************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mmp9x.phase.inp mmp9x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mmp9x.phase.out_freqs : haplotype frequency estimates mmp9x.phase.out_pairs : most likely haplotype pairs for each individual mmp9x.phase.out_recom : estimates of recombination parameters mmp9x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 29 Positions of loci: 70 189 430 1364 2078 2590 3235 3965 4146 4679 4845 5029 5413 6185 6860 6986 7287 7565 8046 8224 8629 8834 9419 9464 9607 10814 10831 11273 11336 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mmp9x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CTCTCTGCGACAGGCCAGAATCGCCTCCA 1.000000 2 CTCTCTGCGACAGGGTCGAACGGCTTTCA 1.000000 3 CTCTCTGCGACAGGGTAGAACCGCTTTCA 1.000000 4 CTCTCTGCGACAGGGTAGAACGGCTTTCA 4.000000 5 CTCTCTGTGACAAGCTCGAACGGTTTTCA 1.000000 6 CTCTCTACGACAGGGTAGAACGGCTTTCA 33.000000 7 CTCTCTACGACAGGGTAAGACGACTTTCA 1.000000 8 CTCTCTATGACAAGCTCGAACGGTTTTCA 35.000000 9 CTCTCTATGACAAGCTAGAACGGTTTTCA 3.000000 10 CTCTTTACGACAGGCTCGAACGGCCCTTC 12.000000 11 CTCTTTACGACAGGCTAGAACGGCCCTTC 1.000000 12 CTCGCCGCGACAGGCCAGAATCGCCTCCA 1.000000 13 CTCGCCGCTGCAGGCTAAGACGGCTTTCA 2.000000 14 CTCGCCACGACAGGCCAGAATCGCCTCCA 9.000000 15 CTCGCTGCGACAGGCTCGAACGGCTTTCA 2.000000 16 TTCTCCGCGGCAGACTAGAGCGGCTTTCA 42.000000 17 TTCTCCGCGGTAGGCTCGAACGGCCTCCA 9.000000 18 TTCTCCGCGGTAGGCTCGAGCGGCTTTCA 1.000000 19 TTCTCCGCGGTAGGCTAGAACGGCCTCCA 3.000000 20 TTCTCCACGGCAGACTAGAGCGGCTTTCA 1.000000 21 TATTCCGCGGCAGGCTAGGACGGCTTTCA 1.000000 22 TATTCCGCTGCAGGCTAAGACGACTTTCA 1.000000 23 TATTCCGCTGCGGGCTAAGACCACTTTCA 1.000000 24 TATTCCGCTGCGGGCTAAGACGACTTTCA 18.000000 25 TATTCCACGACAGGCCAGAATCGCCTCCA 3.000000 26 TATTCCACTGCGGGCTAAGACGACTTTCA 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,16) D002: (6,8) D003: (10,15) D004: (9,14) D005: (4,6) D006: (6,9) D007: (19,24) D008: (6,9) D009: (14,23) D010: (14,16) D011: (16,24) D012: (24,24) D013: (6,20) D014: (12,16) D015: (14,19) DY01: (4,17) DY02: (16,25) DY03: (6,21) DY04: (6,14) DY05: (14,14) DY06: (16,22) DY07: (13,25) DY08: (2,14) DY09: (1,19) DY10: (6,24) DY11: (13,14) DY12: (6,8) E101: (16,24) E102: (8,16) E103: (16,16) E104: (8,16) E105: (8,16) E106: (8,8) E107: (6,24) E108: (8,16) E109: (8,24) E110: (8,24) E111: (8,24) E112: (8,8) E113: (8,8) E114: (8,8) E115: (8,10) E116: (4,16) E117: (8,24) E118: (8,16) E119: (8,8) E120: (8,24) E121: (10,16) E122: (8,8) H101: (6,6) H102: (10,16) H103: (6,24) H104: (6,10) H105: (15,24) H106: (10,16) H107: (8,10) H108: (8,10) H109: (6,8) H110: (16,24) H111: (6,6) H112: (5,16) H113: (8,16) H114: (6,8) H115: (6,6) H116: (8,25) H117: (6,17) H118: (8,8) H119: (6,16) H120: (10,16) H121: (8,17) H122: (4,8) X101: (16,16) X102: (6,16) X103: (10,16) X104: (6,16) X105: (16,16) X106: (6,16) X107: (16,26) X108: (16,17) X109: (16,16) X110: (6,10) X111: (6,16) X112: (16,18) X113: (10,26) X114: (6,16) X115: (17,26) X116: (6,17) X117: (6,11) X118: (24,24) X119: (7,24) X120: (16,17) X121: (6,17) X122: (16,16) X123: (6,16) X124: (6,17) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C T C T C T G C G A C A G G G T [A] G A A C C G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 D002 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 D003 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C C T C G C T G C G A C A G G C T C G A A C G G C T T T C A 0 D004 C T C T C T A T G A C A A G C T A G A A C G G [T] T T T C A C T C G C C A C G A C A G G C C A G A A T C G C C T C C A 0 D005 C T C T C T G C G A C A G G G T A G A A C G G C T T T C A C T C T C T A C G A C A G G G T A G A A C G G C T T T C A 0 D006 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T A G A A C G G [T] T T T C A 0 D007 T T C T C C G C G G T A G [G] C T A G A A C G G C C T C C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 D008 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T A