************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 sftpc.phase.inp sftpc.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST sftpc.phase.out_freqs : haplotype frequency estimates sftpc.phase.out_pairs : most likely haplotype pairs for each individual sftpc.phase.out_recom : estimates of recombination parameters sftpc.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 29 Positions of loci: 1347 1525 1626 2262 2436 2437 2992 3193 3416 4565 4912 5224 5306 5387 5560 5753 5788 5854 6531 6624 6701 6783 6882 7011 7235 7378 7428 7437 7541 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file sftpc.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AACCATGAAGGGGATGACCGTCCGDGCGC 1.000000 2 AACCATGAAGGGGGTACCCACCGGDGTGC 1.000000 3 AACCGGGAAGGCAGCGCCCGCCCGDGCGT 1.000000 4 AACCGGGAGGGGGATGCCCGCCCGIACGC 1.000000 5 AACCGGGGAAAGAGTACCCACCGGDGTGC 3.000000 6 AACCGGCAAGGCAGCGCCCGCCCGIACGC 1.000000 7 AACCGTGAAGGGGGCGCCCGCCCGIACGC 1.000000 8 AACCGTGAAGGGGGCGCCCGCCCGDGCGT 1.000000 9 AACCGTGAAGGGGGCGCCCGCTCGDGCGT 1.000000 10 AACCGTGAAGGGAGCGCACGCCCGIACGC 1.000000 11 AACCGTGAAGGGAGCGACCGCCCGDGCGC 4.000000 12 AACGATGAAGGGGATGCCCGCCCGDGCGC 1.000000 13 AACGATGAAGGGGATGCCCGCTCGDGCGT 1.000000 14 AACGATGAAGGGGATGCCCGCTGGDGCGT 3.000000 15 AACGATGAAGGGGATGACCGCCCGDGCGT 1.000000 16 AACGATGAAGGGGATGACCGCTGGDGCGT 2.000000 17 AACGATGAAGGGGACGCACGCCCGIACGC 2.000000 18 AACGATGAAGGGGGTGACCGCCCGDGCGT 1.000000 19 AACGATGAAGGGGGTGACCGCCCGDGTGC 2.000000 20 AACGATGAAGGGGGTGACCGCCCGDGTCC 4.000000 21 AACGATGAAGGGGGTACCCGCTGGDGCGT 1.000000 22 AACGATGAAGGGAGCGACCGCCCGDGCGC 1.000000 23 AACGATGAGGGGGATGACCGCTGGDGCGT 2.000000 24 AACGATGAGGGGGGTGCCCACCGGDGTGC 1.000000 25 AACGATGAGGGGGGTGACCGCCCGDGCGC 1.000000 26 AACGATGAGGGGGGTGACCGCCCGDGCCC 1.000000 27 AACGATGAGGGGGGTGACAGCCCAIACGC 2.000000 28 AACGATGAGGGGGGCGACCGCCCGDGCGT 1.000000 29 AACGATGAGGGGGGCGACAGCCCAIACGC 1.000000 30 AACGGGGAGGGGAGCGCCCACCGGDGTGC 1.000000 31 AATCGTGAAGGGGGCGACCGTCCGDGCGC 2.000000 32 AATGATGAAGGGGATGCCCGCTCGDGCGT 1.000000 33 AATGATGAAGGGGATGCCCGCTGGDGCGT 1.000000 34 AATGATGAAGGGGATGACCGCTGGDGCGT 1.000000 35 AATGATGAGGGGGGTGACCGCCCGDGCGC 1.000000 36 ACCCGGGAGGGGAGCGACCGCCCAIACGT 1.000000 37 ACCGATGAAGGGGGTGACCGCCCGDGCGT 1.000000 38 ACCGATGAAGGGGGTGACCGCCCGDGTGC 3.000000 39 ACCGATGAAGGGGGTGACCGCCCGDGTCC 1.000000 40 ACCGATGAAGGGGGTGACCGCCCAIACGC 1.000000 41 ACCGATGAGGGGGGTGACCGCTGGDGCGT 1.000000 42 ACCGATGAGGGGGGTGACAGCCCAIACGC 1.000000 43 ACTGATGAAGGGGATGACCGCCCGDGCCC 1.000000 44 ACTGATGAAGGGGATGACCGCCCGDGTGC 1.000000 45 GACCGGGAGGGGGATGACCGCTGGDGCGT 1.000000 46 GACCGGGAGGGGAGCGCCCGCCCGIGCCC 1.000000 47 GACCGGGAGGGGAGCGCCCGCCCAIGCCC 1.000000 48 GACCGGGAGGGGAGCGACAGCCCAIACGC 