************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 abca3.phase.inp abca3.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST abca3.phase.out_freqs : haplotype frequency estimates abca3.phase.out_pairs : most likely haplotype pairs for each individual abca3.phase.out_recom : estimates of recombination parameters abca3.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 51 Positions of loci: 2420 9839 10213 10991 11251 12171 12399 12466 12606 12618 12766 12930 13519 13555 13714 13849 14076 14082 14357 15102 15539 16167 16777 17136 17277 23185 23554 23639 23727 32303 32750 40537 41303 41692 41862 42535 42855 42871 45675 48297 51350 53071 54670 56510 56901 59634 62274 65893 66022 66761 66773 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file abca3.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AGTGCCCGCTGDTGGGACGAACGATAACCTGGCADCCIAAACATGTCTTCT 5.000000 2 AGTGCCCGCTGDTGGGACGAACGATAACCTAACGDGGIAAGCATGCCGCCC 7.000000 3 AGTGCCCGCTGDTGGGACGAACGATACCCCGGCAICGIAAATAAGCTGTTC 1.000000 4 AGTGCCCGCTGDTGGGACGAACGATACCCCGGAGDCCDGGACGATCTGTCC 1.000000 5 AGTGCCCGCTGDTGGGACGAACGATACCCCGGAGDCCDGGATAAGCCGTTC 1.000000 6 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCAICCIAAACATGTCGTTC 1.000000 7 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCAICGIAAATAAGCCGTTC 2.000000 8 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCAICGIAAATAAGCTGTTC 19.000000 9 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCADCCIAAACATGTCGTCC 1.000000 10 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCADCGIAAATAAGCTGTTC 2.000000 11 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCGICGIAAACATGTTTTCC 1.000000 12 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCGDCCDGGACGATCTGTCC 2.000000 13 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGCGDCCDGGATAAGCTGTTC 1.000000 14 AGTGCCCGCTGDTGGGACGAACGATGCCCCGGAGDCCDGGACGATCTGTCC 10.000000 15 AGTGCCCGCTGDTGGGACGAACGATGCCCCGACGDGGIAAGCATGCTGTTC 2.000000 16 AGTGCCCGCTGDTGGGACGAACGATGCCCTGGCADCCIAAACATGTCTTCT 1.000000 17 AGTGCCCGCTGDTGGGACGAACGATGCCCTGGCADCGIAAACATGTCGTTC 1.000000 18 AGTGCCCGCTGDTGGGACGAACGATGCCCTGACGICGIAAACATGCTTTCC 1.000000 19 AGTGCCCGCTGDTGGGACGAACGATGCCCTAACGDGGIAAGCATGCCGCCC 3.000000 20 AGTGCCCGCTGDTGGGACGAACGATGCTTTGGCAICGIAAATAAGCTGTTC 1.000000 21 AGTGCCCGCTGDTGGGACGAACGATGCTTTGGAGDCCDGGACGATCTGTCC 3.000000 22 AGTGCCCGCTGDTGGGACGACCGATGCCCCGGAGDCCDGGACGATCTGTCC 1.000000 23 AGTGCCCGCTGDTGGGACAAACGATGCCCCGGAGDCCDGGACGATCTGTCC 1.000000 24 AGTGCCCACAGICAAGGTAGCCGAGGCCCCGGCAICCIAAACATGTCGTTC 1.000000 25 AGCGCCCGGAGDTGGGATGGACGAGGCCCCGGCAICGIAAATAAGCTGTTC 3.000000 26 AGCGCCCGGAGDTGGGATGGACGAGGCCCTGACGICGIAAACATGCTTTCC 1.000000 27 AGCGCTCGCTADTGGGATGGACGTGGCCCCGGCAICGIAAACATGTCTTCT 2.000000 28 AGCGTCCGGAGDTGGGATGGACGAGGCCCCGGCAICGIAAATAAGCTGTTC 1.000000 29 AACGCCCGCTGDTGGGATGGACGAGGCCCCGGCAICGIAAATAAGCTGTTC 1.000000 30 AACGCCCGCTGDTGGGATGGACGAGGCCCCGACGICGIAAACATGCTTTCC 1.000000 31 AACGCCCGCTGDTGGGATGGACGTGAACCTGGCADCCIAAACATGTCTTCT 2.000000 32 AACGCTCGCTADTGGGATGGACGTGGCCCCGGCAICGIAAATAAGCTGTTC 2.000000 33 AACGCTCGCTADTGGGATGGACGTGGCTTTGGCAICGIAAATAAGCTGTTC 1.000000 34 CACACCCACAGICAAAGTAGCGAAGGCCCCGGCAICGIAAATAAGCTGTTC 1.000000 35 CACATCGACAGDCAAAGTAGCGAAGGCCCCGGCAICCIAAACATGTCGTTC 1.000000 36 CACATCGACAGDCAAAGTAGCGAAGGCTTCGACGDGGIAAGCATGCTGTCC 1.000000 37 CACATCGACAGICAAAGTAGCGAAGAACCCGGCAICCIAAACATGTCGTTC 1.000000 38 CACATCGACAGICAAAGTAGCGAAGAACCTGACGICGIAAACATGCTTTCC 2.000000 39 CACATCGACAGICAAAGTAGCGAAGGCCCCGGCAICCIAAACATGTCGTTC 2.000000 40 