G A A C G G [T] T T T C A 0 D009 C T C G C C A C G A C A G G C C A G A A T C G C C T C C A T A T T C C G C T G C G G G C T A A G A C C A C T T T C A 0 D010 C T C G C C A C G A C A G G C C A G A A T C G C C T C C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 D011 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 D012 T A T T C C G C T G C G G G C T A A G A C G A C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 D013 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C A C G G C A G A C T A G A G C G G C T T T C A 0 D014 C T C G C C G C G A C A G G C C A G A A T C G C C T C C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 D015 C T C G C C A C G A C A G G C C A G A A T C G C C T C C A T T C T C C G C G G T A G [G] C T A G A A C G G C C T C C A 0 DY01 C T C T C T G C G A C A G G G T [A] G A A C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 DY02 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T A T T C C A C G A C A G G C C A G A A T C G C C T C C A 0 DY03 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T A T T C C G C G G C A G G C T A G G A C G G C T T T C A 0 DY04 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C G C C A C G A C A G G C C A G A A T C G C C T C C A 0 DY05 C T C G C C A C G A C A G G C C A G A A T C G C C T C C A C T C G C C A C G A C A G G C C A G A A T C G C C T C C A 0 DY06 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T A T T C C G C T G C A G G C T A A G A C G A C T T T C A 0 DY07 C T C G C C G C T G C A G G C T A A G A C G G C T T T C A T A T T C C A C G A C A G G C C A G A A T C G C C T C C A 0 DY08 C T C T C T (G) C G A C A G G G T (C) G A A C G G C T T T C A C T C G C C (A) C G A C A G G C C (A) G A A T C G C C T C C A 0 DY09 C T C T C T G C G A C A G G C C A G A A T C G C C T C C A T T C T C C G C G G T A G G C T A G A A C G G C C T C C A 0 DY10 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 DY11 C T C G C C G C T G C A G G C T A A G A C G G C T T T C A C T C G C C A C G A C A G G C C A G A A T C G C C T C C A 0 DY12 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E101 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E102 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E103 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E104 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E105 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E106 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E107 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E108 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E109 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E110 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E111 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E112 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E113 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E114 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E115 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T T T A C G A C A G G C T C G A A C G G C C C T T C 0 E116 C T C T C T G C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E117 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E118 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E119 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 E120 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 E121 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 E122 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 H101 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A C G A C A G G G T A G A A C G G C T T T C A 0 H102 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H103 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 H104 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T T T A C G A C A G G C T C G A A C G G C C C T T C 0 H105 C T C G C T G C G A C A G G C T C G A A C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 H106 