1.000000 49 GACCGGGGAAAGAGTACCCACCGGDGTGC 1.000000 50 GACCGGCAAGGCAGTGCCCGCCCGIACGC 1.000000 51 GACCGGCAAGGCAGCGCCCGCCCGIACGC 1.000000 52 GACCGTGAAGGGGGCGCCCGCCCGDGCGT 1.000000 53 GACCGTGAAGGGGGCGCCCGCCGGDGCGT 1.000000 54 GACCGTGAAGGGGGCGCCCGCTGGDGCGT 2.000000 55 GACCGTGAAGGGGGCGACCGCCCAIACGT 1.000000 56 GACCGTGAAGGGAGCGCCCGCCCGDGCGC 1.000000 57 GACCGTGAAGGGAGCGACCGCCCGIACGC 2.000000 58 GACCGTGAAGGGAGCGACCGCCCGDACGC 1.000000 59 GACCGTGAAGGGAGCGACCGCCCGDGTGC 1.000000 60 GACGATGAAGGGGATGCCCGCTGGDGCGT 3.000000 61 GACGATGAAGGGGATGACCGCTGGDGCGT 1.000000 62 GACGATGAAGGGGGTGACCGCCCGDGCGT 1.000000 63 GACGATGAAGGGGGTGACCGCCCGDGTGC 1.000000 64 GACGATGAGGGGGGCGACCGCCCGDGCGT 1.000000 65 GACGATGAGGGGAGCGACCGCCCGDGCGC 3.000000 66 GATCGTGAAGGGGGCGACCGCCCAIACGT 1.000000 67 GATGATGAAGGGGATGACCGCTGGDGCGT 1.000000 68 GCCCGTGAAGGGGGCGACCGTCCGDGCGC 1.000000 69 GCCCGTGAAGGGGGCGACAGCCCAIACGC 1.000000 70 GCCCGTGGAGGGGGCGACCGTCCGDGCCC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (60,4) D002: (11,47) D003: (14,54) D004: (17,65) D005: (6,12) D006: (56,65) D007: (25,60) D008: (21,58) D009: (11,35) D010: (22,57) D011: (7,10) D012: (9,57) D013: (14,53) D014: (38,60) D015: (17,54) D016: (24,44) D033: (8,11) D034: (50,13) D035: (3,14) D036: (52,63) D037: (32,46) D038: (51,59) D039: (33,65) D040: (11,38) E001: (2,31) E002: (5,61) E003: (18,20) E004: (38,45) E005: (19,48) E006: (16,31) E007: (29,64) E008: (37,42) E009: (23,40) E010: (66,28) E011: (39,49) E012: (16,69) E013: (1,20) E014: (26,23) E015: (67,70) E016: (5,15) E017: (55,68) E018: (5,34) E019: (19,27) E020: (20,41) E021: (27,30) E022: (20,62) E023: (36,43) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 (G) A C (G) (A) (T) G A (A) G G G G A T G C C C G C T G G D G C G T (A) A C (C) (G) (G) G A (G) G G G G A T G C C C G C C C G I A C G C 0 D002 (A) A C C G T G A A G G G A G C G (A) C C G C C C G D G C G C (G) A C C G G G A G G G G A G C G (C) C C G C C C A I G C [C] [C] 0 D003 (A) A C G A T G A A G G G G A T G C C C G C T G G D G C G T (G) A C C G T G A A G G G G G C G C C C G C T G G D G C G T 0 D004 (A) A C G A T G A A G G G G A C G C A C G C C C G I A C G C (G) A C G A T G A G G G G A G C G A C C G C C C G D G C G C 0 D005 A A C C G G C A A G G C A G C G C C C G C C C G (I) (A) [C] G C A A C G A T G A A G G G G A T G C C C G C C C G (D) (G) C G C 0 D006 G A C (C) (G) T G A (A) G G G A G C G (C) C C G C C C G D G C G [C] G A C (G) (A) T G A (G) G G G A G C G (A) C C G C C C G D G C G C 0 D007 (A) A C G A T G A (G) G G G G (G) T G A C C G C C C G D G [C] [G] C (G) A C G A T G A (A) G G G G (A) T G C C C G C T G G D G C G T 0 D008 (A) A C (G) (A) T G A A G G G (G) G (T) (A) (C) C C G C (T) (G) G D (G) C G [T] (G) A C (C) (G) T G A A G G G (A) G (C) (G) (A) C C G C (C) (C) G D (A) C G C 0 D009 A A (C) C G T G A A G G G (A) G (C) G A C C G C C C G D G C G C A A (T) G A T G A G G G G (G) G (T) G A C C G C C C G D G C G C 0 D010 (A) A C (G) (A) T G A A G G G A G C G A C C G C C C G (D) (G) C G C (G) A C (C) (G) T G A A G G G A G C G A C C G C C C G (I) (A) C G C 0 D011 A A C C G T G A A G G G (G) G C G C C C G C C C G I A C G C A A C C G T G A A G G G (A) G C G C A C G C C C G I A C G C 0 D012 (A) A C C G T G A A G G G (G) G C G (C) C C G C (T) C G D G C G T (G) A C C G T G A A G G G (A) G C G (A) C C G C (C) C G I A C G C 0 D013 (A) A C G A T G A A G G G G A T G C C C G C (T) G G D G C G T (G) A C C G T G A A G G G G G C G C C C G C (C) G G D G C G T 0 D014 (A) (C) C G A T G A A G G G G G T G A C C G C C C G D G T G C (G) (A) C G A T G A A G G G G A T G C C C G C T G G D G C G T 0 D015 (A) A C G A T G A A G G G G A C G C A C G C C C G I A C G C (G) A C C G T G A A G G G G G C G C C C G C T G G D G C G T 0 D016 A (A) (C) G A T G A (G) G G G G (G) T G (C) C C A C C G G D G T G C A (C) (T) G A T G A (A) G G G G (A) T G (A) C C G C C C G D G T G C 0 D033 A A C C G T G A A G G G G G C G C C C G C C C G D G C G T A A C C G T G A A G G G A G C G A C C G C C C G D G C G C 0 D034 (G) A C C G G C A A G G C A G T G C C C G C (C) C G (I) (A) C G (C) (A) A C G A T G A A G G G G A T G C C C G C (T) C G (D) (G) C G (T) 0 D035 A A C (C) (G) (G) G A A G G C A G C G C C C G C C (C) G D G C G T A A C (G) (A) (T) G A A G G G G A T G C C C G C T (G) G D G C G T 0 D036 G A C C G T G A A G G G G G C G C C C G C C C G D G (C) G (T) G A C G A T G A A G G G G G T G A C C G C C C G D G (T) G (C) 0 D037 (A) A (T) G A T G A A G G G G A T G C C C G C (T) C G (D) G C (G) (T) (G) A (C) C G G G A G G G G A G C G C C C G C (C) C G (I) G C (C) (C) 0 D038 G A C C G G C A A G G C A G C G C C C G C C C G (I) (A) (C) G C G A C C G T G A A G G G A G C G A C C G C C C G (D) (G) (T) G C 0 D039 (A) A (T) G A T G A (A) G G G G A T G (C) C C G C T G G D G C G T (G) A (C) G A T G A (G) G G G A G C G (A) C C G C C C G D G C G C 0 D040 A (A) C C G T G A A G G G A G C G A C C G C C C G D G C G C A (C) C G A T G A A G G G G G T G A C C G C C C G D G T G C 0 E001 A A (C) C (A) T G A A G G G G G (T) A C C C A C C G G D G T G C A A (T) C (G) T G A A G G G G G (C) G A C C G T C C G D G C G C 0 E002 (A) A C C G G G G A A A G A G T A C C C A C C G G D G T G C (G) A C G A T G A A G G G G A T G A C C G C T G G D G C G T 0 E003 A A C G A T G A A G G G G G T G A C C G C C C G D G C G T A A C G A T G A A G G G G G T G A C C G C C C G D G T C C 0 E004 (A) (C) C (G) (A) (T) G