************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 il110.phase.inp il110.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il110.phase.out_freqs : haplotype frequency estimates il110.phase.out_pairs : most likely haplotype pairs for each individual il110.phase.out_recom : estimates of recombination parameters il110.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 51 Positions of loci: 248 996 1241 1283 1303 2122 2228 2379 2563 2631 2915 2954 2955 3037 3552 3659 3954 4001 4015 4255 4581 4590 4606 4734 4870 4890 5392 5678 5865 5996 6025 6074 6213 6329 6357 6844 7082 7096 7744 7781 8228 8468 8489 9137 9995 10186 10590 10895 10976 10991 11041 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il110.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GACTCTTCAATCADAGAGCCGCCATGTTAAGGCCGGTCCAGTCCTTGCAGT 1.000000 2 GACTCTTCAATCADAGAGTCGCAATATTAAGGTTGGCTCATCACCTCCCAC 1.000000 3 GACTCTTCAATCADAGAGTCGCAATATTAATGCCGATCCAGTACTCGTAGT 1.000000 4 GACTCTTCAATCADAGCGTCGCAATATTAAGGTTGGCTCATCACCTCCCAC 3.000000 5 GACTCTTCAATCADAGCGTCGCAATATTAAGGTTGGCCCATCACCTCCCAC 1.000000 6 GACTCTTCAATCADAGCGTCGCAATATTAGGGTCGGCTCAGCACTTCCCAC 1.000000 7 GACTCTTCAATCADAGCGTTGCAATATTAAGGTTGGCTCATCACCTCCCAC 1.000000 8 GACTCTTGAATCADAGAGCCGCAGTGTTAAGGCCGGCTCAGTCCTCGCAGT 6.000000 9 GACTCTTGAATCADAGAGCCGCAGTGTTAAGGCCGATCAAGTACTTGTAGT 1.000000 10 GACTCTGCAATCADAGAGCCGCAATATTAGGGCCTATCAGGTCCTCGCAGT 2.000000 11 GATTCTTCAACTGDAGAGCTGCCATGTTAATGCCGATCCAGCACTTCCCAC 2.000000 12 GATTCTTCAACTGDGGAGCCGCAGTGATGAGGCCTGTCCAGTCCTTGCAGT 2.000000 13 GATTCTTCAACTGDGGAGCCGCAGTGATGAGGCCTATCCAGCACTTCCCAC 1.000000 14 GATTCTTCAACTGIAGAGCTGCCATGTTAATGCCGATCCAGCACTTCCCAC 1.000000 15 GATTCTTCAACTGIGGAGCCGCAGTGATGAGGCCTGTCCAGTCCTTGCAGT 8.000000 16 GATTCTTCAACTGIGGAGCCGCAGTGATGAGGCCTATCCAGTACTTGTAGT 1.000000 17 GATTCTTCAACTGIGGAGCCGCAGTGATGAGGCCTATCCAGCACTTCCCAC 2.000000 18 GATTCTTCGACTGIGGAGCCGCAGTGATGAGGCCTGTCCAGTCCTTGCAGT 1.000000 19 GTCTCCTCAGTCADAGAGCCGCAGTGTTAAGGCCGGCTCAGTCCTCGCAGT 2.000000 20 GTCTCCTCAGTCADAGAGCCGCAGTGTTAAGGCCTGCTCAGCACCTCCCAC 1.000000 21 GTCTCCTCAGTCADAGAGCCGCCATGTTAAGGTCGGCTCAGCACTTCCCAC 1.000000 22 GTCTCCTCAGTCADAGAGCCGCCATGTTAATGCTGGTCCAGTCCTTGCAGT 1.000000 23 GTCTCCTCAGTCADAGAGCCGCCATGTTAGGTCTTGCTCAGCACTTCCCAC 1.000000 24 GTCTCCTCAGTCADAGAGCCGCCATGTTAGGTCTTGTCAGGTCCTCGCAGT 1.000000 25 GTCTCCTCAGTCADAGAGCCACCATGTCGAGGCCGGCTCAGCACTTCCCAC 3.000000 26 GTCTCCTCAGTCADAGAGCCACCATGTCGAGGCCTATCCAGTACTTGTAGT 5.000000 27 GTCTCCTCAGTCADAGAGCCACCATGTCGGGGCCTGCTCAGCACCTCCCAC 3.000000 28 GTCTCCTCAGTCADAGAGCTGCCATGTTAATGCCGATCCAGCACTTCCCAC 2.000000 29 GTCTCCTCAGTCADAGAGCTGCCATGTTAATGCCGATCCAGCATTTCCCAC 9.000000 30 GTCTCCTCAGTCADAGAGCTGCCATGTTAATGCTGATCCAGCACTTCCCAC 3.000000 31 GTCTCCTCAGTCADAGAGCTGCCATGTTGAGGCCTGTCCAGTCCTTGCAGT 1.000000 32 GTCTCCTCAGTCADAGAGTCGCAATATTAAGTCCGGCTCAGTACTCGTAGT 2.000000 33 GTCTCCTCGGTCADAGAGCTGCCATGTTAATGCCGATCCAGCATTTCCCAC 1.000000 34 GTCCATGCAGTCADACAACTGCCATGTTAATGCCGATCCAGCATTTCCCAC 1.000000 35 TTCCATGCAATCADAGAGCCGCCATGTTAAGGTCGGCTCAGCACTTCCCAC 1.000000 36 TTCCATGCAACTGDAGAGCCGCCATGTTAGGGCCTGTCCAGTCCTTGCAGT 1.000000 37 TTCCATGCAGTCADACAGCTGCCATGTTAATGCCGATCCAGCATTTCCCAC 1.000000 38 TTCCATGCAGTCADACAACCGTAGTGTCGAGGCCGGCTCAGCACTTCCCAC 1.000000 39 TTCCATGCAGTCADACAACCGTAGAGTTAAGGCTGATCCAGCACTTCCCAC 7.000000 40 TTCCATGCGATCADAGAGCCGCCATGTTAAGGCCGGTCCAGTCCTTGCAGT 1.000000 41 TTCCATGCGATCADAGAGCCGCCATGTTAAGTCTTGCTAGTCACCTCCCAC 1.000000 42 TTCCATGCGATCADAGAGCCGCCATGTTAGGGCTGATCAAGTACTTGTAGT 2.000000 43 TTCCATGCGATCADAGAGCCGCCATGTTAGGTCTTGTCAGGTCCTCGCAGT 1.000000 44 TTCCATGCGATCADAGAGTCGCAATATTAAGGTCGGCTCAGCATTTCCCAC 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (8,19) DY02: (9,39) DY03: (39,44) DY04: (21,22) DY05: (10,25) DY06: (3,27) DY07: (32,36) DY08: (1,23) DY09: (40,44) DY10: (4,44) DY11: (7,28) DY12: (10,32) DY13: (39,43) DY14: (4,42) DY15: (4,25) DY16: (2,44) DY17: (6,41) DY18: (5,42) DY19: (25,26) DY20: (26,35) DY21: (8,24) DY22: (8,19) DY23: (39,44) DY24: (20,38) E101: (15,27) E102: (26,29) E103: (12,13) E104: (15,26) E105: (29,29) E106: (18,33) E107: (15,30) E108: (17,29) E109: (29,29) E110: (11,34) E111: (17,30) E112: (8,30) E113: (15,16) E114: (11,12) E115: (15,31) E116: (15,39) E117: (15,37) E118: (14,39) E119: (29,39) E120: (8,29) E121: (26,29) E122: (8,28) E123: (15,27) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T 0 DY02 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G A T C A A G T A C T T G T A G T T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C 0 DY03 T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C T T C C A T G C G A T C A D A G A G T C G C A A T A T T A A G G T C G G C T C A G C A T T T C C C A C 0 DY04 G T C T C C T C A G T C A D A G A G C C G C C A T G T T A A G G T (C) G G C T C A G C A C T T C C C A C G T C T C C T C A G T C A D A G A G C C G C C A T G T T A A T G C (T) G G T C C A G T C C T T G C A G T 0 DY05 G A C T C T G C A A T C A D A G A G C C G C A A T A T T A G G G C C T A T C A G G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C G G C T C A G C A C T T C C C A C 0 DY06 G A C T C T T C A A T C A D A G A G T C G C A A T A T T A A T G C C G A T C C A G T A C T C G T A G T G T C T C C T C A G T C A D A G A G C C A C C A T G T C G G G G C C T G C T C A G C A C C T C C C A C 0 DY07 (G) T C (T) (C) (C) (T) C A (G) (T) (C) (A) D A G A G (T) C G C A A T A T T A A G T C C G G C T C A G T A C T C G T A G T (T) T C (C) (A) (T) (G) C A (A) (C) (T) (G) D A G A G (C) C G C C A T G T T A G G G C C T G T C C A G T C C T T G C A G T 0 DY08 G (A) C T C (T) T C A A T C A D A G A G C C G C C A T G T T A (A) G (G) C (C) (G) G T C C A G T C C T T G C A G T G (T) C T C (C) T C A [G] T C A D A G A G C C G C C A T G T T A (G) G (T) C (T) (T) G C T C A G C A C T T C C C A C 0 DY09 T T C C A T G C [G] A T C A D A G A G C C G C C A T G T T A A G G C C G G T C C A G T C C T T G C A G T T T C C A T G C G A T C A D A G A G T C G C A A T A T T A A G G T C G G C T C A G C A T T T C C C A C 0 DY10 G A C T C T T C A A T C A D A G [C] G T C G C A A T A T T A A G G T T G G C T C A T C A C C T C C C A C T T C C A T G C G A T C A D A G A G T C G C A A T A T T A A G G T C G G C T C A G C A T T T C C C A C 0 DY11 G A C T C T T C A A T C A D A G C G T T G C A A T A T T A A G G T T G G C T C A T C A C C T C C C A C G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A C T T C C C A C 0 DY12 G A C T C T G C A A T C A D A G A G C C G C A A T A T T A G G G C C T A T C A G G T C C T C G C A G T G T C T C C T C A G T C A D A G A G [T] C G C A A T A T T A A G T C C G G C T C A G T A C T C G T A G T 0 DY13 T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C T T C C A T G C G A T C A D A G A G C C G C C A T G T T A G G T C T T G T C A G G T C C T C G C A G T 0 DY14 G A C T C T T C A A T C A D A G C G T C G C A A T A T T A A G G T T G G C T C A T C A C C T C C C A C T T C C A T G C G A T C A D A G A G C C G C C A T G T T A G G G C T G A T C A A G T A C T T G T A G T 0 DY15 G A C T C T T C A A T C A D A G C G T C G C A A T A T T A A G G T T G G C T C A T C A C C T C C C