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H107 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T T T A C G A C A G G C T C G A A C G G C C C T T C 0 H108 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T T T A C G A C A G G C T C G A A C G G C C C T T C 0 H109 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 H110 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 H111 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A C G A C A G G G T A G A A C G G C T T T C A 0 H112 C T C T C T G T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H113 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H114 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 H115 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T C T A C G A C A G G G T A G A A C G G C T T T C A 0 H116 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T A T T C C A C G A C A G G C C A G A A T C G C C T C C A 0 H117 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 H118 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A C T C T C T A T G A C A A G C T C G A A C G G T T T T C A 0 H119 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H120 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 H121 C T C T C T A T G A C A A G C T C G A A C G G T T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 H122 C T C T C T (G) C G A C A G G G T A G A A C G G C T T T C A C T C T C T (A) T G A C A A G C T C G A A C G G T T T T C A 0 X101 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X102 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X103 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X104 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X105 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X106 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X107 T T C T C C (G) C G G C A G A C T A G A G C G G C T T T C A T A T T C C (A) C T G C G G G C T A A G A C G A C T T T C A 0 X108 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 X109 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X110 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T T T A C G A C A G G C T C G A A C G G C C C T T C 0 X111 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X112 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G T A G G C T C G A G C G G C T T T C A 0 X113 C T C T T T A C G A C A G G C T C G A A C G G C C C T T C T A T T C C A C T G C G G G C T A A G A C G A C T T T C A 0 X114 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X115 T T C T C C G C G G T A G G C T C G A A C G G C C T C C A T A T T C C A C T G C G G G C T A A G A C G A C T T T C A 0 X116 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 X117 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A C T C T T T A C G A C A G G C T A G A A C G G C C C T T C 0 X118 T A T T C C G C T G C G G G C T A A G A C G A C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 X119 C T C T C T A C G A C A G G G T A A G A C G A C T T T C A T A T T C C G C T G C G G G C T A A G A C G A C T T T C A 0 X120 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 X121 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 0 X122 T T C T C C G C G G C A G A C T A G A G C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X123 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G C A G A C T A G A G C G G C T T T C A 0 X124 C T C T C T A C G A C A G G G T A G A A C G G C T T T C A T T C T C C G C G G T A G G C T C G A A C G G C C T C C A 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 ? = = = = T = = = A = = = ? G = ? = = A = C = = = = = = = ? = = = = C = = = G = = = ? C = ? = = G = G = = = = = = = 0 D002 = = = = ? = = C = = = = G = G = ? = = = = = = ? = = = = = = = = = ? = = T = = = = A = C = ? = = = = = = ? = = = = = 0 D003 = = = T T = A = = = = = = = = = = = = = = = = = C ? ? T C = = = G C = G = = = = = = = = = = = = = = = = = T ? ? C A 0 D004 = = = T ? T = T = = = = A ? = T = = = = C G = ? T = T = = = = = G ? C = C = = = = G ? = C = = = = T C = ? C = C = = 0 D005 = = = = = = G = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = A = = = = = = = = = = = = = = = = = = = = ? ? 