A (A) G G G G (G) T G A C C G C (C) (C) G D G (T) G (C) (G) (A) C (C) (G) (G) G A (G) G G G G (A) T G A C C G C (T) (G) G D G (C) G (T) 0 E005 (A) A C (G) (A) (T) G A A G G G (G) G (T) G A C (C) G C C C (G) (D) (G) (T) G C (G) A C (C) (G) (G) G A G G G G (A) G (C) G A C (A) G C C C (A) (I) (A) (C) G C 0 E006 A A (C) G A T G A A G G G G A T G A C C G C T G G D G C G T A A (T) C G T G A A G G G G G C G A C C G T C C G D G C G C 0 E007 (A) A C G A T G A G G G G G G C G A C A G C C C A I A C G C (G) A C G A T G A G G G G G G C G A C C G C C C G D G C G T 0 E008 A C C G A T G A (A) G G G G G T G A C C G C C C G D G C G T A C C G A T G A (G) G G G G G T G A C A G C C C A I A C G C 0 E009 A (A) C G A T G A (G) G G G G (A) T G A C C G C T G G D G C G T A (C) C G A T G A (A) G G G G (G) T G A C C G C C C A I A C G C 0 E010 (G) A (T) C G T G A A G G G G G C G A C C G C C C A I A C G T (A) A (C) G A T G A G G G G G G C G A C C G C C C G D G C G T 0 E011 (A) (C) C G A T G A A G G G G G T G A C C G C C C G D G T C C (G) (A) C C G G G G A A A G A G T A C C C A C C G G D G T G C 0 E012 (A) (A) C (G) (A) T G A A G G G G A T G A C C G C T G G D G C G T (G) (C) C (C) (G) T G A A G G G G G C G A C A G C C C A I A C G C 0 E013 A A C (C) A T G A A G G G G (A) T G A C C G T C C G D G C (G) C A A C (G) A T G A A G G G G (G) T G A C C G C C C G D G T (C) C 0 E014 A A C G A T G A G G G G G (G) T G A C C G C C C G D G C (C) C A A C G A T G A G G G G G (A) T G A C C G C T G G D G C (G) T 0 E015 G (A) (T) G A T G (A) A G G G G A T G A C C G C T G G D G C (G) T G (C) (C) C G T G (G) A G G G G G C G A C C G T C C G D G C (C) C 0 E016 A A C C G G G G A A A G A G T A C C C A C C G G D G T G C A A C G A T G A A G G G G A T G A C C G C C C G D G C G T 0 E017 G (A) C C G T G A A G G G G G C G A C C G C C C A I A C G [T] G (C) C C G T G A A G G G G G C G A C C G T C C G D G C G C 0 E018 A A (C) C G G G G A A A G A G T A C C C A C C G G D G T G C A A (T) G A T G A A G G G G A T G A C C G C T G G D G C G T 0 E019 A A C G A T G A A G G G G G T G A C C G C C C G D G [T] [G] C A A C G A T G A G G G G G G T G A C A G C C C A I A C G C 0 E020 A (A) C G A T G A A G G G G G T G A C C G C C C G D G T (C) C A (C) C G A T G A G G G G G G T G A C C G C T G G D G C (G) T 0 E021 A A C G (A) (T) G A G G G G (G) G (T) G A C A G C C C A I A C G C A A C G (G) (G) G A G G G G (A) G (C) G C C C A C C G G D G T G C 0 E022 (A) A C G A T G A A G G G G G T G A C C G C C C G D G T C C (G) A C G A T G A A G G G G G T G A C C G C C C G D G C G T 0 E023 A C (C) C G G G A (G) G G G (A) (G) (C) G A C C G C C C (A) (I) (A) C (G) (T) A C (T) G A T G A (A) G G G (G) (A) (T) G A C C G C C C (G) (D) (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 D001 (G) = = (G) (A) (T) = = (A) = = = = = = = = = = = = T G = D G ? ? ? (A) = = (C) (G) (G) = = (G) = = = = = = = = = = = = C C = I A ? ? ? 