************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 pct1a.phase.inp pct1a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST pct1a.phase.out_freqs : haplotype frequency estimates pct1a.phase.out_pairs : most likely haplotype pairs for each individual pct1a.phase.out_recom : estimates of recombination parameters pct1a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 47 Positions of loci: 146 426 722 1832 2125 2880 3574 3842 4735 4796 5768 6478 7103 18049 19795 19969 20014 20582 22506 30336 30542 30618 31246 33506 40918 41266 42021 42958 43487 44150 44187 44193 44377 44378 47016 47921 48707 48887 49944 50693 50884 51087 51515 51529 51530 51904 52292 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file pct1a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AGCCATGDCGAAACTGAGATATTAGAATGCAGTGCTTCTACAAATCG 1.000000 2 AGCCGTGDCGAAACTGAGATATTAGAATGCAGTGCTTCTACAAATCG 1.000000 3 AGCCGTGDCGAAACTGAGATATTAGAATGCAGTGCTTCTGCAAATCG 4.000000 4 AGCGGTGDCGAAACTGAGATACTAGAATGCAGTGCCTCTACAATCCG 5.000000 5 AGCGGTGDTGAAACTGAGACGCTAGAATGCAGTGCCTCTACAATCCG 1.000000 6 AGCGGTADCGGGACCGAGGCGCCAGTGTCTGACACTTCTACTATCCG 1.000000 7 AGCGGTADCGGGACCGAGGCGCCAGTGTCTGACACTGCTACTATCCG 1.000000 8 AGCGGTADCGGGACCGAGGCGCCAGTGTCTGACACTGCTATAATCCG 2.000000 9 AGTGGTADCGGGACCGAGGCGCCAGTGTCTGACACTGCTATAATCCG 1.000000 10 TGCCGTGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTGTCCG 2.000000 11 TGCCGTGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTGTCTG 1.000000 12 TGCCGTGDTGAAACCGAGACGCTAGAACGCAGTGCCTCTGCAATCCG 1.000000 13 TGCCGTGDTGAAACTGAGACGCTAGAATCCAGTGCCTCTACAATCCG 1.000000 14 TGCCGTGDTGAAACTGAGACGCTAGAATGCAGTGCCTCTACAATCCG 2.000000 15 TGCCGTADTGAAACTGAGACGCTAGAATGCAGTGCCTCTATAATCCG 1.000000 16 TGCGATADCGAAACCGAGGCGCCAGTGTCTGACACTGCTATAATCCG 2.000000 17 TGCGATADCGAAACCGAGGCGCTAGTGTCTGACACTGCTATAATCCG 1.000000 18 TGCGATADCGGAACCGAGGCGCCAGTGTCCAACACTGCTATAATCCG 1.000000 19 TGCGATADCGGAACCGAGGCGCCAGTGTCTAACACTGCTATAATCCG 3.000000 20 TGCGATADCGGAACCGAGGCGCCAGTGTCTAACACTGCCACTGTCTG 1.000000 21 TGCGATADCGGAACCGAGGCGCCAGTGTCTGACACTGCTACTGTCCG 1.000000 22 TGTGATGDCGAAACTGAGATACTAGAATGCAGTGCTTCTACAATCCG 1.000000 23 TGTGATGDCGAAACTGAGATACTAGAATGCAGTGCCTCTACAATCCG 1.000000 24 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACAAATCG 1.000000 25 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACAATCCG 5.000000 26 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACAGTCCG 1.000000 27 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTATCCG 3.000000 28 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTGTCCG 4.000000 29 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTGTCTG 8.000000 30 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTATAATCCG 1.000000 31 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCTGCAAATCG 1.000000 32 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTCCACTGTCTG 3.000000 33 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTTTACAATCCG 2.000000 34 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTTTACAATCCA 1.000000 35 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCTTTTACTATCCG 1.000000 36 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGCCTCTACAATCCG 1.000000 37 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGTTTTTACAATCCG 6.000000 38 TGTGATGDCGGAACCGGGGCGCCAGAACCCAGTGTTTTTGCAATCCG 1.000000 39 TGTGATGDCGGAACCGGGGCGCCAGAATCCAGTGCTTCCACTGTCTG 1.000000 40 TGTGATGICGGAACCGGGGCGCCAGAACCCAGTGCTTCTACTATCCG 1.000000 41 TGTGATADCGGAACCGGGGCGCCAGAATGCAGTGCTTCTACAATCCA 1.000000 42 TGTGGTGDCGGAACCGGGGCGCCAGAACGCAGTGCCTCTACAATCCG 1.000000 43 TTCCACGITAAATTTCAAACGCTGCAATGCAGTGCCTCTGCAATCCA 1.000000 44 TTCCGCGDCGGAACCGGGATACTAGAACGCAGTGCTTCTATTGTCTG 1.000000 45 TTCCGCGITAAAACTCAAACGCTGCAATGCAGTGCCTCTACTGTCTG 1.000000 46 TTCCGCGITAAAATTCAAACGCTGCAATGCAGTGCCTCTACAATCCG 1.000000 47 TTCCGCGITAAAATTCAAACGCTGCAATGCAGTGCCTCTACAATCCA 