0 D006 = = = = ? = = C = = = = G = G = = = = = = = ? ? = = = = = = = = = ? = = T = = = = A = C = = = = = = = ? ? = = = = = 0 D007 ? T C = = = = = G = T A = ? = = = G A = = = G = C = C = = ? A T = = = = = T = C G = ? = = = A G = = = A = T = T = = 0 D008 ? = = = = = = C = = = = G = G = = = = = = = ? ? ? ? ? = = ? = = = = = = T = = = = A = C = = = = = = = ? ? ? ? ? = = 0 D009 C T C G = = A = G A = A = = = C = G A ? T = G = C = C = = T A T T = = G = T G = G = = = T = A G ? C = A = T = T = = 0 D010 C = = G = = A = = A = = = G = C = = = A T C = = C = C = = T = = T = = G = = G = = = A = T = = = G C G = = T = T = = 0 D011 = T C = = = = = G = = A = A = = = G A G = = G = = = = = = = A T = = = = = T = = G = G = = = A G A = = A = = = = = = 0 D012 = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = 0 D013 C = = = = T = = = A = = = G G = = = = A = = = = = = = = = T = = = = C = = = G = = = A C = = = = G = = = = = = = = = 0 D014 C = = G = = = = = A = = = ? = C = = = A T C = = C ? ? = = T = = T = = = = = G = = = ? = T = = = G C G = = T ? ? = = 0 D015 C = = G = = A = = A C = = ? = C = = = = T C = = = = ? = = T = = T = = G = = G T = = ? = T = = = = C G = = = = ? = = 0 DY01 ? = = = = T = = = A C = = ? G = ? = = = = = = = T ? ? = = ? = = = = C = = = G T = = ? C = ? = = = = = = = C ? ? = = 0 DY02 = T C = = = G = = G = = = A = T = = = G C G = = T = T = = = A T = = = A = = A = = = G = C = = = A T C = = C = C = = 0 DY03 C T C = = T A = = A = = = = G = = = A = = = = = = = = = = T A T = = C G = = G = = = = C = = = G = = = = = = = = = = 0 DY04 = = = T = T = = = = = = = ? G T = = = = C G = = T = T = = = = = G = C = = = = = = = ? C C = = = = T C = = C = C = = 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = 0 DY06 = T C = = = = = G = = = = A = = = G A G = = G = = = = = = = A T = = = = = T = = = = G = = = A G A = = A = = = = = = 0 DY07 C T C G = = G = T G = = = ? = T = A G = C G = = T = T = = T A T T = = A = G A = = = ? = C = G A = T C = = C = C = = 0 DY08 = = = T = T (G) = = = = = = = G T (C) = = = C G = = T = T = = = = = G = C (A) = = = = = = = C C (A) = = = T C = = C = C = = 0 DY09 C = = = = T = = = A C = = ? = C = = = = T C = = = ? ? = = T = = = = C = = = G T = = ? = T = = = = C G = = = ? ? = = 0 DY10 C T C = = T A = G A = A = = G = = G A = = = G = = = = = = T A T = = C G = T G = G = = C = = A G = = = A = = = = = = 0 DY11 = = = = = = G = T G = = = = = T = A G = C G = = T = T = = = = = = = = A = G A = = = = = C = G A = T C = = C = C = = 0 DY12 = = = = = = = C = = = = G ? G = A = = = = = = C = = = = = = = = = = = = T = = = = A ? C = C = = = = = = T = = = = = 0 E101 = T C = = = = = G = = A = A = = = G A G = = G = = = = = = = A T = = = = = T = = G = G = = = A G A = = A = = = = = = 0 E102 C = = = = T A T = A = = A G = = C = = A = = = T = = = = = T = = = = C G C = G = = G A = = A = = G = = = C = = = = = 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E104 C = = = = T A T = A = = A ? = = C = = A = = = T = = = = = T = = = = C G C = G = = G ? = = A = = G = = = C = = = = = 0 E105 C = = = = T A T = A = = A G = = C = = A = = = T = = = = = T = = = = C G C = G = = G A = = A = = G = = = C = = = = = 0 E106 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 E107 C T C = = T A = G A = A = = G = = G A = = = G = = = = = = T A T = = C G = T G = G = = C = = A G = = = A = = = = = = 0 E108 C = = = = T A T = A = = A G = = C = = A = = = T = = = = = T = = = = C G C = G = = G A = = A = = G = = = C = = = = = 0 E109 C T C = = T A T G A = A A = = = C G A = = = G T = = = = = T A T = = C G C T G = G G = = = A A G = = = A C = = = = = 0 E110 C T C = = T A T G A = A A = = = C G A = = = G T = = = = = T A T = = C G C T G = G