************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 f2rl2.phase.inp f2rl2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST f2rl2.phase.out_freqs : haplotype frequency estimates f2rl2.phase.out_pairs : most likely haplotype pairs for each individual f2rl2.phase.out_recom : estimates of recombination parameters f2rl2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 38 Positions of loci: 419 506 507 512 535 1430 2448 2535 2800 2866 3116 3281 3565 3694 3734 3976 4264 4305 4556 4580 4627 4635 4778 5126 5312 5416 5439 6384 6863 6896 7176 7325 7767 8181 8453 8571 8704 8769 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file f2rl2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AATGCACCGAGGCCCDGCCGTCCCACGAGTGTTACITA 1.000000 2 AATGCACCGAGGCCCDGCCGTTCCACGAGTGTTACITA 1.000000 3 AATGCACCGAGGCTCDGCCGTTCCATGAGTGTTACDTA 7.000000 4 AATGCACCGAGGCTCIGCCGTTCCATGAGTGTTACDTA 1.000000 5 AATGCACCGAGGCTTICGCGCTCCTTGAATGCCGAIGG 10.000000 6 AATGCACCGTAGTTCIGCCGTTCCATGAATGTTACITA 2.000000 7 AATGCACTGAGGCTTICGCGTTCCATGAATGTTACITA 2.000000 8 AATGCACTGTGGCTCDGCCGTTCCATGAATGTTACITA 3.000000 9 AATGCACTGTGGCTCDGCCGTTCCATGAGTGTTACITA 4.000000 10 AATGCATCGAGGCTTICGCGCTCCTTGAATGCCGAIGG 2.000000 11 AATGCATTGTGGCTCDGCCGTTAAATAGATGCCGCITA 2.000000 12 AATGCATTGTGATTCDGCCGTTCCTTGAATGCCGAIGG 4.000000 13 AATGCGCCGAGGCTTICGCGCTCCTTGAATGCCGAIGG 1.000000 14 AGTGCACCGAGGCCCDGCCGTCCCACGAGTGTTACITA 2.000000 15 AGTGCACCGAGGCTCDGCCGTTCCATGAGTGTTACDTA 11.000000 16 AGTGCACCGAGGCTCIGCCGTTCCATGAGTGTTACDTA 1.000000 17 AGTGCACCGAGGCTTICGCGCTCCTTGAATGCCGAIGG 5.000000 18 AGTGCACCGTGGCTCDGCCGTTCCATGAGTGTTACDTA 1.000000 19 AGTGCACTGTGGCTCDGCCGTTCCATGAGTGTTACITA 2.000000 20 AGTGCACTATGGCCCDGCCGTCCCACGAGTGTTACITA 2.000000 21 AGTGCACTATGGCTCDGCCGTTCCATGAGTCTTACITA 1.000000 22 AGTGCATTGTGGCTCDGCCGTTCCATGAATGTTACITA 2.000000 23 AGCGCACCGTAGTTCIGCCGTTCCATGAATGTTACITA 1.000000 24 GATGCATTGTGGCTCDGCCGTTCCATGAGCCTTACITA 1.000000 25 GATGCGCCGAGGCTCDGCCGTTCCATGAGTGTTACDTA 1.000000 26 GATGCGCTGAGGCTCIGGAATTAAATAGATGCCGCITA 2.000000 27 GATGCGTTGTGGCTCDGCCGTTCCATGAGCCTTACITA 1.000000 28 GACATACCGAGGCTTICGCGCTCCTTGAATGCCGAIGG 9.000000 29 GACATACCGAGGCTTICGCGCTCCTTGAATGCCGADGG 1.000000 30 GACATACCGTGGCTCDGCCGTTCCATGAATGTTACITA 1.000000 31 GACATACTGAGGCTCIGGAATTAAATAGATGCCGCITA 1.000000 32 GACATACTGTGGCTCDGCCATTCCATGAATGTTACITA 1.000000 33 GACATACTGTGGCTCDGCCATTCCATGAGTGTTACITA 1.000000 34 GACATACTGTGGCTCDGCCGTTCCATGAATGTTACITA 3.000000 35 GACATACTATGGCCCDGCCGTCCCACGAGTGTTACITA 1.000000 36 GACATATTGTGGCTCDGCCGTTCCATGAATGTTACITA 2.000000 37 GACATATTGTGGCTCDGCCGTTCCATGAGCCTTACITA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (14,26) D002: (7,15) D003: (6,20) D004: (5,14) D005: (15,36) D006: (1,8) D007: (5,5) D008: (5,6) D009: (32,34) D010: (8,15) D011: (21,33) D012: (8,27) D013: (7,34) D014: (3,20) D015: (24,28) D016: (31,35) D033: (26,30) D034: (19,36) D035: (18,28) D036: (2,5) D037: (23,34) D038: (5,3) D039: (17,22) D040: (22,37) E001: (12,17) E002: (3,9) E003: (12,15) E004: (10,15) E005: (15,28) E006: (5,19) E007: (10,28) E008: (5,28) E009: (5,28) E010: (11,12) E011: (15,15) E012: (4,16) E013: (25,28) E014: (12,3) E015: (17,9) E016: (5,15) E017: (3,15) E018: (9,28) E019: (3,29) E020: (11,13) E021: (15,17) E022: (9,17) E023: (3,28) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 (A) (G) T G C (A) C C G A G G C C C D G C C G T C C C A C G A G T G T T A C I T A (G) (A) T G C (G) C T G A G G C T C I G G A A T T A A A T A G A T G C C G C I T A 0 D002 A (A) T G C A C T G A G G C T T I C G C G T T C C A T G A A T G T T A C I T A A (G) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 D003 A (A) T G C A C C G T A G T T C I G C C G T T C C A T G A A T G T T A C I T A A (G) T G C A C T A T G G C C C D G C C G T C C C A C G A G T G T T A C I T A 0 D004 A (A) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A (G) T G C A C C G A G G C C C D G C C G T C C C A C G A G T G T T A C I T A 0 D005 (A) (G) (T) (G) (C) A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A (G) (A) (C) (A) (T) A T T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D006 A A T G C A C C G A G G C C C D G C C G T C C C A C G A G T G T T A C I T A A A T G C A C T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D007 A A T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A A T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 D008 A A T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A A T G C A C C G T A G T T C I G C C G T T C C A T G A A T G T T A C I T A 0 D009 G A C A T A C T G T G G C T C D G C C A T T C C A T G A A T G T T A C I T A G A C A T A C T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D010 A (A) T G C A C T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A A (G) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 D011 A G T G C A C T (A) T G G C T C D G C C (G) T T C C A T G A G T (C) T T A C I T A G A C A T A C T (G) T G G C T C D G C C (A) T T C C A T G A G T (G) T T A C I T A 0 D012 (A) A T G C (A) C T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A (G) A T G C (G) T T G T G G C T C D G C C G T T C C A T G A G C C T T A C I T A 0 D013 (A) A (T) (G) (C) A C T G A G G C T T I C G C G T T C C A T G A A T G T T A C I T A (G) A (C) (A) (T) A C T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D014 A (A) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A A (G) T G C A C T A T G G C C C D G C C G T C C C A C G A G T G T T A C I T A 0 D015 G A (T) (G) (C) A T T G T G G C T C D G C C G T T C C A T G A G C C T T A C I T A G A (C) (A) (T) A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 D016 G A C A T A C T G A G G C T C I G G A A T T A A A T A G A T G C C G C I T A G A C A T A C T A T G G C C C D G C C G T C C C A C G A G T G T T A C I T A 0 D033 G A (T) (G) (C) (G) C (T) G A G G C T C I G G A A T T A A A T A G A T G C C G C I T A G A (C) (A) (T) (A) C (C) G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D034 A G T G C A (C) T G T G G C T C D G C C G T T C C A T G A (G) T G T T A C I T A G A C A T A (T) T G T G G C T C D G C C G T T C C A T G A (A) T G T T A C I T A 0 D035 [A] (G) (T) (G) (C) A C C G (T) G G C T C D G C C G T T C C A T G A G T G T T A C D T A [G] (A) (C) (A) (T) A C C G (A) G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 D036 A [A] T G C A C C G A G G C C C D G C C G T T C C A C G A G T G T T A C I T A A [A] T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 D037 A G C G C A C (C) G T (A) G (T) T C (I) G C C G T T C C A T G A A T G T T A C I T A G A C A T A C (T) G T (G) G (C) T C (D) G C C G T T C C A T G A A T G T T A C I T A 0 D038 A [A] T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A [A] T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 D039 A G T G C A (C) C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A G T G C A (T) T G T G G C T C D G C C G T T C C A T G A A T G T T A C I T A 0 D040 A G T G C A T T G T G G C T C D G C C G T T C C A T G A (A) (T) (G) T T A C I T A G A C A T A T T G T G G C T C D G C C G T T C C A T G A (G) (C) (C) T T A C I T A 0 E001 A (A) T G C A T T G T G A T T C D G C C G T T C C T T G A A T G C C G A I G G A (G) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E002 A A T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A A A T G C A C T G T G G C T C D G C C G T T C C A T G A G T G T T A C I T A 0 E003 A (A) T G C A T T G T G A T T C D G C C G T T C C T T G A A T G C C G A I G G A (G) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E004 A (A) T G C A T C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A (G) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E005 (A) (G) (T) (G) (C) A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A (G) (A) (C) (A) (T) A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E006 A (A) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A (G) T G C A C T G T G G C T C D G C C G T T C C A T G A G T G T T A C I T A 0 E007 A A T G C A (T) C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G G A C A T A (C) C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E008 