 2 GTIGAC 1.000000 9 DICGCGTCAIAAC 2 GTDGAC 19.000000 10 DICGCCTCAIAAC 2 GTDGAC 1.000000 11 DIGGCGCTGIAAC 2 GTDGAT 1.000000 12 DIGGCGTTGIAAC 2 GTDGAT 7.000000 13 DIGGCGTTAIAAC 2 GTDGAT 12.000000 14 DDCATGCCGIAAT 2 GADAAC 4.000000 15 DDCATGCCGIAAT 2 GAIAAC 2.000000 16 DDCATGTCGIAAC 2 GTDGAC 4.000000 17 DDCATGTCGIAGT 1 GAIAAC 2.000000 18 DDCATGTCGDAAC 2 GTDGAC 2.000000 19 DDCATGTCGDAAC 2 GTDGAT 1.000000 20 DDCGTGCCGDAAC 2 GTDGGC 1.000000 21 DDCGTGTCGIAAC 4 GTDGAC 1.000000 22 DDCGTGTCGDAAC 2 GTDGGC 1.000000 23 IICATGCCGIGGT 2 CAIAAC 1.000000 24 IDCATGCCGIGGT 2 CADGAC 1.000000 25 IDCATGCCGIGGT 2 CAIAAC 21.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,14) D002: (4,25) D003: (20,25) D004: (3,14) D005: (4,5) D006: (3,14) D007: (5,18) D008: (4,17) D009: (4,25) D010: (3,17) D011: (15,22) D012: (5,25) D013: (5,25) D014: (3,25) D015: (3,12) DY01: (5,19) DY02: (4,4) DY03: (3,4) DY04: (3,3) DY05: (4,12) DY06: (3,12) DY07: (7,14) DY08: (18,25) DY09: (4,25) DY10: (4,25) DY11: (11,15) DY12: (4,4) E101: (3,3) E102: (1,5) E103: (9,25) E104: (3,25) E105: (5,25) E106: (9,24) E107: (5,13) E108: (5,16) E109: (3,13) E110: (6,13) E111: (9,25) E112: (9,13) E113: (3,13) E114: (9,13) E115: (5,9) E116: (5,5) E117: (9,13) E118: (3,25) E119: (3,5) E120: (3,13) E121: (3,13) E122: (3,9) H101: (2,9) H102: (7,7) H103: (3,25) H104: (7,9) H105: (3,7) H106: (3,7) H107: (10,13) H108: (7,7) H109: (7,7) H110: (4,9) H111: (5,9) H112: (3,7) H113: (3,9) H114: (3,9) H115: (3,4) H116: (7,9) H117: (3,21) H118: (3,16) H119: (7,13) H120: (3,7) H121: (3,13) H122: (3,7) X101: (3,7) X102: (3,7) X103: (12,25) X104: (5,12) X105: (3,25) X106: (8,16) X107: (3,25) X108: (7,16) X109: (7,23) X110: (3,7) X111: (3,7) X112: (7,12) X113: (7,9) X114: (3,25) X115: (7,9) X116: (7,25) X117: (3,12) X118: (7,9) X119: (3,7) X120: (3,9) X121: (3,7) X122: (3,7) X123: (3,7) X124: (7,25) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 D I C G T G T C G I A A C 4 G T D G A C D D C A T G C C G I A A T 2 G A D A A C 0 D002 D I C G T G T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 D003 D D C G T G C C G D A A C 2 G T D G G C I D C A T G C C G I G G T 2 C A I A A C 0 D004 D I C G T G T C G I A A C 4 G T D G A C D D C A T G C C G I A A T 2 G A [D] A A C 0 D005 D I C G T G T C G D A A C 2 G T D G A C D I C G T G T C G D A A C 2 G T D G G C 0 D006 D I C G T G T C G I A A C 4 G T D G A C D D C A T G C C G I A A T 2 G A D A A C 0 D007 D I C G T G T C G D A A C 2 G T D G G C D D C A T G T C G D A A C 2 G T D G A C 0 D008 D I C G T G T C G D A A C 2 G T D G A C D D C A T G T C G I A G T 1 G A I A A C 0 D009 D I C G T G T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 D010 D I C G T G T C G I A A C 4 G T D G A C D D C A T G T C G I A G T 1 G A I A A C 0 D011 D D C A T G C C G I A A T 2 G A I A A C D D C G T G T C G D A A C 2 G T D G G C 0 D012 D I C G T G T C G D A A C 2 G T D G G C I D C A T G C C G I G G T 2 C A I A A C 0 D013 D I C G T G T C G D A A C 2 G T D G G C I D C A T G C C G I G G T 2 C A I A A C 0 D014 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 D015 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T G I A A C 2 G T D G A T 0 DY01 D (I) C G T G T C G D A A C 2 G T D G (G) (C) D (D) C [A] T G T C G D A A C 2 G T D G (A) (T) 0 DY02 D I C G T G T C G D A A C 2 G T D G A C D I C G T G T C G D A A C 2 G T D G A C 0 DY03 D I C G T G T C G I A A C 4 G T D G A C D I C G T G T C G D A A C 2 G T D G A C 0 DY04 D I C G T G T C G I A A C 4 G T D G A C D I C G T G T C G I A A C 4 G T D G A C 0 DY05 D I C G T G T C G D A A C 2 G T D G A C D I G G C G T T G I A A C 2 G T D G A T 0 DY06 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T G I A A C 2 G T D G A T 0 DY07 D I C G T [C] T C G D A A C 2 G T D G A C D D C A T G C C G I A A T 2 G A D A A C 0 DY08 D D C A T G T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 DY09 D I C G T G