G = = = A A G = = = A C = = = = = 0 E111 C T C = = T A T G A = A A = = = C G A = = = G T = = = = = T A T = = C G C T G = G G = = = A A G = = = A C = = = = = 0 E112 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E115 = = = = C = = T = = = = A ? = = = = = = = = = T T T = C A = = = = T = = C = = = = G ? = = = = = = = = = C C C = T C 0 E116 C = = = = T = = = A = = = ? G = = = = A = = = = = = = = = T = = = = C = = = G = = = ? C = = = = G = = = = = = = = = 0 E117 C T C = ? T A T G A = A A = = = C G A = = = G T = = = = = T A T = ? C G C T G = G G = = = A A G = = = A C = = = = = 0 E118 C = = = = T A T = A = = A G = = C = = A = = = T = = = = = T = = = = C G C = G = = G A = = A = = G = = = C = = = = = 0 E119 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 E120 C T C = = T A T G A = A A = = = C G A = = = G T = = = = = T A T = = C G C T G = G G = = = A A G = = = A C = = = = = 0 E121 C = = = T T A = = A = = = ? = = C = = A = = = = C C = T C T = = = C C G = = G = = = ? = = A = = G = = = = T T = C A 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H102 ? = = = T ? A = = A = = = G = = C = = A = = = = C C = T C ? = = = C ? G = = G = = = A = = A = = G = = = = T T = C A 0 H103 C T C = = T A = G A = A = = G = = G A = = = G = = = = = = T A T = = C G = T G = G = = C = = A G = = = A = = = = = = 0 H104 = = = = C = = = = = = = = = G = A = = = = = = = T T = C A = = = = T = = = = = = = = = C = C = = = = = = = C C = T C 0 H105 C T C G = T = = G A = A = ? = = C G A = = = G = = = = = = T A T T = C = = T G = G = ? = = A A G = = = A = = = = = = 0 H106 ? = = = T T A = = A = = = G = = C = = A = = = = C ? ? T C ? = = = C C G = = G = = = A = = A = = G = = = = T ? ? C A 0 H107 = = = = C = = T = = = = A = = = = = = = = = = T T T = C A = = = = T = = C = = = = G = = = = = = = = = = C C C = T C 0 H108 = = = = C = = T = = = = A = = = = = = = = = = T T T = C A = = = = T = = C = = = = G = = = = = = = = = = C C C = T C 0 H109 = = = = = = = C = = = = G = G = A = = = = = = C = = = = = = = = = = = = T = = = = A = C = C = = = = = = T = = = = = 0 H110 ? T C = = = = = G = = A = A = = = G A G = = G = = = = = = ? A T = = = = = T = = G = G = = = A G A = = A = = = = = = 0 H111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H112 C = = = = T = T = A = = A G = = C = = A = = = T = = = = = T = = = = C = C = G = = G A = = A = = G = = = C = = = = = 0 H113 C = = = = T A T = A = = A G = = C = = A = = = T = = = = = T = = = = C G C = G = = G A = = A = = G = = = C = = = = = 0 H114 = = = = = = = C = = = = G = G = A = = = = = = C = = = = = = = = = = = = T = = = = A = C = C = = = = = = T = = = = = 0 H115 ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H116 C T C = = T = T = = = = A = = T C = = = C G = T T = T = = T A T = = C = C = = = = G = = C A = = = T C = C C = C = = 0 H117 C = = = = T A = = A C = = ? G = A = = = = = = = T = T = = T = = = = C G = = G T = = ? C = C = = = = = = = C = C = = 0 H118 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H119 C = = = = T A = = A = = = G G = = = = A = = = = = = = = = T = = = = C G = = G = = = A C = = = = G = = = = = = = = = 0 H120 ? = = = T T A = = A = = = G = = C = = A = = = = C C = T C ? = = = C C G = = G = = = A = = A = = G = = = = T T = C A 0 H121 C = = = = T A T = A C = A ? = = = = = = = = = T T = T = = T = = = = C G C = G T = G ? = = = = = = = = = C C = C = = 0 H122 = = = = = = (G) C = = = = G = G = A = = = = = = C = ? ? ? ? = = = = = = (A) T = = = = A = C = C = = = = = = T = ? ? ? ? 