2.000000 48 TTCCGCGITAAATCTCAAACGCTGCAATGCAGTGCCTCTACAATCCA 5.000000 49 TTCCGCGITAAATTTCAAACGCTGCAATGCAGTGCCTCTACAATCCG 2.000000 50 TTCCGCAITAGATTTCAAACGCTGCAATGCAGTGCCTCTACAATCCG 1.000000 51 TTTCGCGITAAATCTCAAACGCTGCAATGCAGTGCCTCTACTGTCTG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,33) DY02: (28,35) DY03: (13,34) DY04: (27,28) DY05: (4,19) DY06: (19,36) DY07: (4,14) DY08: (23,42) DY09: (28,29) DY10: (4,26) DY11: (3,22) DY12: (31,33) DY13: (12,27) DY14: (9,27) DY15: (25,28) DY16: (25,29) DY17: (25,40) DY18: (5,7) DY19: (4,4) DY20: (8,25) DY21: (6,15) DY22: (8,14) DY23: (18,25) DY24: (24,29) E101: (46,49) E102: (3,32) E103: (19,47) E104: (20,29) E105: (3,37) E106: (10,44) E107: (37,48) E108: (29,30) E109: (29,29) E110: (29,51) E111: (16,48) E112: (21,37) E113: (3,39) E114: (32,37) E115: (32,50) E116: (43,48) E117: (2,37) E118: (38,49) E119: (16,37) E120: (17,47) E121: (11,41) E122: (10,45) E123: (48,48) 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 A T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T A C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T T T A C A A T C C G 0 DY02 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T (C) T A C T G T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T (T) T A C T A T C C G 0 DY03 T G C C G T G D T G A A A C T G A G A C G C T A G A A T C C A G T G C C T C T A C A A T C C (G) T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T T T A C A A T C C (A) 0 DY04 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T [C] T A C T A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C C G 0 DY05 A G C G G T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A A T C C G T G C G A T A D C G G A A C C G A G G C G C C A G T G T C T A A C A C T G C T A T A A T C C G 0 DY06 T G C G A T A D C G G A A C C G A G G C G C C A G T G T C T A A C A C T G C T A T A A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C C T C T A C A A T C C G 0 DY07 A G C G G T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A A T C C G T G C C G T G D T G A A A C T G A G A C G C T A G A A T G C A G T G C C T C T A C A A T C C G 0 DY08 T G T G A T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A A T C C G T G T G G T G D C G G A A C C G G G G C G C C A G A A C G C A G T G C C T C T A C A A T C C G 0 DY09 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G 0 DY10 A G C G G T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A (A) T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C A (G) T C C G 0 DY11 A G C C G T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T G C A A A T C G T G T G A T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C T T C T A C A A T C C G 0 DY12 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T (C) T (G) C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T (T) T (A) C A A T C C G 0 DY13 T G C C G T G D T G A A A C C G A G A C G C T A G A A C G C A G T G C C T C T (G) C (A) A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T [C] T (A) C (T) A T C C G 0 DY14 A G T G G T A D C G G G A C C G A G G C G C C A G T G T C T G A C A C T G C T A (T) (A) A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A (C) (T) A T C C G 0 DY15 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C (A) A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C (T) G T C C G 0 DY16 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T [C] T A C A A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G 0 DY17 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T [C] T A C A A T C C G T G T G A T G I C G G A A C C G G G G C G C C A G A A C C C A G T G C T T [C] T A C T A T C C G 0 DY18 A G C G G T G D T G A A A C T G A G A C G C T A G A A T G C A G T G C C T C T A C (A) A T C C G A G C G G T A D C G G G A C C G A G G C G C C A G T G T C T G A C A C T G C T A C (T) A T C C G 0 DY19 A G C G G