CACATCGACAGICAAAGTAGCGAAGGCCCCGGCAICGIAAATAAGCTGTTC 1.000000 41 CACATCGACAGICAAAGTAGCGAAGGCCCTGGCADCCIAAACATGTCTTCT 1.000000 42 CACATCGACAGICAAAGTAGCGAAGGCTCTGGCADCGIAAACATGTCGTTC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,8) DY02: (7,7) DY03: (17,24) DY04: (6,25) DY05: (31,42) DY06: (33,31) DY07: (3,27) DY08: (8,28) DY09: (34,40) DY10: (1,35) DY11: (8,30) DY12: (32,38) DY13: (15,29) DY14: (1,13) DY15: (1,27) DY16: (16,36) DY17: (15,25) DY18: (18,39) DY19: (8,39) DY20: (38,41) DY21: (11,25) DY22: (20,37) DY23: (1,32) DY24: (5,26) E101: (10,12) E102: (12,14) E103: (2,9) E104: (8,14) E105: (8,14) E106: (4,14) E107: (8,14) E108: (2,2) E109: (21,22) E110: (2,2) E111: (14,14) E112: (8,14) E113: (2,21) E114: (8,14) E115: (8,8) E116: (8,21) E117: (8,19) E118: (8,10) E119: (14,19) E120: (2,23) E121: (8,8) E122: (8,8) E123: (8,19) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T G G C A D C C I A A A C A T G T C T T C T A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY02 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C C G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C C G T T C 0 DY03 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C (T) G G C A (D) C (G) I A A A C A T G T C G T T C A G T G C C C A C A G [I] C A A G G T A G C C G A G G C C C (C) G G C A (I) C (C) I A A A C A T G T C G T T C 0 DY04 A G (T) G C C C G (C) (T) G D T G G G A (C) G (A) A C G A (T) G C C C C G G C A I C C I A A A C A T G T C G T T C A G (C) G C C C G (G) (A) G D T G G G A (T) G (G) A C G A (G) G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY05 A A C G C C C G C T G D T G G G A T G G A C G T G A A (C) C T G G C A D C C I A A A C A T G T C T T C T C A C A T C G A C A G [I] C A A A G T A G C G A A G G C (T) C T G G C A D C G I A A A C A T G T C G T T C 0 DY06 A [A] C G C (T) C G C T (A) D T G G G A T G G A C G T G G C T T T G G C A I C G I A A A T A A G C T G T T C A [A] C G C (C) C G C T (G) D T G G G A T G G A C G T G A A C C T G G C A D C C I A A A C A T G T C T T C T 0 DY07 A G T G C C C G C T G D T G G G A C G A A C G A T (A) C C C C G G C A I C G I A A A T A A G C [T] G T T C A G [C] G C T C G C T A D T G G G A T G G A C G T G (G) C C C C G G C A I C G I A A A C A T G T C T T C T 0 DY08 A G T G (C) C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G C G (T) C C G G A G D T G G G A T G G A C G A G G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY09 C A C A C C C A C A G I C A A A G T A G C G A A G G C C C C G G C A I C G I A A A T A A G C T G T T C C A C A T C G A C A G I C A A A G T A G C G A A G G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY10 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T G G C A D C C I A A A C A T G T C T T C T C A C A T C G A C A G D C A A A G T A G C G A A G G C C C C G G C A I C C I A A A C A T G T C G T T C 0 DY11 A (G) (T) G C C C G C T G D T G G G A (C) G (A) A C G A (T) G C C C C G G C A I C G I A A A T A A G C T G T T C A (A) (C) G C C C G C T G D T G G G A (T) G (G) A C G A (G) G C C C C G A C G I C G I A A A C A T G C T T T C C 0 DY12 A A C G C T C G C T A D T G G G A T G G A C G T G G C C C C G G C A I C G I A A A T A A G C T G T T C C A C A T C G A C A G I C A A A G T A G C G A A G A A C C T G A C G I C G I A A A C A T G C T T T C C 0 DY13 A (G) (T) G C C C G C T G D T G G G A (C) G (A) A C G A (T) G C C C C G A C G D G G I A A G C A T G C T G T T C A (A) (C) G C C C G C T G D T G G G A (T) G (G) A C G A (G) G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY14 