************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 il1f5.phase.inp il1f5.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il1f5.phase.out_freqs : haplotype frequency estimates il1f5.phase.out_pairs : most likely haplotype pairs for each individual il1f5.phase.out_recom : estimates of recombination parameters il1f5.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 54 Positions of loci: 100 364 537 1215 1616 1637 2771 2828 3640 3645 4100 4193 5043 5045 5437 5505 5558 5616 5669 5822 5858 5868 6735 6805 7110 7256 7280 7363 7439 7487 7524 7544 7555 7556 7719 8581 8635 8685 8760 8777 8837 8919 9222 9305 9441 9758 9992 9993 10240 10273 10346 10553 11256 11470 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il1f5.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GACCCTTIDACACACGTTTITCGGCDGCCTGAATCTAC 1 ATCTTCTCAGCGTTC 1.000000 2 GACCCTTIDACACACGTTTITCGGCDGTACAAGGTTAC 1 ATCTTCTCAGCGCGC 7.000000 3 GACCCTTIDATAGCCATACDCTACGIGCCTGAGTCTAC 1 ATCTTCTCAGCGTTC 1.000000 4 GGCTCCCIITTACACATACDCTACGIACCTGGGTCCGA 4 GCGTCCCCAGCGCTC 6.000000 5 GGCTCTCIITTACACATACDCTACGIACCTGGGTCCGA 4 GCGTCCCCAGCGCTC 4.000000 6 GGCTCTTIIATAGCCATACDCTACGIACCTGGGTCCGA 4 GCGTCCCCAGCGCTC 1.000000 7 GGCTCTTIDATAGCCATACDCTACGIACCTGGGTCCGA 4 GCGTCCCCAGCGCTC 16.000000 8 GGCTCTTIDATAGCCATACDCTACGIACCTGGGTCTAC 1 ATCTCCCCAGCGCTC 1.000000 9 AACCCTCIITTACACATACDCTACGIACCTGGGTCCGA 4 GCGTCCCCAGCGCTC 4.000000 10 AACCCTCIITTACACATACDCTACGIACCTGGGTCTGA 4 GCGTCCCCAGCGCTC 1.000000 11 AACCCTCIITTACACACACDCTACGIACCTGGGTCCGA 4 GCGTCACTGTTACTT 10.000000 12 AACCCTCIDATAGCCATACDCTACGIACCTGAGTCCGA 4 GCGTCCCCAGCGCTC 2.000000 13 AGCCCTTIDACACATATACDCTACGIACCTGAATCCGA 4 GCGTCACTGTTACTT 9.000000 14 AGCCCTTIDACACATATACDCTACGIACCTGAATCTAC 1 ATCTTCTCAGCGTTC 9.000000 15 AGCCCTTDDATACACGTTTITCGGCDGTACAAGGTCGA 2 GCGTCACTGTTACTT 2.000000 16 AGCCCTTDDATACACGTTTITCGGCDGTACAAGGTCGA 4 GCGTCCCCAGCGCTC 1.000000 17 AGCCCTTDDATAGCCATACDCTACGIACCTGGGTCCGA 4 GCGTCACTGTTACTT 1.000000 18 AGACGTTDDACTCACGTTTITCGGCDGTACAAGGTTAC 1 ATCTTCTCAGCGCTC 1.000000 19 AGACGTTDDACTCACGTTTITCGGCDGTACAAGGTTAC 1 ATCCTCTCAGCGCTC 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,4) DY02: (2,11) DY03: (11,13) DY04: (7,12) DY05: (7,14) DY06: (1,7) DY07: (5,15) DY08: (3,12) DY09: (13,15) DY10: (13,14) DY11: (9,14) DY12: (5,14) DY13: (11,17) DY14: (13,14) DY15: (4,14) DY16: (13,14) DY17: (13,14) DY18: (13,14) DY19: (4,9) DY20: (13,16) DY21: (2,4) DY22: (2,4) DY23: (11,13) DY24: (4,11) E101: (5,18) E102: (7,10) E103: (19,19) E104: (9,19) E105: (7,7) E106: (7,19) E107: (7,19) E108: (7,19) E109: (7,7) E110: (11,19) E111: (7,19) E112: (2,7) E113: (19,19) E114: (19,19) E115: (6,19) E116: (11,19) E117: (11,19) E118: (11,19) E119: (7,11) E120: (2,7) E121: (7,9) E122: (2,8) E123: (5,19) 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 C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 DY02 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T 0 DY03 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T 0 DY04 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A A C C C T C I [D] [A] T A G C C A T A C D C T A C G I A C C T G A G T C C G A 4 G C G T C C C C A G C G C T C 0 DY05 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY06 G A C C C T T I D A C A C A C G T T T I T C G G C D G C C T G A A T C T A C 1 A T C T T C T C A G C G T T C G G C T C T T I D A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 DY07 G G C T C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G C C C T T D D A T A C A C G T T T I T C G G C D G T A C A A G G T C G A 2 G C G T C A C T G T T A C T T 0 DY08 (G) A C C C T (T) I [D] A T A G C C A T A C D C T A C G I (G) C C T G A G T C T A C 1 A T C T T C T C A G C G T T C (A) A C C C T (C) I [D] [A] T A G C C A T A C D C T A C G I (A) C C T G A G T C C G A 4 G C G T C C C C A G C G C T C 0 DY09 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T D D A T A C A C G T T T I T C G G C D G T A C A A G G T C G A 2 G C G T C A C T G T T A C T T 0 DY10 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY11 A A C C C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY12 G G C T C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY13 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T D D A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T 0 DY14 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY15 G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY16 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY17 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY18 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C T A C 1 A T C T T C T C A G C G T T C 0 DY19 G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A A C C C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 