T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A A T C C G A G C G G T G D C G A A A C T G A G A T A C T A G A A T G C A G T G C C T C T A C A A T C C G 0 DY20 A G C G G T A D C G G G A C C G A G G C G C C A G T G T C T G A C A C T [G] C T A (T) A A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A (C) A A T C C G 0 DY21 A G C G G T A D C G G G A C C G A G G C G C C A G T G T C T G A C A C T T C T A (C) (T) A T C C G T G C C G T A D T G A A A C T G A G A C G C T A G A A T G C A G T G C C T C T A (T) (A) A T C C G 0 DY22 A G C G G T A D C G G G A C C G A G G C G C C A G T G T C T G A C A C T G C T A (T) A A T C C G T G C C G T [G] D T G A A A C T G A G A C G C T A G A A T G C A G T G C C T C T A (C) A A T C C G 0 DY23 T G C G A T A D C G G A A C C G A G G C G C C A G T G T C C A A C A C T G C T A T A A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C A A T C C G 0 DY24 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G 0 E101 T T C C G C G I T A A A A T T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C G T T C C G C G I T A A A T T T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C G 0 E102 A G C C G T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T G C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A [C] C C A G T G C T T C C A C T G T C T G 0 E103 T G C G A T A D C G G A A C C G A G G C G C C A G T G T C T A A C A C T G C T A T A A T C C G T T C C G C G I T A A A A T T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C A 0 E104 T G C G A T A D C G G A A C C G A G G C G C C A G T G T C T [A] A C A C T G C (C) A C T G T C T G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C (T) A C T G T C T G 0 E105 A G C C G T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T G C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C A A T C C G 0 E106 T [G] C C G (T) G D C G G A A C C G G G G C G C C A G A A C (C) C A G T G C T T C T A (C) T G T C (C) G T [T] C C G (C) G D C G G A A C C G G G A T A C T A G A A C (G) C A G T G C T T C T A (T) T G T C (T) G 0 E107 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C A A T C C G T T C C G C G I T A A A T C T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C A 0 E108 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A T A A T C C G 0 E109 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G 0 E110 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G T T T C G C G I T A A A T C T C A A A C G C T G C A A T G C A G T G C C T C T A C T G T C T G 0 E111 T G C G A T A D C G A A A C C G A G G C G C C A G T G T C T G A C A C T G C T A T A A T C C G T T C C G C G I T A A A T C T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C A 0 E112 T G C G A T A D C G G A A C C G A G G C G C C A G T G T C T G A C A C T G C T A C (T) (G) T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C (A) (A) T C C G 0 E113 A G C C G T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T G C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A T C C A G T G C T T C C A C T G T C T G 0 E114 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C C A C T G T C T G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C A A T C C G 0 E115 T G T G A T (G) D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C C A C T G T C T G T T C C G C (A) I T A G A [T] [T] T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C G 0 E116 T T C C (A) C G I T A A A T (T) T C A A A C G C T G C A A T G C A G T G C C T C T (G) C A A T C C A T T C C (G) C G I T A A A T (C) T C A A A C G C T G C A A T G C A G T G C C T C T (A) C A A T C C A 0 E117 A G C C G T G D C G A A A C T G A G A T A T T A G A A T G C A G T G C T T C T A C A A A T C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C A A T C C G 0 E118 T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T G C A A T C C G T T C C G C G I T A A A T T T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C