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T G G C A D C C I A A A C A T G T C T T C T A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C G D C C D G G A T A A G C T G T T C 0 DY15 A G T G C C C G C T G D T G G G A C G A A C G A T (A) (A) C C (T) G G C A (D) C (C) I A A A C A T G T C T T C T A G C G C T C G C T A D T G G G A T G G A C G T G (G) (C) C C (C) G G C A (I) C (G) I A A A C A T G T C T T C T 0 DY16 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C T G G C A D C C I A A A C A T G T C T T C T C A C A T C G A C A G D C A A A G T A G C G A A G G C T T C G A C G D G G I A A G C A T G C T G T C C 0 DY17 A G (T) G C C C G (C) (T) G D T G G G A (C) G (A) A C G A (T) G C C C C G A C G D G G I A A G C A T G C T G T [T] C A G (C) G C C C G (G) (A) G D T G G G A (T) G (G) A C G A (G) G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY18 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C (T) G (A) C (G) I C (G) I A A A C A T G (C) (T) [T] T (C) C C A C A T C G A C A G I C A A A G T A G C G A A G G C C C (C) G (G) C (A) I C (C) I A A A C A T G (T) (C) [G] T (T) C 0 DY19 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C (G) I A A A (T) A (A) G (C) (T) G T T C C A C A T C G A C A G I C A A A G T A G C G A A G G C C C C G G C A I C (C) I A A A (C) A (T) G (T) (C) G T T C 0 DY20 C A C A T C G A C A G I C A A A G T A G C G A A G A A C C T G A C G I C G I A A A C A T G C T T T C C C A C A T C G A C A G I C A A A G T A G C G A A G G C C C T G G C A D C C I A A A C A T G T C T T C T 0 DY21 A G (T) G C C C G (C) (T) G D T G G G A (C) G (A) A C G A (T) G C C C C G G C (G) I C G I A A A (C) A (T) G (T) [T] (T) T (C) C A G (C) G C C C G (G) (A) G D T G G G A (T) G (G) A C G A (G) G C C C C G G C (A) I C G I A A A (T) A (A) G (C) T (G) T (T) C 0 DY22 A G T G C C C G C T G D T G G G A C G A A C G A T (G) (C) (T) (T) (T) G G C A I C (G) I A A A (T) A (A) G (C) (T) G T T C C A C A T C G A C A G I C A A A G T A G C G A A G (A) (A) (C) (C) (C) G G C A I C (C) I A A A (C) A (T) G (T) (C) G T T C 0 DY23 A (G) (T) G C (C) C G C T (G) D T G G G A (C) G (A) A C G (A) (T) A A C C T G G C A D C C I A A A C A T G T C T T C T A (A) (C) G C (T) C G C T (A) D T G G G A (T) G (G) A C G (T) (G) G C C C C G G C A I C G I A A A T A A G C T G T T C 0 DY24 A G (T) G C C C G (C) (T) G D T G G G A (C) G (A) A C G A (T) A C C C C G G A G D C C D G G A [T] A A G C C G T T C A G (C) G C C C G (G) (A) G D T G G G A (T) G (G) A C G A (G) G C C C T G A C G I C G I A A A C A T G C T T T C C 0 E101 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A D C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C G D C C D G G A C G A T C T G T C C 0 E102 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C G D C C D G G A C G A T C T G T C C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E103 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A D C C I A A A C A T G T [C] G T C C 0 E104 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E105 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C [T] G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E106 A G T G C C C G C T G D T G G G A C G A A C G A T A C C C C G G A G D C C D G G A C G A T C T G T C C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E107 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E108 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C 0 E109 A G T G C C C G C T G D T G G G A C G A (A) C G A T G C T T T G G A G D C C D G G A C G A T C T G T C C A G T G C