0 X101 ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 X102 C = = = = T A = = A = = = G G = = = = A = = = = = = = = = T = = = = C G = = G = = = A C = = = = G = = = = = = = = = 0 X103 C = = = T T A = = A = = = G = = C = = A = = = = C C = T C T = = = C C G = = G = = = A = = A = = G = = = = T T = C A 0 X104 ? = = = = T A = = A = = = G G = = = = A = = = = = = = = = ? = = = = C G = = G = = = A C = = = = G = = = = = = = = = 0 X105 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 X106 ? ? ? = = T A = = A = = = G G = = = = A = = = = = = = = = ? ? ? = = C G = = G = = = A C = = = = G = = = = = = = = = 0 X107 ? T C = = = (G) = G = = A = A = = = G A G = = G = = = = = = ? A T = = = (A) = T = = G = G = = = A G A = = A = = = = = = 0 X108 = = = = = = = = = = C = = ? = = A = = G = = = = T = T = = = = = = = = = = = = T = = ? = = C = = A = = = = C = C = = 0 X109 = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? = = 0 X110 = = = = C = = = = = = = = = G = A = = = = = = = T ? ? C A = = = = T = = = = = = = = = C = C = = = = = = = C ? ? T C 0 X111 C = = = = T A = = A = = = ? G = = = = A = = = = = = = = = T = = = = C G = = G = = = ? C = = = = G = = = = = = = = = 0 X112 = = = = = = = = = = C = = ? = = A = = = = = = = = = = = = = = = = = = = = = = T = = ? = = C = = = = = = = = = = = = 0 X113 C T C = T T = = G A = A = = = = C G A = = = G = C C = T C T A T = C C = = T G = G = = = = A A G = = = A = T T = C A 0 X114 ? = = = = T A = = A = = = G G = = = = A = = = = = = = = = ? = = = = C G = = G = = = A C = = = = G = = = = = = = = = 0 X115 = T C = = = G = G = T A = ? = = C G A = = = G = C = C = = = A T = = = A = T = C G = ? = = A A G = = = A = T = T = = 0 X116 C = = = = T A = = A C = = ? G = A = = = = = = = T = T = = T = = = = C G = = G T = = ? C = C = = = = = = = C = C = = 0 X117 = = = = C = = = = = = = = = G = = = = = = = = = T T = C A = = = = T = = = = = = = = = C = = = = = = = = = C C = T C 0 X118 = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = 0 X119 C T C = = T A = G A = A = = G = = = = = = = ? = = = = = = T A T = = C G = T G = G = = C = = = = = = = ? = = = = = = 0 X120 = = = = = = = = = = C = = ? = = A = = G = = = = T = T = = = = = = = = = = = = T = = ? = = C = = A = = = = C = C = = 0 X121 C = = = = T A = = A C = = ? G = A = = = = = = = T = T = = T = = = = C G = = G T = = ? C = C = = = = = = = C = C = = 0 X122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X123 C = = = = T A = = A = = = G G = = = = A = = ? ? ? = = = = T = = = = C G = = G = = = A C = = = = G = = ? ? ? = = = = 0 X124 C = = = = ? A = = A C = = ? G = ? = = ? = ? ? ? ? ? ? = = T = = = = ? G = = G T = = ? 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 = 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 = = 0.97 = 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 0.93 = = 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 = = = = = = 0.97 0.97 0.97 0.97 = = 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 = = = = = = = 1.00 1.00 0.61 = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 = = ? = 1.00 = = = = 1.00 1.00 = = = ? ? = = 1.00 1.00 1.00 = = 1.00 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 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 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 0.99 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 0.99 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 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 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 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 = = = = = = = = 0.74 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 = = = 0.81 = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = ? = = 1.00 = = 1.00 = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 = = = = = = = 1.00 ? ? 1.00 1.00 1.00 = = = = 1.00 1.00 = = 1.00 = = = ? 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = 1.00 = = ? = = 1.00 = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 = 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 0.97 = 1.00 1.00 = 1.00 = = 1.00 = = = = = = = ? = = = = = = = = = = = = = = = = 1.00 = = ? = = 1.00 = = 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = = 1.00 1.00 = = 1.00 1.00 = = ? 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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