T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 DY10 D I C G T G T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 DY11 D I G G C G C T G I A A C 2 G T D G A T D D C A T G C C G I A A T 2 G A I A A C 0 DY12 D I C G T G T C G D A A C 2 G T D G A C D I C G T G T C G D A A C 2 G T D G A C 0 E101 D I C G T G T C G I A A C 4 G T D G A C D I C G T G T C G I A A C 4 G T D G A C 0 E102 D I C A T G T C G I A A C 2 G T D G A C D I C G T G T C G D A A C 2 G T D G G C 0 E103 D I C G C G T C A I A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 E104 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 E105 D I C G T G T C G D A A C 2 G T D G G C I D C A T G C C G I G G T 2 C A I A A C 0 E106 D I C G C G T C A I A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A D G A C 0 E107 D I C G T G T C G D A A C 2 G T D G G C D I G G C G T T A I A A C 2 G T D G A T 0 E108 D I C G T G T C G D A A C 2 G T D G G C D D C A T G T C G I A A C 2 G T D G A C 0 E109 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E110 D I C G (T) G T C A I A A C 2 G T D G A C D I G G (C) G T T A I A A C 2 G T D G A T 0 E111 D I C G C G T C A I A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 E112 D I C G C G T C A I A A C 2 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E113 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E114 D I C G C G T C A I A A C 2 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E115 D I C G T G T C G D A A C 2 G T D G G C D I C G C G T C A I A A C 2 G T D G A C 0 E116 D I C G T G T C G D A A C 2 G T D G G C D I C G T G T C G D A A C 2 G T D G G C 0 E117 D I C G C G T C A I A A C 2 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E118 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 E119 D I C G T G T C G I A A C 4 G T D G A C D I C G T G T C G D A A C 2 G T D G G C 0 E120 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E121 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 E122 D I C G T G T C G I A A C 4 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H101 D I C G T G T C G I A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H102 D I C G T C T C G D A A C 2 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H103 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 H104 D I C G T C T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H105 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H106 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H107 D I C G C (C) T C A I A A C 2 G T D G A C D I G G C (G) T T A I A A C 2 G T D G A T 0 H108 D I C G T C T C G D A A C 2 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H109 D I C G T C T C G D A A C 2 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H110 D I C G T G T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H111 D I C G T G T C G D A A C 2 G T D G G C D I C G C G T C A I A A C 2 G T D G A C 0 H112 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H113 D I C G T G T C G I A A C 4 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H114 D I C G T G T C G I A A C 4 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H115 D I C G T G T C G I A A C 4 G T D G A C D I C G T G T C G D A A C 2 G T D G A C 0 H116 D I C G T C T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 H117 D I C G T G T C G I A A C 4 G T D G A C D D C G T G T C G I A A C 4 G T D G A C 0 H118 D I C G T G T C G I A A C 4 G T D G A C D D C A T G T C G I A A C 2 G T D G A C 0 H119 D I C G T C T C G D A A C 2 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 H120 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 H121 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T A I A A C 2 G T D G A T 0 H122 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X101 D I C G T G T C G I A A C 4 G T D G A C D I C G T [C] T C G D A A C 2 G T D G A C 0 X102 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X103 