C C G C T G D T G G G A C G A (C) C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E110 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C 0 E111 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E112 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E113 A G T G C C C G C T G D T G G G A C G A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C A G T G C C C G C T G D T G G G A C G A A C G A T G C T T T G G A G D C C D G G A C G A T C T G T C C 0 E114 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E115 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C [T] G T T C 0 E116 A G T G C C C G C T G D T G G G A C G A A C G A T G C (C) (C) (C) G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C (T) (T) (T) G G A G D C C D G G A C G A T C T G T C C 0 E117 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C T A A C G D G G I A A G C A T G C C G C C C 0 E118 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A D C G I A A A T A A G C T G T T C 0 E119 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C T A A C G D G G I A A G C A T G C C G C C C 0 E120 A G T G C C C G C T G D T G G G A C (G) A A C G A T A A C C T A A C G D G G I A A G C A T G C C G C C C A G T G C C C G C T G D T G G G A C (A) A A C G A T G C C C C G G A G D C C D G G A C G A T C T G T C C 0 E121 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C 0 E122 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C 0 E123 A G T G C C C G C T G D T G G G A C G A A C G A T G C C C C G G C A I C G I A A A T A A G C T G T T C A G T G C C C G C T G D T G G G A C G A A C G A T G C C C T A A C G D G G I A A G C A T G C C G C C C END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 DY01 = ? = = ? = = = = = = = = = = = = = = = = = = = = A A = = T = = = = D = C = = ? = C ? T = T C T = C T = ? = = ? = = = = = = = = = = = = = = = = = = = = G C = = C = = = = I = G = = ? = T ? A = C T G = T C 0 DY02 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY03 = = = = = = = G ? ? ? ? T G G = A C G A A = = = T = = = = (T) = = = = (D) = (G) = = = = = = = = = ? = = = = = = = = = = = A ? ? ? ? C A A = G T A G C = = = G = = = = (C) = = = = (I) = (C) = = = = = = = = = ? = = = = 0 DY04 = ? (T) = = = = = (C) (T) = = = = = = = (C) = (A) = = = = (T) = = = = = = = = = = = C = = = = C = T = T ? = = = ? = ? (C) = = = = = (G) (A) = = = = = = = (T) = (G) = = = = (G) = = = = = = = = = = = G = = = = T = A = C ? = = = ? 0 DY05 A = = G C = C G ? ? ? ? T G G G A = G = A C G T = A A (C) = = = = = = = = C = = = = = = = = = = T = C T C = = A T = G A ? ? ? ? C A A A G = A = C G A A = G C (T) = = = = = = = = G = = = = = = = = = = G = T C 0 DY06 = ? = = = (T) = = = = (A) = = = = = = = = = = = = = = G C T T = = = = = I = G = = = = T = A = C T G = T C = ? = = = (C) = = = = (G) = = = = = = = = = = = = = = A A C C = = = = = D = C = = = = C = T = T C T = C T 0 DY07 = = ? = = C = = = = G = = = = = = C = A ? = = A T (A) = = = = = = = = = = = = = = = T = A = C ? G = T C = = ? = = T = = = = A = = = = = = T = G ? = = T G (G) = = = = = = = = = = = = = = = C = T = T ? T = C T 0 DY08 = = T = (C) = = = C T = = ? ? ? ? = C = A = = = = T = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = C = (T) = = = G A = = ? ? ? ? = T = G = = = = G = = = = = = = = = = = = = = = = = = = = = = = = ? ? 