A A T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G G A C A T A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E009 A A T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G G A C A T A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E010 A A T G C A T T G T G G C T C D G C C G T T A A A T A G A T G C C G C I T A A A T G C A T T G T G A T T C D G C C G T T C C T T G A A T G C C G A I G G 0 E011 A G T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A A G T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E012 A A T G C A C C G A G G C T C I G C C G T T C C A T G A G T G T T A C D T A A G T G C A C C G A G G C T C I G C C G T T C C A T G A G T G T T A C D T A 0 E013 G A (T) (G) (C) (G) C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A G A (C) (A) (T) (A) C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E014 A A T G C A T T G T G A T T C D G C C G T T C C T T G A A T G C C G A I G G A [A] T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E015 A (G) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A (A) T G C A C T G T G G C T C D G C C G T T C C A T G A G T G T T A C I T A 0 E016 A (A) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G A (G) T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E017 A A T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A A G T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A 0 E018 (A) A (T) (G) (C) A C T G T G G C T C D G C C G T T C C A T G A G T G T T A C I T A (G) A (C) (A) (T) A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E019 (A) A (T) (G) (C) A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A (G) A (C) (A) (T) A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A D G G 0 E020 A A T G C (A) T T G T G G C T C D G C C G T T A A A T A G A T G C C G C I T A A A T G C (G) C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E021 A G T G C A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A A G T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E022 A (A) T G C A C T G T G G C T C D G C C G T T C C A T G A G T G T T A C I T A A (G) T G C A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 0 E023 (A) A (T) (G) (C) A C C G A G G C T C D G C C G T T C C A T G A G T G T T A C D T A (G) A (C) (A) (T) A C C G A G G C T T I C G C G C T C C T T G A A T G C C G A I G G 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 (A) (G) = = = (A) = C = = ? ? = C = D = C C G = C C C = C G A G = = T T A = = = = (G) (A) = = = (G) = T = = ? ? = T = I = G A A = T A A = T A G A = = C C G = = = = 0 D002 = (A) = = = = = T = = = = = = T I C G = = = = = = = = = = A = = = = = = I = = = (G) = = = = = C = = = = = = C D G C = = = = = = = = = = G = = = = = = D = = 0 D003 = (A) = = = = = C G = A = T T = I = = = = = T = = ? ? ? = A = = = = = = = = = = (G) = = = = = T A = G = C C = D = = = = = C = = ? ? ? = G = = = = = = = = = 0 D004 = (A) = = = = = = = = = = = T T I C G = = C T = = T T = = A = = C C G A = G G = (G) = = = = = = = = = = = C C D G C = = T C = = A C = = G = = T T A C = T A 0 D005 (A) (G) (T) (G) (C) = C C = A = = = = = = = = = = = = = = = = = = G = = = = = = D = = (G) (A) (C) (A) (T) = T T = T = = = = = = = = = = = = = = = = = = A = = = = = = I = = 0 D006 = = = = = = = C = A = = ? ? ? = = = = = = C = = = C = = G = = = = = = = = = = = = = = = = T = T = = ? ? ? = = = = = = T = = = T = = A = = = = = = = = = 0 D007 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D008 = = = = = = = = = A G = C = T = C G = = C = = = T = = = = = = C C G A = G G = = = = = = = = = T A = T = C = G C = = T = = = A = = = = = = T T A C = T A 0 D009 = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = 0 D010 = (A) = = = = = T = T = = = = = = = = = = = = = = = = = = A = = = = = ? ? = = = (G) = = = = = C = A = = = = = = = = = = = = = = = = = = G = = = = = ? ? = = 0 D011 A G T G C = = = (A) = = = = = = = = = = (G) = = = = = = = = = = (C) = = = ? ? = = G A C A T = = = (G) = = = = = = = = = = (A) = = = = = = = = = = (G) = = = ? ? = = 0 D012 (A) = = = = (A) C = = = = = = = = = = = = = = = = = = = = = A T G = = = = = = = (G) = = = = (G) T = = = = = = = = = = = = = = = = = = = = = G C C = = = = = = = 0 D013 (A) = (T) (G) (C) = = = = A = = = = T I C G = = = = = = = = = = = = = = = = = = = = (G) = (C) (A) (T) = = = = T = = = = C D G C = = = = = = = = = = = = = = = = = = = = 0 D014 = (A) = = = = = C G A = = = T = = = = = = = T = = = T = = = = = = = = = D = = = (G) = = = = = T A T = = = C = = = = = = = C = = = C = = = = = = = = = I = = 0 D015 = = (T) (G) (C) = T T = T = = = = C D G C = = T = = = A = = = G C C T T A C = T A = = (C) (A) (T) = C C = A = = = = T I C G = = C = = = T = = = A T G C C G A = G G 0 D016 = = = = = = = = G A = = = T = I = G A A = T A A = T A G A = = C C G = = = = = = = = = = = = A T = = = C = D = C C G = C C C = C G A G = = T T A = = = = 0 D033 = = (T) (G) (C) (G) = (T) = A = = = = = I = G A A = = A A = = A G = = = ? C G = = = = = = (C) (A) (T) (A) = (C) = T = = = = = D = C C G = = C C = = G A = = = ? T A = = = = 0 D034 A G T G C = (C) = = ? = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = G A C A T = (T) = = ? = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = 0 D035 ? (G) (T) (G) (C) = = = = (T) = = = = C D G C = = T = = = A = = = G = = T T A C D ? A ? (A) (C) (A) (T) = = = = (A) = = = = T I C G = = C = = = T = = = A = = C C G A I ? G 0 D036 ? ? ? ? ? = = = = = = = = C C D G C = = T = = = A C = = G = = T T ? C = T A ? ? ? ? ? = = = = = = = = T T I C G = = C = = = T T = = A = = C C ? A = G G 0 D037 ? G = G C = = (C) = ? (A) = (T) = = (I) = = = = = = ? = ? ? ? = = = = = = = ? ? ? = ? A = A T = = (T) = ? (G) = (C) = = (D) = = = = = = ? = ? ? ? = = = = = = = ? ? ? = 0 D038 ? ? ? ? ? = = = = = = = ? = T I C G = = C = = = T = = = A = = C C G A I G G ? ? ? ? ? = = = = = = = ? = C D G C = = T = = = A = = = G = = T T A C D T A 0 D039 = = = = = = (C) C = A = = ? ? ? ? C G = = C = = = T = = = = = = C C G A = G G = = = = = = (T) T = T = = ? ? ? ? G C = = T = = = A = = = = = = T T A C = T A 0 D040 A G T G C = = = = = = = = = = = = = = = = = = = ? ? ? = (A) (T) (G) = = = = = = = G A C A T = = = = = = = = = = = = = = = = = = = ? ? ? = (G) (C) (C) = = = = = = = 0 E001 = (A) = = = = T T = T = A T = C D G C = = T = = = = = = = = = = = = = = = = = = (G) = = = = C C = A = G C = T I C G = = C = = = = = = = = = = = = = = = = = 0 E002 = = = = = = = C = A = = = = = = = = = = = = = = = = = = = = = = = = = D = = = = = = = = = T = T = = = = = = = = = = = = = = = = = = = = = = = = = I = = 0 E003 = (A) = = = = T T = ? = A T = = = = = = = = = = = T = = = A = = C C G A I G G = (G) = = = = C C = ? = G C = = = = = = = = = = = A = = = G = = T T A C D T A 0 E004 = (A) = = = = T = = = = = = = T I C G = = C = = = T = = = A = = C C G ? ? G G = (G) = = = = C = = = = = = = C D G C = = T = = = A = = = G = = T T A ? ? T A 0 E005 (A) (G) (T) (G) (C) = = = = = = = = = C D G C = = T = = = A = = = G = = T T A C D T A (G) (A) (C) (A) (T) = = = = = = = = = T I C G = = C = = = T = = = A = = C C G A I G G 0 E006 = (A) = = = = = C = A = = = = T I C G = = C = = = T = = = A = = C C G A = G G = (G) = = = = = T = T = = = = C D G C = = T = = = A = = = G = = T T A C = T A 0 E007 A = T G C ? (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = C A T ? (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 A = T G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = C A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 A = T G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = C A T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = = = = = = = = = = = G C = = = = = = = = = A A A = A G = = = = = = C = T A = = = = = = = = = = = A T = = = = = = = = = C C T = G A = = = = = = A = G G 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = = (T) (G) (C) (G) = = = = = = = = C D G C = = T = = = A = = = G = = T ? A C D T A = = (C) (A) (T) (A) = = = = = = = = T I C G = = C = = = T = = = A = = C ? G A I G G 0 E014 ? ? ? ? ? = T T = T = A T = = = = = = = = = = = T = = = A = = C C G A I G G ? ? ? ? ? = C C = A = G C = = = = = = = = = = = A = = = G = = T T A C D T A 0 E015 = (G) = = = ? = C = A = = = = T I C G = = C = = = T = = ? A = = C C G A = G G = (A) = = = ? = T = T = = = = C D G C = = T = = = A = = ? G = = T T A C = T A 0 E016 = (A) = = = = = = = = = = = = T I C G = = C = = = T = = = A = = C C G A ? G G = (G) = = = = = = = = = = = = C D G C = = T = = = A = = = G = = T T A C ? T A 0 E017 = A = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 E018 (A) = (T) (G) (C) = = T = T = = = = C D G C = = T = = = A = = = G = = T T A C = T A (G) = (C) (A) (T) = = C = A = = = = T I C G = = C = = = T = = = A = = C C G A = G G 0 E019 (A) = (T) (G) (C) = = = = = = = = = C D G C = = T = = = A = = = G = = T T A C = ? A (G) = (C) (A) (T) = = = = = = = = = T I C G = = C = = = T = = = A = = C C G A = ? G 0 E020 = = = = = (A) T T = T = = = = C D G C = = T = A A A = A G = = = = ? = ? ? ? A = = = = = (G) C C = A = = = = T I C G = = C = C C T = G A = = = = ? = ? ? ? G 0 E021 = = = = = = = = = = = = = = C D G C = = T = = = A = = = G = = T T A C D ? A = = = = = = = = = = = = = = T I C G = = C = = = T = = = A = = C C G A I ? G 0 E022 = (A) = = = = = T = T ? ? ? = C D G C = = T = = = A = = = G = = T T A C = T A = (G) = = = = = C = A ? ? ? = T I C G = = C = = = T = = = A = = C C G A = G G 0 E023 (A) = (T) (G) (C) ? = = = = = = = = C D G C = = T = = = ? ? ? = G = = ? T A C D T A (G) = (C) (A) (T) ? = = = = = = = = T I C G = = C = = = ? ? ? = A = = ? C G A I G G END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.75 0.75 = = = 0.75 = 1.00 = = ? ? = 1.00 = 1.00 = 1.00 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 = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = 1.00 = = = = = = 1.00 = = = 0.66 = = = = = 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 0.56 0.54 0.56 0.56 0.56 = 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 = = = = = = = = = = = = = = = = = = = 0.69 = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? ? = = 1.00 1.00 1.00 1.00 1.00 = = = 0.52 = = = = = = = = = = 0.65 = = = = = = = = = = 0.52 = = = ? ? = = 0.61 = = = = 0.55 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = 0.71 = 0.71 0.71 0.71 = = = = 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 0.51 = = = = = 0.98 0.98 0.98 = = = 1.00 = = = = = = = 1.00 = = = 1.00 = = = = = = = = = 1.00 = = = = 0.52 0.52 0.52 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 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 = 0.56 = 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 = 0.51 = = ? = = = = = = = = = = = = = = = = = = 0.52 = = = = = = = = = ? 0.62 0.62 0.62 0.62 = = = = 0.56 = = = = 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 = = 0.68 = ? 0.68 = 0.68 = = 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 = = = = = = 0.90 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 0.98 0.98 0.98 = = = = = = = = = = = = = = = = = = = ? ? ? = 0.63 0.63 0.63 = = = = = = = = 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 = = = 0.70 = = = = 1.00 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 = = = = 0.93 = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 ? ? 1.00 1.00 0.65 0.65 0.65 0.65 0.65 = = = = = = = = = 1.00 1.00 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 ? 0.63 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = = = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 0.58 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 ? ? ? ? ? = 1.00 1.00 = 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 = = ? 0.99 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 0.63 = = = = = = = = = = = = 1.00 1.00 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 0.59 0.59 = = 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 0.52 = 0.52 0.52 0.52 = = = = = = = = = 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 = = 1.00 = = = 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 ? 1.00 = 0.51 = = = = = 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 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 END PHASEPROBS