G 0 E119 T G C G A T A D C G A A A C C G A G G C G C C A G T G T C T G A C A C T G C T A T A A T C C G T G T G A T G D C G G A A C C G G G G C G C C A G A A C C C A G T G T T T T T A C A A T C C G 0 E120 T G C G A T A D C G A A A C C G A G G C G C T A G T G T C T G A C A C T G C T A T A A T C C G T T C C G C G I T A A A A T T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C A 0 E121 T G (C) (C) (G) T (G) D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C T G T G (T) (G) (A) T (A) D C G G A A C C G G G G C G C C A G A A T G C A G T G C T T C T A C A A T C C A 0 E122 T G C C G T G D C G G A A C C G G G G C G C C A G A A C C C A G T G C T T C T A C T G T C (C) G T T C C G C G I T A A A A C T C A A A C G C T G C A A T G C A G T G C C T C T A C T G T C (T) G 0 E123 T T C C G C G I T A A A T C T C A A A C G C T G C A A T G C A G T G C C T C T A C A A T C C A T T C C G C G I T A A A T C T C A A A C G C T G C A A T G C A G T G C C T C T A C A A 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 DY01 A = C C = = = = = = A = = = T = A = A T A T T = = = = T G = = = = = = ? = C = = = = = A T = = T = T G = = = = = = G = = = C = G = G C G C C = = = = C C = = = = = = ? = T = = = = = T C = = 0 DY02 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = (C) ? = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = (T) ? = = = A = = = = 0 DY03 = = C C G = = = T = A = = = T = A = A = = ? T = = = = T = = = = = = = C = C ? = = = = = = = (G) = = T G A = = = C = G = = = C = G = G = = ? C = = = = C = = = = = = = T = T ? = = = = = = = (A) 0 DY04 = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = ? ? ? = = = = A = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = ? ? ? = = = = G = = = = 0 DY05 A = = = G = G = = = A = = = T = = = A T A = T = = A A = G C ? ? T G = C T = = = C = = = = = = T = = = A = A = = = G = = = C = = = G C G = C = = T G = C T ? ? C A = T G = = = T = = = = = = 0 DY06 = = C = = = A = = = = = = = = = A = = = ? ? = = = T G T = T = ? C A = T G = = = T = = = = = = = = T = = = G = = = = = = = = = G = = = ? ? = = = A A C = C = ? T G = C T = = = C = = = = = = 0 DY07 A = = G = = = = C = = = = = = = = = = T A = = = = = = = = = = = = = = = = = ? = = = = = = = = T = = C = = = = T = = = = = = = = = = C G = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 DY08 ? = = = A = = = = = A = = ? T = A ? A ? ? ? ? = = = = T = = = = = = = = ? ? = = = = = = = = = ? = = = G = = = = = G = = ? C = G ? G ? ? ? ? = = = = C = = = = = = = = ? ? = = = = = = = = = 0 DY09 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = 0 DY10 A = C = G = = = = = A = = = T = A = A T A = T = = = = T G = = = = = = C = = = = = = (A) = = = = T = T = A = = = = = G = = = C = G = G C G = C = = = = C C = = = = = = T = = = = = = (G) = = = = 0 DY11 A = C C G = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = ? ? = G = = = A T = ? T = T G A = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = ? ? = A = = = T C = ? 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = (C) = (G) = = = A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = (T) = (A) = = = T C = = 0 DY13 = = C C G = = = T = ? ? = = = = A = A = = = T = = = = = G = = = = = = ? ? ? = (G) = (A) = = = = = = = T G A = = = C = ? ? = = = = G = G = = = C = = = = = C = = = = = = ? ? ? = (A) = (T) = = = = = 0 DY14 A = = = G = A = = = = G = = = = A = = = = = = = = T G T = T G A C A = = G = = = (T) (A) = = = = = T = = = A = G = = = = A = = = = G = = = = = = = = A A C = C A G T G = = T = = = (C) (T) = = = = = 0 DY15 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) G = = = = 0 DY16 ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = A A = = C = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = T G = = T = 0 DY17 = = = = = = ? D = = = = = ? = = = = = = = = ? = = = = = ? = = = = = = = ? ? = = = A = = = = = = = = = = = ? I = = = = = ? = = = = = = = = ? = = = = = ? = = = = = = = ? ? = = = T = = = = = 0 DY18 = = = = = = G = T = A A = = T = = = A = = = T = = A A = G C A G T G = ? T = = = = (A) = = = = = = = = = = = A = C = G G = = C = = = G = = = C = = T G = C T G A C A = ? G = = = = (T) = = = = = 0 DY19 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY20 A = C = G = A = = = ? G = = = = A = = = = = = = = T G T = T G A C A = ? ? ? = = (T) = = = = = = T = T = A = G = = = ? A = = = = G = = = = = = = = A A C = C A G T G = ? ? ? = = (C) = = = = = = 0 DY21 A = = G = = = = C = ? G = = ? = = = G = = = C = = T G = C T G A C A = ? = = = = (C) (T) = = = = = T = = C = = = = T = ? A = = ? = = = A = = = T = = A A = G C A G T G = ? = = = = (T) (A) = = = = = 0 DY22 A = = G = = ? = C = ? G = = C = = = G = = = C = = T G = C T G A C A = T G = = = (T) = = = = = = T = = C = = ? = T = ? A = = T = = = A = = = T = = A A = G C A G T G = C T = = = (C) = = = = = = 0 DY23 ? = C = = = A = = = = = = = = = A = = = = = = = = T G T = = ? ? C A = = G = = = T = = = = = = ? = T = = = G = = = = = = = = = G = = = = = = = = A A C = = ? ? T G = = T = = = C = = = = = = 0 DY24 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = A A A T C ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = T G T C T ? 0 E101 = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 A = C C G = = = = = ? = = = T = A ? A T A T ? = = = = ? G = ? ? = = = = = = T G = A A A T C = T = T G A = = = = = ? = = = C = G ? G C G C ? = = = = ? C = ? ? = = = = = = C A = T G T C T = 0 E103 = G = G A T ? D C G G = = C C G = G G = = = C A G T G = C T = A C A = T G = = = T = = = = = G = T = C G C ? I T A A = = T T C = A A = = = T G C A A = G C = G T G = C T = = = C = = = = = A 0 E104 = = C = = = A = = = = = = = = = A = = = = = = = = T G T = T ? ? C A = ? G = (C) = = = = = = = = = = T = = = G = = = = = = = = = G = = = = = = = = A A C = C ? ? T G = ? T = (T) = = = = = = = = 0 E105 A = C C G = = = = = A = = = T = A = A T A T T = = = = T G = = = = = C ? = C = G = = = A T = = T = T G A = = = = = G = = = C = G = G C G C C = = = = C C = = = = = T ? = T = A = = = T C = = 0 E106 ? ? ? = = (T) ? = = = ? = = = = = = = G C G = C = = = = = (C) = ? ? = = = = = = = = (C) = = = = (C) = ? ? ? = = (C) ? = = = ? = = = = = = = A T A = T = = = = = (G) = ? ? = = = = = = = = (T) = = = = (T) = 0 E107 = G T G A T = D C G G = A = C G G G G = = = C A G = = C C = = = = = T T = T = = = = = = = = G = T C C G C = I T A A = T = T C A A A = = = T G C = = T G = = = = = C C = C = = = = = = = = A 0 E108 = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = C T G = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = T A A = = C = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 E110 = G = G A T = D C G G = A = C G G G G = = = ? A G = = C ? = = = = = = T = = = = = = = = = = = = T = C G C = I T A A = T = T C A A A = = = ? G C = = T ? = = = = = = C = = = = = = = = = = = 0 E111 = G = G A T A D C G = = A = C G = G G = = = C A G T G = C T G A C A = T G = = = T = = = = = G = T = C G C G I T A = = T = T C = A A = = = T G C A A = G C A G T G = C T = = = C = = = = = A 0 E112 = = C = = = A = = = = = = = = = A = = = = = = = = T G T = T G A C A C = G C = = = (T) (G) = = = = = = T = = = G = = = = = = = = = G = = = = = = = = A A C = C A G T G T = T T = = = (A) (A) = = = = 0 E113 A = C C G = = = = = ? = = = T = A = A T A T T = = = = = G = = = = = = = = ? T G = A A A T C = T = T G A = = = = = ? = = = C = G = G C G C C = = = = = C = = = = = = = = ? C A = T G T C T = 0 E114 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = ? ? = = C = = C C = = T G = = T = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = ? = ? ? = = T = = T T = = A A = = C = 0 E115 = G T G A T (G) D C G = = ? ? C G G G G = = = C A G = = C C = = = = = = T = = C = = T G = = T = = T C C G C (A) I T A = = ? ? T C A A A = = = T G C = = T G = = = = = = C = = T = = A A = = C = 0 E116 = = = = (A) = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = (G) = = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = 0 E117 A = C C G = = = = = ? = = = T = A = A T A T T = = = = T G = = = = = C = = C = = = = = A T = = T = T G A = = = = = ? = = = C = G = G C G C C = = = = C C = = = = = T = = T = = = = = T C = = 0 E118 = G T G A T = D C G ? ? A C C G G G G = = = C A G = = C C = = = = = T T ? ? ? G = = = = = = = = T C C G C = I T A ? ? T T T C A A A = = = T G C = = T G = = = = = C C ? ? ? A = = = = = = = 0 E119 = = C = = = A = = = ? = ? = = = A = = ? = = = = = T G T = T G A C A C = G C = = T = = = = = ? = = T = = = G = = = ? = ? = = = G = = ? = = = = = A A C = C A G T G T = T T = = C = = = = = ? 0 E120 = G = G A T A D C G ? = ? C ? G = G G = = = = A G T G = C T G A C A = ? ? ? = = T = = = = = G = T = C G C G I T A ? = ? T ? C = A A = = = = G C A A = G C A G T G = ? ? ? = = C = = = = = A 0 E121 = = (C) (C) (G) = (G) = = = = = = = ? = = = = = = = = = = = = C C = = = ? ? = = ? ? = = = T G = = T G = = (T) (G) (A) = (A) = = = = = = = ? = = = = = = = = = = = = T G = = = ? ? = = ? ? = = = A A = = C A 0 E122 = G = = = T = D C G G = = = C G G G G = = = C A G = = C C = = = = = = T = = = = = = = = = (C) = = T = = = C = I T A A = = = T C A A A = = = T G C = = T G = = = = = = C = = = = = = = = = (T) = 0 E123 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = 0.94 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = 0.68 ? = = = 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 ? = = = = = = = 0.59 = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = ? ? ? = = = = 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 = = = = = = 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 = = = = = = 0.69 = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = ? ? = 0.96 = = = 0.96 0.96 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0.63 = 0.90 = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 = ? ? = = = = 1.00 = 1.00 = = = 1.00 = = = = = 1.00 = = = = = = ? ? ? = 0.88 = 0.88 = = = = = 1.00 = = = 1.00 = 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 0.59 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.85 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 = = = = 0.68 = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = = ? 1.00 = = = = 1.00 = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = ? ? ? = = 0.66 = = = = = = 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 = ? = = = = 0.61 0.61 = = = = = 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 = = = 0.61 = = = = = = ? = 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 = 0.53 = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 = = = = = 1.00 ? = 1.00 = 0.94 = = = 1.00 1.00 = = ? ? ? = = 0.59 ? = = = ? = = = = = = = 0.97 0.97 0.97 = 0.97 = = = = = 0.89 = ? ? = = = = = = = = 0.72 = = = = 0.57 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 0.95 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 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 = = = = = 1.00 = = 1.00 = = = 1.00 = = = = = = = = = 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 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 0.57 1.00 1.00 1.00 = = ? ? 1.00 1.00 1.00 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 = = = = = = = = 0.73 = = = = = = = = = = = = = = = = = = = = = = = = = 0.83 = = = = = = = 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 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 ? ? ? 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 = = 0.57 0.57 0.57 = 0.63 = = = = = = = ? = = = = = = = = = = = = 0.93 0.93 = = = ? ? = = ? ? = = = 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 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = = = = = = = = = 0.55 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS