************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 apo3g.phase.inp apo3g.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST apo3g.phase.out_freqs : haplotype frequency estimates apo3g.phase.out_pairs : most likely haplotype pairs for each individual apo3g.phase.out_recom : estimates of recombination parameters apo3g.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 39 Positions of loci: 310 673 1324 1805 2445 2751 5141 5882 6136 6150 6325 6731 7060 7100 7101 7186 7864 8111 8112 8279 8333 8922 9422 9456 9946 10152 10154 10421 10619 10654 10782 10787 11130 11386 11568 12591 12603 12726 12937 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file apo3g.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AGCCC 2 ATCTAGGTCGCGTGCGCACCGCCGCGCGGCCTC 2.000000 2 AGCCC 3 GTCTAGATCGCGTGCGCACCGCCGCGCGGCCTC 1.000000 3 AGCCC 4 ATCTAGGTCGCGTGCGCACCGCCGCGCGGCCTC 19.000000 4 AGCCG 2 GTCTAGATCGCGTGCGCACCGCCGCGCGGCCTC 3.000000 5 AGCCG 3 GTCTAGATCGCGTGCGCACCGCCGCGCGGCCTC 3.000000 6 AGCGC 2 ATCTAGGTCGCGAGCGCGCCGCCGCGCGGCCCG 1.000000 7 AGCGC 2 ATCTAGGTCGCGAGGGTGTGGCGAAGCGGCCCC 1.000000 8 AGCGC 2 ATGCGTGAAACGATCACGCGACGAAGCGATTCG 14.000000 9 AGCGC 2 ATGCGTGTCACGATCGCGCGACGAAGCGACCCG 2.000000 10 AGCGC 4 ATCTAGGTCGCGTGCGCACCGCCGCGCGGCCTC 1.000000 11 AGGCC 2 ATCTAGGTCGCGAGCGCGCCGCCACGCGGCCTC 2.000000 12 AGGCC 2 ATCTAGGTCGCGTGCGCACCGCCGCGCGGCCTC 6.000000 13 AACGC 2 ATCTAGGTCGCGAGGGTGTGGCGAAGCGGCCCC 9.000000 14 AACGC 2 ATGCGTGTCACGAGCGCGCGACGAAGCGACCCG 3.000000 15 AACGC 2 ACCTAGGTCGCGAGGGCGTGGCGAAGCGGCCCC 2.000000 16 AACGC 2 ACCTAGGTCGCGAGGGTGTGGCGAAGCGGCCCC 14.000000 17 AACGC 2 ACCTAGGTCGCGTGCGCACCGCCGCGCGGCCTC 2.000000 18 TGCGC 2 ATCTAGGTCGGAAGCGCGCGGTGAAAGGATCCG 1.000000 19 TGCGC 2 ATCTAGGTCGGAAGCGCGCGGTGAAAGAACCCC 1.000000 20 TGCGC 2 ATCTAGGTCGGAAGCGCGCGGTGAAAGAACCCG 5.000000 21 TGCGC 2 ATCTAGGTCGGAAGCGCGCGGTGAAAGAGCCTC 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,8) DY02: (3,12) DY03: (9,11) DY04: (5,8) DY05: (8,8) DY06: (8,16) DY07: (5,8) DY08: (5,12) DY09: (19,20) DY10: (1,8) DY11: (8,20) DY12: (8,21) DY13: (8,11) DY14: (3,4) DY15: (8,18) DY16: (3,20) DY17: (3,20) DY18: (12,1) DY19: (13,21) DY20: (6,8) DY21: (3,3) DY22: (4,4) DY23: (3,9) DY24: (8,14) E101: (15,16) E102: (3,7) E103: (13,16) E104: (8,14) E105: (3,16) E106: (3,16) E107: (3,16) E108: (3,16) E109: (10,13) E110: (13,13) E111: (16,16) E112: (3,12) E113: (3,12) E114: (13,13) E115: (3,16) E116: (13,16) E117: (3,13) E118: (15,16) E119: (16,17) E120: (3,17) E121: (3,14) E122: (3,20) E123: (12,16) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A G C C C 3 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY02 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G [G] C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY03 A G C G C 2 A T G C G T G T C A C G A T C G C G C G A C G A A G C G A C C C G A G G C C 2 A T C T A G G T C G C G A G C G C G C [C] G C C [A] C G C G G C C T C 0 DY04 A G C C G 3 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY05 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY06 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G A A C G C 2 A [C] C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 DY07 A G C C G 3 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY08 A G C C G 3 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C A G [G] C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY09 T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C C T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C G 0 DY10 A G C C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY11 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C G 0 DY12 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A G C C T C 0 DY13 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G A G G C C 2 A T C T A G G T C G C G A G C G C