A C G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C G G C T C A G C A C T T C C C A C 0 DY16 G A C T C T T C A A T C A D A G A G T C G C A A T A T T A A G G T T G G C T C A T C A C C T C C C A C T T C C A T G C G A T C A D A G A G T C G C A A T A T T A A G G T C G G C T C A G C A T T T C C C A C 0 DY17 G A C T C T T C A A T C A D A G C G T C G C A A T A T T A G G G T C G G C T C A G C A C T T C C C A C T T C C A T G C G A T C A D A G A G C C G C C A T G T T A A G T C T T G C T A G T C A C C T C C C A C 0 DY18 G A C T C T T C A A T C A D A G C G T C G C A A T A T T A A G G T T G G C C C A T C A C C T C C C A C T T C C A T G C G A T C A D A G A G C C G C C A T G T T A G G G C T G A T C A A G T A C T T G T A G T 0 DY19 G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C G G C T C A G C A C T T C C C A C G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C T A T C C A G T A C T T G T A G T 0 DY20 (G) T C (T) (C) (C) (T) C A (G) T C A D A G A G C C A C C A T G T C G A G G C C T A T C C A G T A C T T G T A G T (T) T C (C) (A) (T) (G) C A (A) T C A D A G A G C C G C C A T G T T A A G G T C G G C T C A G C A C T T C C C A C 0 DY21 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C C G C C A T G T T A G G T C T T G T C A G G T C C T C G C A G T 0 DY22 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T 0 DY23 T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C T T C C A T G C G A T C A D A G A G T C G C A A T A T T A A G G T C G G C T C A G C A T T T C C C A C 0 DY24 G T C T C C T C A G T C A D A G A G C C G C [A] [G] T G T T A A G G C C (T) G C T C A G C A C (C) T C C C A C T T C C A T G C A G T C A D A C A A C C [G] [T] [A] [G] [T] G T C G A G G C C (G) G C T C A G C A C (T) T C C C A C 0 E101 G A T T C T T C A A C T G [I] G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C A G T C A D A G A G C C A C C A T G T C G G G G C C T G C T C A G C A C C T C C C A C 0 E102 G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C T A T C C A G T A C T T G T A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E103 G A T T C T T C A A C T G D G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G A T T C T T C A A C T G D G G A G C C G C A G T G A T G A G G C C T A T C C A G C A [C] T T C C C A C 0 E104 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C T A T C C A G T A C T T G T A G T 0 E105 G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E106 G A T T C T T C G A C T G [I] G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C G G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E107 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C T G A T C C A G C A C T T C C C A C 0 E108 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T A T C C A G C A C T T C C C A C G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E109 G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E110 G A T T C T T C A A C T G D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A C T T C C C A C G T C C A T G C A G T C A D A C A A C T G C C A T G T T A A T G C C G A T C C A G C A [T] T T C C C A C 0 E111 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T A T C C A G C A C T T C C C A C G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C T G A T C C A G C A C T T C C C A C 0 E112 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C T G A T C C A G C A C T T C C C A C 0 E113 G A T T C T T C A A C T G [I] G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G A T T C T T C A A C T G [I] G G A G C C G C A G T G A T G A G G C C T A