DY20 A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T D D A T A C A C G T T T I T C G G C D G T A C A A G G T C G A 4 G C G T C C C C A G C G C T C 0 DY21 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 DY22 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 DY23 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G C C C T T I D A C A C A T A T A C D C T A C G I A C C T G A A T C C G A 4 G C G T C A C T G T T A C T T 0 DY24 G G C T C C C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T 0 E101 G G C T C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C T C 0 E102 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C (C) G A 4 G C G T C C C C A G C G C T C A A C C C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C (T) G A 4 G C G T C C C C A G C G C T C 0 E103 A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E104 A A C C C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E105 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 E106 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E107 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E108 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E109 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 E110 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E111 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E112 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 E113 A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E114 A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E115 G G C T C T T I (I) A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D (D) A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E116 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E117 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E118 A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T A G A C G T T D [D] A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T C 0 E119 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A A C C C T C I I T T A C A C A C A C D C T A C G I A C C T G G G T C C G A 4 G C G T C A C T G T T A C T T 0 E120 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 E121 G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A A C C C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C 0 E122 G A C C C T T I D A C A C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C T T C T C A G C G C G C G G C T C T T I [D] A T A G C C A T A C D C T A C G I A C C T G G G T C T A C 1 A T C T C C C C A G C G C T C 0 E123 G G C T C T C I I T T A C A C A T A C D C T A C G I A C C T G G G T C C G A 4 G C G T C C C C A G C G C T C A G A C G T T D D A C T C A C G T T T I T C G G C D G T A C A A G G T T A C 1 A T C C T C T C A G C G C T 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 = C = T T = D A C = = = = G = T T I T C G G ? ? ? ? ? ? ? ? ? ? ? T A C 1 A T C = T = T = = = = = = G = = G = T = C C = I T T = = = = A = A C D C T A C ? ? ? ? ? ? ? ? ? ? ? C G A 4 G C G = C = C = = = = = = T = 0 DY02 G = = = = = T = ? ? C = = = = G T T T I T C G G C D G T A C A A = G ? T A ? 1 A T C = T C T C A G C G = G C A = = = = = C = ? ? T = = = = A C A C D C T A C G I A C C T G G = T ? C G ? 4 G C G = C A C T G T T A = T T 0 DY03 = A = = = = C = ? ? T = = = C = C = = = = = = = = = = = = = = G G = = = = = = = = = = = = = = = = = = = = = = G = = = = T = ? ? C = = = T = T = = = = = = = = = = = = = = A A = = = = = = = = = = = = = = = = = = = = = 0 DY04 G G = T = = T = ? ? = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = A A = C = = C = ? ? = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = 0 DY05 G = = T = = = = ? ? T = G C C = = = = = = = = = = = = = = = = G G = ? C G A 4 G C G = C = C = = = = = C = = A = = C = = = = ? ? C = C A T = = = = = = = = = = = = = = = = A A = ? T A C 1 A T C = T = T = = = = = T = = 0 DY06 = A = C = = = = = = C = C A = G = T T I T C G G C D G = = = = A A = ? T ? ? 1 A T C = T = T = = = = = T = = = G = T = = = = = = T = G C = A = A C D C T A C G I A = = = = G G = ? C ? ? 4 G C G = C = C = = = = = C = = 0 DY07 G = = T = = C I ? ? = = = = = A = A C D C T A C ? I A C C T G G = T ? = = = 4 = = = = = C = C A G C G = = C A = = C = = T D ? ? = = = = = G = T T I T C G G ? D G T A C A A = G ? = = = 2 = = = = = A = T G T T A = = T 0 DY08 (G) = = = = = (T) = ? ? = = = = = = = = = = = = = = = = (G) = = = = = = = ? ? ? ? 1 A T C = T = T = = = = = T = = (A) = = = = = (C) = ? ? = = = = = = = = = = = = = = = = (A) = = = = = = = ? ? ? ? 