G C [C] G C C [A] C G C G G C C T C 0 DY14 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G C C G 2 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY15 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G G A T C C G 0 DY16 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C G 0 DY17 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C G 0 DY18 A G [G] C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G [C] C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY19 A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A G C C T C 0 DY20 A G [C] G C 2 A T C T A G G T C G C G A G C G C G C C G C C G C G C G G C C C G A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G 0 DY21 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY22 A G C C G 2 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C A G C C G 2 G T C T A G A T C G C G T G C G C A C C G C C G C G C G G C C T C 0 DY23 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T G C G T G T C A C G A T C G C G C G A C G A A G C G A C C C G 0 DY24 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G A [A] C G C 2 A T G C G T G T C A C G A [G] C G C G C G A C G A A G C G A C C C G 0 E101 A A C G C 2 A C C T A G G T C G C G A G G G C G T G G C G A A G C G G C C C C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E102 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E103 A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E104 A G C G C 2 A T G C G T G A A A C G A T C A C G C G A C G A A G C G A T T C G A A C G C 2 A T G C G T G T C A C G A G C G C G C G A C G A A G C G A C C C G 0 E105 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E106 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E107 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E108 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E109 A G C G C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E110 A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A [A] C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E111 A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E112 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G [G] C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 E113 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A G G C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 E114 A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E115 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E116 A A C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E117 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A [A] C G C 2 A T C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E118 A A C G C 2 A C C T A G G T C G C G A G G G C G T G G C G A A G C G G C C C C A A C G C 2 A [C] C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C 0 E119 A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C C A A C G C 2 A C C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 E120 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C 0 E121 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A T G C G T G T C A C G A G C G C G C G A C G A A G C G A C C C G 0 E122 A G C C C 4 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C T G C G C 2 A T C T A G G T C G G A A G C G C G C G G T G A A A G A A C C C G 0 E123 A G G C C 2 A T C T A G G T C G C G T G C G C A C C G C C G C G C G G C C T C A A C G C 2 A C C T A G G T C G C G A G G G T G T G G C G A A G C G G C C C 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 = ? ? C = 3 G = C T A G A T C G = = T G = ? = ? = C G = C G C = = = G C C T C = ? ? G = 2 A = G C G T G A A A = = A T = ? = ? = G A = G A A = = = A T T C G 0 DY02 = ? ? = = 4 = = = = ? = = = = = = = = = = ? = = = ? ? = ? ? = = = = = = = = = = ? ? = = 2 = = = = ? = = = = = = = = = = ? = = = ? ? = ? ? = = = = = = = = = 0 DY03 = ? ? G = = = = G C G T = = = A = = = T = ? = = = ? ? = ? ? A = = = A = = C G = ? ? C = = = = C T A G = = = G = = = G = ? = = = ? ? = ? ? C = = = G = = T C 0 DY04 = ? ? C G 3 G = C T A G A T C G = = T G = ? = A = ? ? = ? ? C = = = G C C T C = ? ? G C 2 A = G C G T G A A A = = A T = ? = G = ? ? = ? ? A = = = A T T C G 0 DY05 = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? = ? ? = = = = = = = = = 0 DY06 = ? = = = = = ? G C G T = A A A = = = T C ? C = C = A = ? ? = = = = A T T = G = ? = = = = = ? C T A G = T C G = = = G G ? T = T = G = ? ? = = = = G C C = C 0 DY07 = = ? C G 3 G = C T A G A T C G = = T G = G = A = C G = C ? C = = = ? C C T C = = ? G C 2 A = G C G T G A A A = = A T = A = G = G A = G ? A = = = ? T T C G 0 DY08 = ? ? = G 3 G ? = = = = A = = = = = = = = ? = ? = = = = = = = = = = = = = = = = ? ? = C 2 A ? = = = = G = = = = = = = = ? = ? = = = = = = = = = = = = = = = 0 DY09 ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = = = = = = C ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = = = = = = G 0 DY10 ? = = C = = = = C T A G = T C G = = T G = ? = A = C G = C ? C = = = G C C T C ? = = G = = = = G C G T = A A A = = A T = ? = G = G A = G ? A = = = A T T C G 0 DY11 A = = = = = = = G C G T = ? ? ? C G = T = A = = = = A C = = = G C G = T T = = T = = = = = = = C T A G = ? ? ? G A = G = G = = = = G T = = = A G A = C C = = 0 DY12 A = = = = = = = G C G T ? A A ? C G = T = A = = = = A C ? ? = G C G A T T C G T = = = = = = = C T A G ? T C ? G A = G = G = = = = G T ? ? = A G A G C C T C 0 DY13 = = C G = = = = G C G T = A A A = = = T = A = = ? ? ? ? ? ? A = = = ? T T C G = = G C = = = = C T A G = T C G = = = G = G = = ? ? ? ? ? ? C = = = ? C C T C 0 DY14 = ? ? = C 4 A = = = = = G = = = = = = = = = = = = = = = = ? = = = = = ? ? ? ? = ? ? = G 2 G = = = = = A = = = = = = = = = = = = = = = = ? = = = = = ? ? ? ? 0 DY15 A = = = = = = = G C G T = A A A C G = T = ? = = = = A C = ? = G C = = = T = = T = = = = = = = C T A G = T C G G A = G = ? = = = = G T = ? = A G = = = C = = 0 DY16 A = = C = 4 = = = = = = = = = = C G T = = ? = A = C = C C G C G C G G = = T C T = = G = 2 = = = = = = = = = = G A A = = ? = G = G = T G A A A G A A = = C G 0 DY17 A = = C ? 4 = = = = = = = = = = C G T = = ? = A = C = C C G C G C G G = = T C T = = G ? 2 = = = = = = = = = = G A A = = ? = G = G = T G A A A G A A = = C G 0 DY18 = ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = 0 DY19 A A = = = = = = = = = = = = = = C G = = G = T = T = = C = = = G C G = = = C = T G = = = = = = = = = = = = = = G A = = C = C = C = = T = = = A G A = = = T = 0 DY20 = = ? = = = = = C T A G = T C ? = = = G = G = = = C G = C G C = = = G C C = = = = ? = = = = = G C G T = A A ? = = = T = A = = = G A = G A A = = = A T T = = 0 DY21 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY22 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 0 DY23 = = = C = 4 = = C T A G = = = G = = T G = = = A = C G = C G C = = = G = = T C = = = G = 2 = = G C G T = = = A = = A T = = = G = G A = G A A = = = A = = C G 0 DY24 = ? ? = = = = = = = = = = A A = ? ? ? ? ? ? = = = ? ? = = ? = = = = = T T = = = ? ? = = = = = = = = = = T C = ? ? ? ? ? ? = = = ? ? = = ? = = = = = C C = = 0 E101 = = ? = ? = = = = = = = ? = = = = = = = = ? C = = = = = = ? = = = = = = = = = = = ? = ? = = = = = = = ? = = = = = = = = ? T = = = = = = ? = = = = = = = = = 0 E102 = = ? C = 4 = = = = = = = = = = = = T = C ? C A C C = = C ? C = = = = = = T = = = ? G = 2 = = = = = = = = = = = = A = G ? T G T G = = G ? A = = = = = = C = 0 E103 = = = = = = = T = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = 0 E104 = G = = = = = = = = = = = A A = = = = T = A = = = = = = = ? = = = = = ? ? = = = A = = = = = = = = = = = T C = = = = G = G = = = = = = = ? = = = = = ? ? = = 0 E105 = G = C = 4 = T = = = = = = = = = = ? = C = C A C C ? = C G C = = = = = = T = = A = G = 2 = C = = = = = = = = = = ? = G = T G T G ? = G A A = = = = = = C = 0 E106 = G = C = 4 = T = = = = = = = = = = T = C = C A C C = = C G C = = = = = = T = = A = G = 2 = C = = = = = = = = = = A = G = T G T G = = G A A = = = = = = C = 0 E107 = G = C = 4 = T = = = = = = = = = = T = C = C A C C ? = C ? C = = = = = = T = = A = G = 2 = C = = = = = = = = = = A = G = T G T G ? = G ? A = = = = = = C = 0 E108 = ? ? C = 4 = T = = = = = = = = = = T = C ? C A C C = = C G C = = = = = = T = = ? ? G = 2 = C = = = = = = = = = = A = G ? T G T G = = G A A = = = = = = C = 0 E109 = G = = = 4 = = = = = = = = = = = = T = C ? C A C ? ? = C G C = = = = = = T = = A = = = 2 = = = = = = = = = = = = A = G ? T G T ? ? = G A A = = = = = = C = 0 E110 = ? ? = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 E111 = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = = = = = = = 0 E112 = = ? = = 4 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 2 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = C = = 4 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = G = = 2 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = 0 E114 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = G = C = 4 = T = = = = = = = = = = T = C = C A C C = = C ? C = = = = = = T = = A = G = 2 = C = = = = = = = = = = A = G = T G T G = = G ? A = = = = = = C = 0 E116 = = ? = = = = T = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? ? = = = ? = = = = C = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? ? = 0 E117 ? ? ? ? = 4 = = = = = = = = = = = ? ? = ? ? C A C C = = C G C = = = = = = T = ? ? ? ? = 2 = = = = = = = = = = = ? ? = ? ? T G T G = = G A A = = = = = = C = 0 E118 = ? ? = = = = ? = = = = = = = = = = = = = = C = = ? ? ? ? ? = = = = = ? ? ? ? = ? ? = = = = ? = = = = = = = = = = = = = = T = = ? ? ? ? ? = = = = = ? ? ? ? 0 E119 = ? ? = = = = = = = = = = = = = = = A = G = T G T G ? = G A A = = = = = = C = = ? ? = = = = = = = = = = = = = = = T = C = C A C C ? = C G C = = = = = = T = 0 E120 = G ? C = 4 = T = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = A ? G = 2 = C = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = 0 E121 = G ? C = 4 = = C T A G = = = G = = T = = = = A = C G = C G C = = = G = = T C = A ? G = 2 = = G C G T = = = A = = A = = = = G = G A = G A A = = = A = = C G 0 E122 A = = C = 4 = = = = = = = = = = C G T = = = = A = C = C C ? C G C G G = = T C T = = G = 2 = = = = = = = = = = G A A = = = = G = G = T G ? A A G A A = = C G 0 E123 = G G C = = = T = = = = = = = = = = T = C = C A ? ? ? = C ? C = = = ? = = T = = A C G = = = C = = = = = = = = = = A = G = T G ? ? ? = G ? A = = = ? = = C = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? 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= = = = = = = = 1.00 ? = = 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 = ? = 1.00 = 1.00 1.00 = 1.00 ? 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = ? ? ? 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 ? 1.00 1.00 ? 1.00 1.00 = 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 = = = 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 = = = = = = ? = = = = = = = = = = = ? 0.97 = 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 = = 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 = = = = = = 1.00 = = ? ? = = = = ? = = = = = = = = = = = = = = 1.00 = = ? ? ? ? ? = = = = = ? ? ? ? = ? ? = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 ? = 1.00 1.00 1.00 = = = = = = 1.00 = = 1.00 ? 1.00 = 1.00 = 1.00 = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 ? 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = 1.00 1.00 1.00 = = = = 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 = = = 0.99 = = = = = = = = = = 1.00 = 1.00 = 1.00 1.00 ? ? ? = 1.00 ? 1.00 = = = ? = = 1.00 = END PHASEPROBS