T C C A G T A C T T G T A G T 0 E114 G A T T C T T C A A C T G D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A C T T C C C A C G A T T C T T C A A C T G D G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T 0 E115 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T G A G G C C T G T C C A G T C C T T G C A G T 0 E116 G A T T C T T C A A C T G [I] G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C 0 E117 G A T T C T T C A A C T G [I] G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T T T C C A T G C A G T C A D A C A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E118 G A T T C T T C A A C T G (I) [A] G A G C [T] G C C A T G T T A A T G C C G A T C C A G C A C T T C C C A C T T C C A T G C A G T C A (D) A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C 0 E119 G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C T T C C A T G C A G T C A D A C A A C C G T A G A G T T A A G G C T G A T C C A G C A C T T C C C A C 0 E120 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E121 G T C T C C T C A G T C A D A G A G C C A C C A T G T C G A G G C C T A T C C A G T A C T T G T A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A T T T C C C A C 0 E122 G A C T C T T G A A T C A D A G A G C C G C A G T G T T A A G G C C G G C T C A G T C C T C G C A G T G T C T C C T C A G T C A D A G A G C T G C C A T G T T A A T G C C G A T C C A G C A C T T C C C A C 0 E123 G A T T C T T C A A C T G I G G A G C C G C A G T G A T G A G G C C T G T C C A G T C C T T G C A G T G T C T C C T C A G T C A D A G A G C C A C C A T G T C G G G G C C T G C T C A G C A C C T C C C 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 DY01 = A = = = T = G = A = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = T = = = C = C = G = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0 DY02 G A = T C = T G ? ? ? ? ? ? = G = G = = = C = = T = = = = = = = = C = = = = A = = T = = = = G ? ? ? ? T T = C A = G C ? ? ? ? ? ? = C = A = = = T = = A = = = = = = = = T = = = = C = = C = = = = C ? ? ? ? 0 DY03 = = = = = = = = ? ? ? ? ? ? = C = A C = = T = G A G = = = = = = C T = A T C = = = = = C = = = = = = = = = = = = = = = ? ? ? ? ? ? = G = G T = = C = A T A = = = = = = T C = G C T = = = = = T = = = = = = = 0 DY04 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = T (C) = = C T = = = C A = = = C = C A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C (T) = = T C = = = T C = = = G = A G T 0 DY05 = A = = = T G = = A = = = ? = = = = = = G = A = = A = T A G = = = = T A T C A G = T C = ? C G = A G T = T = = = C T = = G = = = ? = = = = = = A = C = = G = C G A = = = = G G C T C A = C A = ? T C = C A C 0 DY06 = A = = = T = = = A = = = = = = = = T = G = A = = A = T A A T = = = G A T C = = = T = = T C G T A G T = T = = = C = = = G = = = = = = = = C = A = C = = G = C G G G = = = T G C T = = = C = = C T C C C A C 0 DY07 (G) = = (T) (C) (C) (T) = = (G) (T) (C) (A) = = = = = (T) = = = A = = A = = = A = T = = G = C T = = = = A = = C = T = = = (T) = = (C) (A) (T) (G) = = (A) (C) (T) (G) = = = = = (C) = = = C = = G = = = G = G = = T = T C = = = = C = = T = C = = = 0 DY08 = (A) = = = (T) = = ? ? ? ? ? ? = = = = = = = = = = = = = = = (A) = (G) = (C) (G) = T C = = = T C = = = G = A G T = (T) = = = (C) = = ? ? ? ? ? ? = = = = = = = = = = = = = = = (G) = (T) = (T) (T) = C T = = = C A = = = C = C A C 0 DY09 = = = = = = = = ? ? ? ? ? ? = = = = C = = = C = = G = = = = ? = C = = = T C = = = T C C = = G ? ? ? ? = = = = = = = = ? ? ? ? ? ? = = = = T = = = A = = A = = = = ? = T = = = C T = = = C A T = = C ? ? ? ? 