4 G C G = C = C = = = = = C = = 0 DY09 = = = = = = = I = = C = = = T A = A C D C T A C G I A C C T G = A T C = = = 4 = = = = = = = = = = = = = = = = = = = = = = D = = T = = = C G = T T I T C G G C D G T A C A = G G T = = = 2 = = = = = = = = = = = = = = = 0 DY10 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C G A 4 G C G = C A C T G T T A C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A C 1 A T C = T C T C A G C G T = C 0 DY11 = A = = = = C = I T T = = = C = = = = = = = = = = = = = = = = G G = = C G A 4 G C G = C = C = = = = = C = = = G = = = = T = D A C = = = T = = = = = = = = = = = = = = = = A A = = T A C 1 A T C = T = T = = = = = T = = 0 DY12 G = = T = = C = ? ? T = = = C = = = = = = = = = = = = = = = = G G = = C G A 4 G C G = C = C = = = = = C = = A = = C = = T = ? ? C = = = T = = = = = = = = = = = = = = = = A A = = T A C 1 A T C = T = T = = = = = T = = 0 DY13 = A = = = = C I I T = = C A = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = T D D A = = G C = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY14 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = C G A 4 G C G = C A C T G T T A C = T = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = T A C 1 A T C = T C T C A G C G T = C 0 DY15 G = = T = C C = I T T = = = C = = = = = = = = = = ? ? ? ? ? ? ? ? ? = C G A 4 G C G = C = C = = = = = C = = A = = C = T T = D A C = = = T = = = = = = = = = = ? ? ? ? ? ? ? ? ? = T A C 1 A T C = T = T = = = = = T = = 0 DY16 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C G A 4 G C G = C A C T G T T A C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A C 1 A T C = T C T C A G C G T = C 0 DY17 = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? C G A 4 G C G = C A C T G T T A C = T = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? T A C 1 A T C = T C T C A G C G T = C 0 DY18 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C G A 4 G C G = C A C T G T T A C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A C 1 A T C = T C T C A G C G T = C 0 DY19 G G = T = C = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A = C = T = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 = = = = = = = I ? ? C = = = T A = A ? D C T A C G I A C C T G = A T C = = = = = = = = = A = T G T T A = = T = = = = = = = D ? ? T = = = C G = T ? I T C G G C D G T A C A = G G T = = = = = = = = = C = C A G C G = = C 0 DY21 = A = C = T T = ? ? C = = = = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C = T = T = = = = = = G = = G = T = C C = ? ? T = = = = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G = C = C = = = = = = T = 0 DY22 = A = C = T T = ? ? C = = = = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C = T = T = = = = = = G = = G = T = C C = ? ? T = = = = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G = C = C = = = = = = T = 0 DY23 ? A = = = = C = I T T = = = C = C = = = = = = = = = = = = = = G G = = = = = = = = = = = = = = = = = = = = = ? G = = = = T = D A C = = = T = T = = = = = = = = = = = = = = A A = = = = = = = = = = = = = = = = = = = = = 0 DY24 G G = T = C = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C A G C G = = C A A = C = T = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = A = T G T T A = = T 0 E101 G = C T C = C I I T T A = = = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G = C = C = = = = = = = = A = A C G = T D D A C T = = = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C = T = T = = = = = = = = 0 E102 G G = T = = T = ? ? = = G C = = = = = = = = = = = = = = = = = = = = = (C) = = = ? = = = = = = = = = = = = = = A A = C = = C = ? ? = = C A = = = = = = = = = = = = = = = = = = = = = (T) = = = ? = = = = = = = = = = = = = = 0 E103 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 = A C = C = C I ? ? T A = = = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G T C = C = = = = = = = = = G A = G = T D ? ? C T = = = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C C T = T = = = = = = = = 0 E105 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 G = C T C = = I ? ? T A G C = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G T C = C = = = = = = = = A = A C G = = D ? ? C T C A = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C C T = T = = = = = = = = 0 E107 G = C T C = = I ? ? T A G C = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G T C = C = = = = = = = = A = A C G = = D ? ? C T C A = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C C T = T = = = = = = = = 0 E108 G = C T C = = I ? ? T A G C = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G T C = C = = = = = = = = A = A C G = = D ? ? C T C A = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C C T = T = = = = = = = = 0 E109 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = 0 E110 = A C = C = C I ? ? T A = = = A C A C D C T A C G I A C C T G G = T C C G A 4 G ? ? T C A C T G T T A = = T = G A = G = T D ? ? C T = = = G T T T I T C G G C D G T A C A A = G T T A C 1 A ? ? C T C T C A G C G = = C 0 E111 G = C T C = = I ? ? T A ? ? = A = A C D C T ? ? G I A C C T G G = T C C G A 4 G ? ? T C = C = = = = = = ? ? A = A C G = = D ? ? C T ? ? = G = T T I T C ? ? C D G T A C A A = G T T A C 1 A ? ? C T = T = = = = = = ? ? 