0 DY09 = = = = C = C = ? ? = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? ? = = = = = = T = G = ? ? = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? ? = = 0 DY10 A G T G C = C G ? ? ? = T G G G A C G A A C ? = T A A = = T = ? = = D = = = = = = = = = = = = T = C T C A C A T = G A ? ? ? = C A A A G T A G C G ? = G G C = = C = ? = = I = = = = = = = = = = = = G = T C 0 DY11 = (G) (T) = = = = = = = = = = = = = = (C) = (A) = = = = (T) = = = = = = G = A = = = = = = = T = A = = = ? ? T = = (A) (C) = = = = = = = = = = = = = = (T) = (G) = = = = (G) = = = = = = A = G = = = = = = = C = T = = = ? ? C = 0 DY12 A = = G C T C G ? ? A D ? ? ? ? A = G = ? C G T = G C = = C = G = A = = = = = = = T = A = = = ? ? T = C = = A T C G A ? ? G I ? ? ? ? G = A = ? G A A = A A = = T = A = G = = = = = = = C = T = = = ? ? C = 0 DY13 = (G) (T) = = = = = = = = = = = = = = (C) = (A) = = ? = (T) = = = = = ? A = G D G = = = = G C = ? = = = = = = = = (A) (C) = = = = = = = = = = = = = = (T) = (G) = = ? = (G) = = = = = ? G = A I C = = = = A T = ? = = = = = = = 0 DY14 = = = = = = = = = = = = = = = = = = = = = = ? ? ? A A = ? T ? = = A = = = I A A = C = T = T C T = C T = = = = = = = = = = = = = = = = = = = = = = ? ? ? G C = ? C ? = = G = = = D G G = T = A = C T G = T C 0 DY15 = = T = = C = = = = G = = = = = = C = A ? = = A T (A) (A) = = (T) = = = = (D) = (C) = = = = = = = = = = ? ? = = = = C = = T = = = = A = = = = = = T = G ? = = T G (G) (C) = = (C) = = = = (I) = (G) = = = = = = = = = = ? ? = = 0 DY16 A G T G C = C G ? ? ? = T G G G A C G A A C G = T = = C C T = G = A = C C = = = A = = ? = T C ? ? = ? C A C A T = G A ? ? ? = C A A A G T A G C G A = G = = T T C = A = G = G G = = = G = = ? = C T ? ? = ? 0 DY17 = = (T) = = = = = (C) (T) = = = = = = = (C) = (A) = = ? = (T) = = = = = = A = G D G = = = = G C = T = = = = = ? ? = = (C) = = = = = (G) (A) = = = = = = = (T) = (G) = = ? = (G) = = = = = = G = A I C = = = = A T = A = = = = = ? ? 0 DY18 A G T G C = C G ? ? ? D T G G G A C G A A C G = T = = = = (T) = (A) = (G) = = (G) = = = = = = = = (C) (T) ? ? (C) = C A C A T = G A ? ? ? I C A A A G T A G C G A = G = = = = (C) = (G) = (A) = = (C) = = = = = = = = (T) (C) ? ? (T) = 0 DY19 A G T G C = C G ? ? ? D T G G G A C G A A C G = T = = = = = = = = = = = (G) = = = = (T) = (A) = (C) (T) = = = = C A C A T = G A ? ? ? I C A A A G T A G C G A = G = = = = = = = = = = = (C) = = = = (C) = (T) = (T) (C) = = = = 0 DY20 = = = = = = = = ? ? = = = = = = = = = = = = = = = A A = = = = A = G I = G = = = = = = = = ? T = = = C = = = = = = = = ? ? = = = = = = = = = = = = = = = G C = = = = G = A D = C = = = = = = = = ? C = = = T 0 DY21 ? = (T) = = = = = (C) (T) = = = = = = = (C) = (A) ? = = = (T) = = = = = = = = (G) = = = = = = = (C) = (T) = (T) ? (T) = (C) = ? = (C) = = = = = (G) (A) = = = = = = = (T) = (G) ? = = = (G) = = = = = = = = (A) = = = = = = = (T) = (A) = (C) ? (G) = (T) = 0 DY22 A G T G C = C G ? ? ? D T G G G A C G A A C G = T (G) (C) (T) (T) (T) ? = = = = = (G) = = = = (T) = (A) = (C) (T) = = = = C A C A T = G A ? ? ? I C A A A G T A G C G A = G (A) (A) (C) (C) (C) ? = = = = = (C) = = = = (C) = (T) = (T) (C) = = = = 0 DY23 = (G) (T) = = (C) = = = = (G) = ? ? ? ? = (C) = (A) ? = = (A) (T) A A = = T = = = = D = C = = = = C = T = T ? T = C T = (A) (C) = = (T) = = = = (A) = ? ? ? ? = (T) = (G) ? = = (T) (G) G C = = C = = = = I = G = = = = T = A = C ? G = T C 0 DY24 ? = (T) = = = = = (C) (T) = = = = = = = (C) = (A) = = = = (T) A = = = C = G A = D = C D G G = ? = A = = C ? ? T = ? = (C) = = = = = (G) (A) = = = = = = = (T) = (G) = = = = (G) G = = = T = A C = I = G I A A = ? = T = = T ? ? C = 0 E101 ? = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = A = = G I A A = T A = G = = ? ? T = ? = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = G = = C D G G = C G = T = = ? ? C = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = ? ? = = 0 E103 = ? = = = = = = = = = = = = = = = = = = = = = = = A A = = T A A = G = G G = = = G = = = = C ? = C = = = ? = = = = = = = = = = = = = = = = = = = = = = = G C = = C G G = A = C C = = = A = = = = T ? = T = = 0 E104 = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = C A I = G I A A = T A = G = = ? ? T = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = A G D = C D G G = C G = T = = ? ? C = 0 E105 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C A I = G I A A = T A ? G = ? ? ? T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G D = C D G G = C G ? T = ? ? ? C = 0 E106 = = = = = = = = = = = = = = = = = = = = = = ? = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = G = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = C A I = G I A A = T A = G = = = = T = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = A G D = C D G G = C G = T = = = = C = 0 E108 = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = ? = = = ? = = ? ? = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = ? = = = ? = = ? ? 0 E109 = = = = = = = = = = = = ? ? ? ? = = = = (A) = = = = = = T T T ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = (C) = = = = = = C C C ? = = = = = = = = = = = = = = = = = = = = 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E111 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = 0 E112 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C A I = G I A A = T A = G = = = = T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G D = C D G G = C G = T = = = = C = 0 E113 = ? = = = = = = = = = = = = = = = = = = = = ? = = A A C C = A A C = = G G I A A G = A T G = ? = C = = = ? = = = = = = = = = = = = = = = = = = = = ? = = G C T T = G G A = = C C D G G A = G A T = ? = T = = 0 E114 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? = C A I = G I A A = T A = G = = = = T = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? = A G D = C D G G = C G = T = = = = C = 0 E115 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) (C) (C) = = C A I = G I A A = ? A = G = = ? ? T = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) (T) (T) = = A G D = C D G G = ? G = T = = ? ? C = 0 E117 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = C G G = A I C = = = = A T ? ? = = T = T T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = T A A = G D G = = = = G C ? ? = = C = C C = 0 E118 = ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = I = = = = = = = = = = = = ? ? ? ? = ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = D = = = = = = = = = = = = ? ? ? ? 0 E119 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C G G A = = C C D G G A = G A T = T ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T A A C = = G G I A A G = A T G = C ? ? = = 0 E120 = = = = = = = = = = = = = = = = = = (G) = = = = = = A A = = T A A C = = G G I A A G = A ? G = C ? ? = = = = = = = = = = = = = = = = = = = = (A) = = = = = = G C = = C G G A = = C C D G G A = G ? T = T ? ? = = 0 E121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 E122 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 E123 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = C G G = A I C = = = = A T = ? = ? T = T T = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = T A A = G D G = = = = G C = ? = ? C = C C = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = ? = = ? = = = = = = = = = = = = = = = = = = = = 0.99 0.99 = = 1.00 = = = = 1.00 = 1.00 = = ? = 1.00 ? 