0 DY10 G A = T C = T = A = = = = = ? ? ? ? ? = = = = = = = = = = = = = = T = = = = = = T = = C C = = = = = = T T = C A = G = G = = = = = ? ? ? ? ? = = = = = = = = = = = = = = C = = = = = = G = = T T = = = = = = 0 DY11 = A = = = T = = = A = = = = = = C = T = = = A = = A = = = = G = T T = G C T = = T = = = C = = = = = = = T = = = C = = = G = = = = = = A = C = = = C = = G = = = = T = C C = A T C = = G = = = T = = = = = = 0 DY12 = A = = = T G = = A = = = = ? ? ? ? ? = = = = = = = = = = G = G = = T A T C A G = = C = = = = C = = = = T = = = C T = = G = = = = ? ? ? ? ? = = = = = = = = = = A = T = = G G C T C A = = A = = = = T = = = 0 DY13 = = = = = = = = A G = = = = = C = A = = = T A G A = = = = A = G = = G A = = C A = C A = = T C = C A C = = = = = = = = G A = = = = = G = G = = = C C A T = = = = G = T = = T G = = A G = T C = = C G = A G T 0 DY14 G A = T C = T = A = = = = = = = C = T = = = A = = A = = = A = = T = = G C T C = T C = = C = C C C A C T T = C A = G = G = = = = = = = A = C = = = C = = G = = = G = = C = = A T C A = G T = = T = G T A G T 0 DY15 = A = = = T = = = A = = = = = = C = T = G = A = = A = T A = = = T T = = = = = = T = = = C = = = = = = = T = = = C = = = G = = = = = = A = C = A = C = = G = C G = = = C C = = = = = = G = = = T = = = = = = 0 DY16 G A = T C = T = ? ? ? ? ? ? = = = = = = = = = = = = = = ? = = = = T = = = = = = T = = C C = = = = = = T T = C A = G = ? ? ? ? ? ? = = = = = = = = = = = = = = ? = = = = C = = = = = = G = = T T = = = = = = 0 DY17 G A = T C = T = A = = = = = = = C = T = = = A = = A = = ? G = G T C G = = = C A G = = = T = = ? ? ? ? T T = C A = G = G = = = = = = = A = C = = = C = = G = = ? A = T C T T = = = A G T = = = C = = ? ? ? ? 0 DY18 G A = T C ? ? ? A = = = = = = = C = T = = = A = = A = = = A = = T = = ? ? = C = T C = = ? = C C C A C T T = C A ? ? ? G = = = = = = = A = C = = = C = = G = = = G = = C = = ? ? = A = G T = = ? = G T A G T 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G G C T = = = C = = = = C C C A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A T C = = = T = = = = G T A G T 0 DY20 (G) = = (T) (C) (C) (T) = = (G) = = = = = = = = ? = A = = = = = = C G = = = C = T A T C = = = T = = = = G T A G T (T) = = (C) (A) (T) (G) = = (A) = = = = = = = = ? = G = = = = = = T A = = = T = G G C T = = = C = = = = C C C A C 0 DY21 = A = = = T = G = A = = = = ? = = = = = = = A G = = = = = A = G = C G = C T C A = = = = = = = = = = = = T = = = C = C = G = = = = ? = = = = = = = C A = = = = = G = T = T T = T C A G = = = = = = = = = = = 0 DY22 = A = = = T = G = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = T = = = C = C = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = 0 DY23 = = = = = = = = ? ? ? ? ? ? = C = A C = = T = G A G = = = = = = ? T = A T C = = = = = C = = = = = = = = = = = = = = = ? ? ? ? ? ? = G = G T = = C = A T A = = = = = = ? C = G C T = = = = = T = = = = = = = 0 DY24 G = = T C C T = = = = = = = = G = G = ? ? ? ? ? ? ? = T A = = = = = (T) = = = = = = = = = (C) = = = = = = T = = C A T G = = = = = = = = C = A = ? ? ? ? ? ? ? = C G = = = = = (G) = = = = = = = = = (T) = = = = = = 0 E101 = A T = = T = = ? ? ? ? ? ? G = = = = = G = A G = = A T = A = = = = = = T C = = = T C = T = G ? ? ? ? = T C = = C = = ? ? ? ? ? ? A = = = = = A = C A = = T C = G = = = = = = C T = = = C A = C = C ? ? ? ? 0 E102 = = = = = = = = = = = = = = = = = = = C A = = = = = = C G = G = = = T = = = = = = T = C = = G T A G T = = = = = = = = = = = = = = = = = = = T G = = = = = = T A = T = = = G = = = = = = C = T = = C C C A C 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = T C ? = = G = A G T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = C A ? = = C = C A C 0 E104 = A T = = T = = = A C T G I G = = = = = G = A G = = A T = = = = = = = G = = = = = = C = = = = C = = = = T C = = C = = = G T C A D A = = = = = A = C A = = T C = = = = = = = A = = = = = = A = = = = T = = = 0 E105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 = ? ? ? ? T = = = A C T G ? G = = = = C = = A G = = ? ? G = G = = = T G = = = = = T C C = = G = A G T = ? ? ? ? C = = = G T C A ? A = = = = T = = C A = = ? ? A = T = = = G A = = = = = C A T = = C = C A C 0 E107 = A T = = T = = = A C T G I G = = = = C = = A G = = A = G = G = = C T G = = = = = T C = = = G = A G T = T C = = C = = = G T C A D A = = = = T = = C A = = T = A = T = = T G A = = = = = C A = = = C = C A C 0 E108 = A T = = T = = = A C T G I ? ? ? ? ? C = = A G = = A = ? = G = = = T = = = = = = = = C = = = = = = = = T C = = C = = = G T C A D ? ? ? ? ? T = = C A = = T = ? = T = = = G = = = = = = = = T = = = = = = = 0 E109 = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 = A T T C = T = = A C T G ? = G = G = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = T C C A = G = = G T C A ? = C = A = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 E111 = A T = = T = = = A C T G I G = = = = C = = A G = = A = G = G = = C T = = = = = = = = = = = = = = = = = T C = = C = = = G T C A D A = = = = T = = C A = = T = A = T = = T G = = = = = = = = = = = = = = = = 0 E112 = A = = = T = G = A = = = = = = = = = C = = A G = = = = = = G = = C = G C T = = = T C = = C G = A G T = T = = = C = C = G = = = = = = = = = T = = C A = = = = = = T = = T = A T C = = = C A = = T C = C A C 0 E113 = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = G = = = = = = C = = = = C = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = A = = = = = = A = = = = T = = = 0 E114 = = = = = = = = = = = = = = A = = = = T = = C A = = T = A = T = = = G A = = = = = C A = = = C = C A C = = = = = = = = = = = = = = G = = = = C = = A G = = A = G = G = = = T G = = = = = T C = = = G = A G T 0 E115 = A T = = T = = = A C T G I G = = = = C = = A G = = A = = = = = = = = = = = = = = = = = = = = = = = = = T C = = C = = = G T C A D A = = = = T = = C A = = T = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 G A T T C = T = ? ? ? ? ? ? G G = G = = = C = = T = ? ? ? ? ? ? ? ? ? G = = = = = T C = = = G = A G T T T C C A = G = ? ? ? ? ? ? A C = A = = = T = = A = ? ? ? ? ? ? ? ? ? A = = = = = C A = = = C = C A C 0 E117 G ? T ? ? = T = ? ? ? ? ? ? ? G = = = C = = A G = = A = ? ? ? = = = T G = = = = = T C C = = G = A G T T ? C ? ? = G = ? ? ? ? ? ? ? C = = = T = = C A = = T = ? ? ? = = = G A = = = = = C A T = = C = C A C 0 E118 G A T T C = T = = A C T G (I) ? G = G = ? = C C A T = = = = = T = = C = = = = = = = = = = = = = = = = = T T C C A = G = = G T C A (D) ? C = A = ? = T A G A = = = = = G = = T = = = = = = = = = = = = = = = = = 0 E119 G = = T C C T = = = = = = = = G = G = T = C C A T = = = = = T = = C = = = = = = = = = T = = = = = = = T = = C A T G = = = = = = = = C = A = C = T A G A = = = = = G = = T = = = = = = = = = C = = = = = = = 0 E120 ? ? ? ? ? T = G = A = = = = = = = = = C = = A G = = = = ? ? G = = = = G C T ? ? = T C C = C G = A G T ? ? ? ? ? C = C = G = = = = = = = = = T = = C A = = = = ? ? T = = = = A T C ? ? = C A T = T C = C A C 0 E121 = = = = = = = = = = = = = = = = = = = C A = = = = = = C G = G = = = T = = = = = = T = C = = G T A