0 E112 = A = C = = = = ? ? C = C A = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C = T = T = = = = = = G = = G = T = = = = ? ? T = G C = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G = C = C = = = = = = T = 0 E113 = = = ? ? ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = ? ? ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 E114 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 G = C T C = = I (I) = T A G C = A = A C D C T A C G I A C C T G G = T C C G A 4 G C G T C = C = = = = = = = = A = A C G = = D (D) = C T C A = G = T T I T C G G C D G T A C A A = G T T A C 1 A T C C T = T = = = = = = = = 0 E116 = A C = C = C I I T T A = = = A C A C D C T A C G I A C C T G G = T C C ? A 4 G C G T C A C T G T T A = = T = G A = G = T D D A C T = = = G T T T I T C G G C D G T A C A A = G T T ? C 1 A T C C T C T C A G C G = = C 0 E117 = A C = C = ? I ? ? T A = = = A C A C D C T A C G I A C C T G G = T ? C G A ? ? C G ? ? ? C T G T T A = = T = G A = G = ? D ? ? C T = = = G T T T I T C G G C D G T A C A A = G ? T A C ? ? T C ? ? ? T C A G C G = = C 0 E118 = A C = C = C I ? ? T A = = = A C A C D C T A C G I A C C T G G = T ? C G A 4 G C G T C A C ? ? T T A = = T = G A = G = T D ? ? C T = = = G T T T I T C G G C D G T A C A A = G ? T A C 1 A T C C T C T ? ? G C G = = C 0 E119 G G = T = = T = ? ? = = G C = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C A G C G = = C A A = C = = C = ? ? = = C A = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = A = T G T T A = = T 0 E120 = A = C = = = = ? ? C = C A = G = T T I T C G G ? D G T A C A A = G T T A C 1 A T C = T = T = = ? ? ? ? G = = G = T = = = = ? ? T = G C = A = A C D C T A C ? I A C C T G G = T C C G A 4 G C G = C = C = = ? ? ? ? T = 0 E121 G G = T = = T = ? ? = = G C = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = A A = C = = C = ? ? = = C A = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0 E122 = A = C = = = = ? ? C = C A = G = T T I T C G G C D G T A C A A = G T = = = = = = = ? T = T = = = = = = G = = G = T = = = = ? ? T = G C = A = A C D C T A C G I A C C T G G = T C = = = = = = = ? C = C = = = = = = T = 0 E123 G = C T C = C I I T T A = = = A = ? ? D C T A C G I A C C T G G = T C C G A 4 G C G ? C = C = = = = = = = = A = A C G = T D D A C T = = = G = ? ? I T C G G C D G T A C A A = G T T A C 1 A T C ? T = T = = = = = = = = 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 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 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 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = ? 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = 1.00 = = 1.00 = = 1.00 = = 1.00 1.00 ? ? = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? = = = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 0.57 = = = = = 0.57 = ? ? = = = = = = = = = = = = = = = = 0.55 = = = = = = = ? ? ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = 1.00 = = = = = = = = = 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = 1.00 = = 1.00 = = 1.00 = = 1.00 = ? ? 1.00 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 1.00 = = 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 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = ? ? 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = ? ? 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 = ? 1.00 = = = = 1.00 = 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 = ? ? = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 0.50 = = = ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = 1.00 1.00 = 1.00 = 1.00 1.00 ? ? 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 ? ? 1.00 1.00 ? ? = 1.00 = 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 = 1.00 = = = = = = ? ? = 1.00 = 1.00 = = = = ? ? 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 = = = = ? ? ? = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = 1.00 0.59 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = ? 1.00 ? ? 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 ? ? 1.00 1.00 ? ? ? 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 ? ? 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = 1.00 = ? ? = = 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = = ? ? 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = ? ? ? ? 1.00 = 1.00 1.00 = 1.00 = = 1.00 = ? ? = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = ? ? 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = ? 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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