D I G G C G T T G I A A C 2 G T D G A T I D C A T G C C G I G G T 2 C A I A A C 0 X104 D I C G T G T C G D A A C 2 G T D G G C D I G G C G T T G I A A C 2 G T D G A T 0 X105 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 X106 D I C G T C T C G D A A C 2 G T (I) G A C D D C A T G T C G I A A C 2 G T (D) G A C 0 X107 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 X108 D I C G T [C] T C G D A A C 2 G T D G A C D D C A T G T C G I A A C 2 G T D G A C 0 X109 D I C G T [C] T C G D A A C 2 G T D G A C I I C A T G C C G I G G T 2 C A I A A C 0 X110 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X111 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X112 D I C G T C T C G D A A C 2 G T D G A C D I G G C G T T G I A A C 2 G T D G A T 0 X113 D I C G T C T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 X114 D I C G T G T C G I A A C 4 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 X115 D I C G T C T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 X116 D I C G T C T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A A C 0 X117 D I C G T G T C G I A A C 4 G T D G A C D I G G C G T T G I A A C 2 G T D G A T 0 X118 D I C G T C T C G D A A C 2 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 X119 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X120 D I C G T G T C G I A A C 4 G T D G A C D I C G C G T C A I A A C 2 G T D G A C 0 X121 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X122 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X123 D I C G T G T C G I A A C 4 G T D G A C D I C G T C T C G D A A C 2 G T D G A C 0 X124 D I C G T C T C G D A A C 2 G T D G A C I D C A T G C C G I G G T 2 C A I A 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 = I = G = = T = = = = = C 4 = T = G = = = D = A = = C = = = = = T 2 = A = A = = 0 D002 D I = G = = T = = D A A C = G T D G = = I D = A = = C = = I G G T = C A I A = = 0 D003 D = = G = = = = = D A A C = G T D G G = I = = A = = = = = I G G T = C A I A A = 0 D004 = I = G ? ? T = = = = = C 4 = T ? G = = = D = A ? ? C = = = = = T 2 = A ? A = = 0 D005 = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = G = 0 D006 = I = G ? ? T = = = = = C 4 = T = G = = = D = A ? ? C = = = = = T 2 = A = A = = 0 D007 = I = G = = = = = = = = = = = = = = G = = D = A = = = = = = = = = = = = = = A = 0 D008 = I = G = = = = = D = A C 2 = T D G = = = D = A = = = = = I = G T 1 = A I A = = 0 D009 D I = G = = T = = D A A C = G T D G = = I D = A = = C = = I G G T = C A I A = = 0 D010 = I = G = = = = = = = A C 4 = T D G = = = D = A = = = = = = = G T 1 = A I A = = 0 D011 = = = A ? ? C = = I = = T = = A I A A = = = = G ? ? T = = D = = C = = T D G G = 0 D012 D I = G = = T = = ? A A C = G ? D G G = I D = A = = C = = ? G G T = C ? I A A = 0 D013 D ? = ? = = T = = D A A C = G T D G G = I ? = ? = = C = = I G G T = C A I A A = 0 D014 D I = G ? ? T = = ? A A C 4 G T D G = = I D = A ? ? C = = ? G G T 2 C A I A = = 0 D015 = = C = T = = C = = = = = 4 = = = = = C = = G = C = = T = = = = = 2 = = = = = T 0 DY01 = (I) = ? = = = = = = = = = = = = = = (G) (C) = (D) = ? = = = = = = = = = = = = = = (A) (T) 0 DY02 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY03 = = = = = = = = = I = = = 4 = = = = = = = = = = = = = = = D = = = 2 = = = = = = 0 DY04 = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 0 DY05 = = C = ? = = C = D = = = = = = = = = C = = G = ? = = T = I = = = = = = = = = T 0 DY06 = = C = T = = C = = = = = 4 = = = = = C = = G = C = = T = = = = = 2 = = = = = T 0 DY07 = I = G ? ? T = = D = = C = = T = G = = = D = A ? ? C = = I = = T = = A = A = = 0 DY08 D = = = = = T = = D A A C = G T D G = = I = = = = = C = = I G G T = C A I A = = 0 DY09 D I = G = = T = = D A A C = G T D G = = I D = A = = C = = I G G T = C A I A = = 0 DY10 D I = G = = T = = D A A C = G T D G = = I D = A = = C = = I G G T = C A I A = = 0 DY11 = I G G ? ? = T = = = = C = = T D G = T = D C A ? ? = C = = = = T = = A I A = C 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = A = = = = = I = = = = = = = = A = = = = G = = = = = D = = = = = = = = G = 0 E103 D I = G C = T = A = A A C = G T D G = = I D = A T = C = G = G G T = C A I A = = 0 E104 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 E105 D I = G = = T = = D A A C = G T D G G = I D = A = = C = = I G G T = C A I A A = 0 E106 D I = G C = T = A = A A C = G T = = = = I D = A T = C = G = G G T = C A = = = = 0 E107 = = C = T = = C G D = = = = = = = = G C = = G = C = = T A I = = = = = = = = A T 0 E108 = I = G = = = = = D = = = = = = = = G = = D = A = = = = = I = = = = = = = = A = 0 E109 = ? C = T = = C G = = = = 4 = = = = = C = ? G = C = = T A = = = = 2 = = = = = T 0 E110 = = C = (T) = = C = = = = = = = = = = = C = = G = (C) = = T = = = = = = = = = = = T 0 E111 D ? = G ? ? T = A = ? ? ? ? ? T D G = = I ? = A ? ? C = G = ? ? ? ? ? A I A = = 0 E112 = = C = = = = C = = = = = = = = = = = C = = G = = = = T = = = = = = = = = = = T 0 E113 = = C = T = = C G = = = = 4 = = = = = C = = G = C = = T A = = = = 2 = = = = = T 0 E114 = = C ? = = = C = = = = = = = = = = = C = = G ? = = = T = = = = = = = = = = = T 0 E115 = = = = T = = = G D = = = = = = = = G = = = = = C = = = A I = = = = = = = = A = 0 E116 = = = = ? ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 0 E117 = = C = = = = C = = = = = = = = = = = C = = G = = = = T = = = = = = = = = = = T 0 E118 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 E119 = = = = = = = = = I = = = 4 = = = = A = = = = = = = = = = D = = = 2 = = = = G = 0 E120 = = C = T = = C G = = = = 4 = = = = = C = = G = C = = T A = = = = 2 = = = = = T 0 E121 = = C = ? = = C G = = = = 4 = = = = = C = = G = ? = = T A = = = = 2 = = = = = T 0 E122 = = = = T = = = G = = = = 4 = = = = = = = = = = C = = = A = = = = 2 = = = = = = 0 H101 = = = = T = = = G = = = = = = = = = = = = = = = C = = = A = = = = = = = = = = = 0 H102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H103 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 H104 = = = = T C = = G D = = = = = = = = = = = = = = C G = = A I = = = = = = = = = = 0 H105 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 H106 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 H107 = ? C = = (C) = C = = = = = = = = = = = C = ? G = = (G) = T = = = = = = = = = = = T 0 H108 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H110 = = = = T = = = G D ? ? = = = ? = = = = = = = = C = = = A I ? ? = = = ? = = = = 0 H111 = = = = T = = = G D = = = = = = = = G = = = = = C = = = A I = = = = = = = = A = 0 H112 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 H113 = ? = = T = = = G = = = = 4 = = = = = = = ? = = C = = = A = = = = 2 = = = = = = 0 H114 = = = = T = = = G = = = = 4 = = = = = = = = = = C = = = A = = = = 2 = = = = = = 0 H115 = = = = = = = = = I = = = 4 = = = = = = = = = = = = = = = D = = = 2 = = = = = = 0 H116 = = = = T C = = G D = = = = = = = = = = = = = = C G = = A I = = = = = = = = = = 0 H117 = I = = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = 0 H118 = I = G = = = = = = = = = 4 = = = = = = = D = A = = = = = = = = = 2 = = = = = = 0 H119 = = C = T C = C G D = = = = = = = = = C = = G = C G = T A I = = = = = = = = = T 0 H120 = ? = = = G = = = I = = = 4 = = = = = = = ? = = = C = = = D = = = 2 = = = = = = 0 H121 = = C = T = = C G = = = = 4 = = = = = C = = G = C = = T A = = = = 2 = = = = = T 0 H122 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X101 = = = = ? ? = = = I = = = 4 = = = = = = = = = = ? ? = = = D = = = 2 = = = = = = 0 X102 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X103 D I G G C = T T = = A A ? = ? T D G = T I D C A T = C C = = G G ? = ? A I A = C 0 X104 ? ? C = T = = C = D = = = = = = = = G C ? ? G = C = = T = I = = = = = = = = A T 0 X105 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 X106 = I = G = C = = = D = = = = = = (I) = = = = D = A = G = = = I = = = = = = (D) = = = 0 X107 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 X108 = I = G ? ? = = = D = = = = = = = = = = = D = A ? ? = = = I = = = = = = = = = = 0 X109 D = = G ? ? T = = D A A C = G T D G = = I = = A ? ? C = = I G G T = C A I A = = 0 X110 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X111 = = = = = G = = = I = = ? ? ? = = = = = = = = = = C = = = D = = ? ? ? = = = = = 0 X112 = ? C = T C = C = D ? ? = = = = = = = C = ? G = C G = T = I ? ? = = = = = = = T 0 X113 = = = = T C = = G D = = = = = = = = = = = = = = C G = = A I = = = = = = = = = = 0 X114 D I = G = = T = = = A A C 4 G T D G = = I D = A = = C = = = G G T 2 C A I A = = 0 X115 = = = = T C = = G D = = = = = = = = = = = = = = C G = = A I = = = = = = = = = = 0 X116 D ? = G = C T = = D A A C = G T D G = = I ? = A = G C = = I G G T = C A I A = = 0 X117 = = C = T = = C = = = = = 4 = = = = = C = = G = C = = T = = = = = 2 = = = = = T 0 X118 = ? = = T C = = G D = = = = = = = = = = = ? = = C G = = A I = = = = = = = = = = 0 X119 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X120 = = = = T = = = G = = = = 4 = = = = = = = = = = C = = = A = = = = 2 = = = = = = 0 X121 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X122 = = = = = G = = ? I = = = 4 = = = = = = = = = = = C = = ? D = = = 2 = = = = = = 0 X123 = = = = = G = = = I = = = 4 = = = = = = = = = = = C = = = D = = = 2 = = = = = = 0 X124 D I = G = C T = = D ? ? C = G T D G = = I D = A = G C = = I ? ? T = C A I A = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = 1.00 = 1.00 = = 1.00 = = = = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 ? ? 1.00 = = = = = 1.00 1.00 = 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 ? ? 0.97 = = 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 1.00 1.00 1.00 = 1.00 1.00 = 1.00 ? ? 1.00 = = ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = = = = = 1.00 = 0.71 = ? = = = = = = = = = = = = = = 0.89 0.83 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = 1.00 = ? = = 1.00 = 1.00 = = = = = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = = = = = 1.00 = 1.00 = 1.00 ? ? 1.00 = = 1.00 = = 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 ? ? = 1.00 = = = = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.91 = = = = = 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 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 = 0.93 = 1.00 = = = = = 0.99 = = = = = = = = 1.00 = = ? 1.00 = 1.00 = = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = 1.00 = 0.79 = = 1.00 = = = = = = = = = = = 1.00 1.00 ? = 1.00 ? ? 1.00 = 1.00 = ? ? ? ? ? 1.00 1.00 1.00 = = = = 1.00 = = = = 1.00 = = = = = = = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = 1.00 ? = = = 1.00 = = = = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = = = = = = = = 1.00 = = = = = ? ? = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = 1.00 = = = 1.00 = = = = 1.00 = = = 1.00 = 1.00 = = 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 0.98 = = 1.00 1.00 = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = 1.00 = = = = = = = = = = = 1.00 = = = 1.00 = = = 1.00 = = = = = = = ? 1.00 = = 0.54 = 1.00 = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 ? ? = = = ? = = = = = = = = 1.00 = = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = 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 = = = = = = = = = = = = = = = = = = = 0.96 = 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 = 1.00 = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 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 = = = = = = 0.50 = = = 1.00 1.00 = 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 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 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 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 = = END PHASEPROBS