G T = = = = = = = = = = = = = = = = = = = T G = = = = = = T A = T = = = G = = = = = = C = T = = C C C A C 0 E122 = A = = = T = G = A = = = ? = = = = = C = = A G = = = = = = G = = = = G C T = = = T C = = C G = A G T = T = = = C = C = G = = = ? = = = = = T = = C A = = = = = = T = = = = A T C = = = C A = = T C = C A C 0 E123 = A T = = T = = = A C T G I G = = = = = G = A G = = A T = A = = = = = = T C = = = T C = T = G = A G T = T C = = C = = = G T C A D A = = = = = A = C A = = T C = G = = = = = = C T = = = C A = C = C = C A C 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 0.87 = = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = = = ? = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 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 = = = 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 = = = 0.99 = = 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.81 = = 0.81 0.81 0.81 0.81 = = 0.82 0.82 0.82 0.82 = = = = = 0.88 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = 1.00 = = 1.00 = 1.00 = = = = 0.77 = = = 0.77 = = ? ? ? ? ? ? = = = = = = = = = = = = = = = 0.67 = 0.67 = 0.67 0.67 = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = ? ? ? ? ? ? = = = = 1.00 = = = 1.00 = = 1.00 = = = = ? = 1.00 = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 ? ? ? ? 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = ? ? ? ? ? = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = = = 1.00 = = = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = = = = = 1.00 = = = 1.00 1.00 = = 1.00 = = = = ? ? ? ? ? = = = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = 1.00 = = = = = = = = = = = 0.99 0.99 = = = = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = 1.00 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 0.92 = 0.92 0.92 = 0.92 = 0.92 = = = = = = = 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 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 0.56 = = 0.56 0.56 0.56 0.56 = = 0.56 = = = = = = = = ? = 1.00 = = = = = = 1.00 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 = = = 0.92 = 0.92 = 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 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = 1.00 = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = = = = = = ? 1.00 = 1.00 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 = = = = = = = = = 0.80 = = = = = = = 1.00 1.00 = = 1.00 = = ? ? ? ? ? ? 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = 1.00 1.00 = = = 1.00 1.00 = 1.00 = 1.00 ? ? ? ? = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 1.00 ? = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = = 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? 1.00 = = = 1.00 1.00 1.00 1.00 ? 1.00 = = = = 1.00 = = 1.00 1.00 = = ? ? 1.00 = 1.00 = = = 1.00 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 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 = = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = 1.00 1.00 = = = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? ? ? ? ? ? 1.00 1.00 = 1.00 = = = 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 0.77 ? 1.00 = 1.00 = ? = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = = = = ? ? ? ? ? 1.00 = 1.00 = 1.00 = = = = = = = = = 1.00 = = 1.00 1.00 = = = = ? ? 1.00 = = = = 1.00 1.00 1.00 ? ? = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = 1.00 1.00 = 1.00 = = = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 0.99 = = = 0.99 = 0.99 = 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 END PHASEPROBS