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? ? ? ? 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = 0.51 = = = = 0.51 = 0.51 = = = = = = = = = ? = = = = = ? 0.63 = = = = = 0.63 0.63 = = = = = = = 0.63 = 0.63 = = = = 0.63 = = = = = = = = = = = 0.96 = = = = 0.96 = 0.96 = 0.96 ? = = = ? 1.00 = = 1.00 1.00 = 1.00 1.00 ? ? ? ? 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 = = = = = = = = 1.00 = = = = = = = = = = 1.00 = 1.00 1.00 = ? = = = 0.58 = = = = 0.58 = = = = = = = = = = = = = = 1.00 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 = = = = 0.93 = = = = = = 0.93 = 0.93 ? = = 0.93 0.93 0.73 = = = = = = = = = = = = = = = 0.94 = 0.94 = 0.94 ? 0.94 = 0.94 0.94 = = 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 = 0.57 0.57 = = = = = = = = = = = = = = 0.57 = 0.57 = = = = 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 = 1.00 = = = ? ? 1.00 = = 0.54 0.54 = = = = = = = = = = = = = = 0.54 = 0.54 = = ? = 0.54 = = = = = ? 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? 1.00 1.00 = ? 1.00 ? = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 0.96 = = 1.00 = = = = 1.00 = = = = = = 1.00 = 1.00 ? = = 1.00 1.00 0.67 0.67 = = 0.71 = = = = 0.71 = 0.71 = = = = = = = = = = ? ? = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? ? ? = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = ? = 1.00 1.00 ? ? = ? = = 0.60 = = = = = 0.60 0.60 = = = = = = = 0.60 = 0.60 = = ? = 0.60 = = = = = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 = 1.00 = = = = = ? ? 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? ? ? 1.00 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 = 0.69 = 0.69 = = 0.69 = = = = = = = = 0.69 0.69 ? ? 0.69 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? ? ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = 0.73 = = = = 0.73 = 0.73 = 0.73 0.73 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = = = = = = = ? 1.00 = = = 1.00 ? = 0.75 = = = = = 0.75 0.75 = = = = = = = 0.75 = 0.75 ? = = = 0.75 = = = = = = = = 0.76 = = = = = = = 0.76 = 0.76 = 0.75 ? 0.76 = 0.76 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 ? ? ? 1.00 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 0.68 0.68 0.68 0.68 ? = = = = = 0.68 = = = = 0.68 = 0.68 = 0.68 0.68 = = = = = 0.70 0.70 = = 0.70 = = = = 0.70 = ? ? ? ? = 0.70 = 0.70 ? = = 0.70 0.70 1.00 1.00 = = 1.00 = = = = 1.00 = 1.00 = = = = 1.00 = 1.00 = 1.00 ? 1.00 = 1.00 1.00 ? = 0.67 = = = = = 0.67 0.67 = = = = = = = 0.67 = 0.67 = = = = 0.67 1.00 = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = ? = 1.00 = = 1.00 ? ? 1.00 = ? = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = ? ? 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = 0.96 0.96 = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = 1.00 ? = 1.00 = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = ? ? 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 = ? ? ? 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = = 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 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.74 0.74 0.74 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = ? 1.00 = 1.00 = = ? ? 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 ? ? = = 1.00 = 1.00 1.00 = = ? = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 1.00 = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 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 = END PHASEPROBS