0 D002 (A) = = = = T = = A ? = = = = = = (A) = = = = = = G D = ? ? ? (G) = = = = G = = G ? = = = = = = (C) = = = = = = A I = ? ? ? 0 D003 (A) = = G A = = = = = = = = A T = = = = = = = = = = = = = ? (G) = = C G = = = = = = = = G C = = = = = = = = = = = = = ? 0 D004 (A) = = = = = = = A = = = G A = = C A = = = = = = I A ? ? ? (G) = = = = = = = G = = = A G = = A C = = = = = = D G ? ? ? 0 D005 = = = C G G C = = = = C A G C = = = = = = = = = (I) (A) ? ? ? = = = G A T G = = = = G G A T = = = = = = = = = (D) (G) ? ? ? 0 D006 = = = (C) (G) = = = (A) = = = = = = = (C) = = = = = = = = = ? ? ? = = = (G) (A) = = = (G) = = = = = = = (A) = = = = = = = = = ? ? ? 0 D007 (A) = = = = = = = (G) = = = = (G) = = A = = = = C C = = = ? ? ? (G) = = = = = = = (A) = = = = (A) = = C = = = = T G = = = ? ? ? 0 D008 (A) = = (G) (A) = = = = ? = = (G) = (T) (A) (C) = = = = (T) (G) = = (G) ? ? ? (G) = = (C) (G) = = = = ? = = (A) = (C) (G) (A) = = = = (C) (C) = = (A) ? ? ? 0 D009 = = (C) C G = = = A = = = (A) = (C) = = = = = = = = = = = = = = = = (T) G A = = = G = = = (G) = (T) = = = = = = = = = = = = = = 0 D010 (A) = = (G) (A) = = = = = = = = = = = = = = = = = = = (D) (G) = = = (G) = = (C) (G) = = = = = = = = = = = = = = = = = = = (I) (A) = = = 0 D011 = = = = = = = = = = = = (G) = = = = C = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = A = = = = = = = = = = = 0 D012 (A) = = = = = = = = = = = (G) = = = (C) = = = = (T) = = D G = = T (G) = = = = = = = = = = = (A) = = = (A) = = = = (C) = = I A = = C 0 D013 (A) = = G A = = = = = = = = A T = = = = = = (T) = = = = = = = (G) = = C G = = = = = = = = G C = = = = = = (C) = = = = = = = 0 D014 (A) (C) = = = = = = = = = = = G = = A = = = = C C = = = T = C (G) (A) = = = = = = = = = = = A = = C = = = = T G = = = C = T 0 D015 (A) = = G A = = = = = = = = A = = = A = = = C C = I A = = C (G) = = C G = = = = = = = = G = = = C = = = T G = D G = = T 0 D016 = (A) (C) = = = = = (G) = = = = (G) = = (C) = = A = = G = = = = = = = (C) (T) = = = = = (A) = = = = (A) = = (A) = = G = = C = = = = = = 0 D033 = = = = = = = = = = = = G = ? = C = = = = = = = = = = = T = = = = = = = = = = = = A = ? = A = = = = = = = = = = = C 0 D034 (G) = = C G G C = = = = C A G = = = = = = = (C) = = (I) (A) = = (C) (A) = = G A T G = = = = G G A = = = = = = = (T) = = (D) (G) = = (T) 0 D035 = = = (C) (G) (G) = = = = = C A G C = = ? = = = C (C) = = = = = = = = = (G) (A) (T) = = = = = G G A T = = ? = = = T (G) = = = = = = 0 D036 = = = C G = = = = = = = = = C = C = = = = = = = = = (C) = (T) = = = G A = = = = = = = = = T = A = = = = = = = = = (T) = (C) 0 D037 (A) = (T) G A T = = A = = = G A T = = = = = = (T) = = (D) = = (G) (T) (G) = (C) C G G = = G = = = A G C = = = = = = (C) = = (I) = = (C) (C) 0 D038 = = = = = G C = = = = C = = = = C = = = = = = = (I) (A) (C) = = = = = = = T G = = = = G = = = = A = = = = = = = (D) (G) (T) = = 0 D039 (A) = (T) = = = = = (A) = = = G A T = (C) = = = = T G = = = = = T (G) = (C) = = = = = (G) = = = A G C = (A) = = = = C C = = = = = C 0 D040 = (A) = C G = = = = = = = A = C = = = = = = = = = = = C = = = (C) = G A = = = = = = = G = T = = = = = = = = = = = T = = 0 E001 = = (C) = (A) = = = = = = = = = (T) A C = = A C = G = = = T = = = = (T) = (G) = = = = = = = = = (C) G A = = G T = C = = = C = = 0 E002 (A) = = C G G = G = A A = A G = A C = = A = C = = = = T = C (G) = = G A T = A = G G = G A = G A = = G = T = = = = C = T 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = C G T = = = = = = = = = = = = = = = = = = = = = = = = = = T C C 0 E004 (A) (C) = (G) (A) (T) = = (A) = = = = (G) = = = = = = = (C) (C) = = = (T) = (C) (G) (A) = (C) (G) (G) = = (G) = = = = (A) = = = = = = = (T) (G) = = = (C) = (T) 0 E005 (A) = = (G) (A) (T) = = A = = = (G) = (T) = = = (C) = = = = (G) (D) (G) (T) = = (G) = = (C) (G) (G) = = G = = = (A) = (C) = = = (A) = = = = (A) (I) (A) (C) = = 0 E006 = = (C) G A = = = = = = = = A T = = = = = C T G = = = = = T = = (T) C G = = = = = = = = G C = = = = = T C C = = = = = C 0 E007 (A) = = = = = = = = = = = = = = = = = A = = = = A I A = = C (G) = = = = = = = = = = = = = = = = = C = = = = G D G = = T 0 E008 = = = = = = = = (A) = = = = = = = = = C = = = = G D G = = T = = = = = = = = (G) = = = = = = = = = A = = = = A I A = = C 0 E009 = (A) = = = = = = (G) = = = = (A) = = = = = = = T G G D G = = T = (C) = = = = = = (A) = = = = (G) = = = = = = = C C A I A = = C 0 E010 (G) = (T) C G = = = A = = = = = = = = = = = = = = A I A = = = (A) = (C) G A = = = G = = = = = = = = = = = = = = G D G = = = 0 E011 (A) (C) = G A T = A = G G = G = = G A = = G = = C = = = = C = (G) (A) = C G G = G = A A = A = = A C = = A = = G = = = = G = 0 E012 (A) (A) = (G) (A) = = = = = = = = A T = = = C = = T G G D G = = T (G) (C) = (C) (G) = = = = = = = = G C = = = A = = C C A I A = = C 0 E013 = = = (C) = = = = = = = = = (A) = = = = = = T = = = = = C (G) = = = = (G) = = = = = = = = = (G) = = = = = = C = = = = = T (C) = 0 E014 = = = = = = = = = = = = = (G) = = = = = = = C C = = = = (C) C = = = = = = = = = = = = = (A) = = = = = = = T G = = = = (G) T 0 E015 = (A) (T) G A = = (A) = = = = = A T = = = = = C T G = = = = (G) T = (C) (C) C G = = (G) = = = = = G C = = = = = T C C = = = = (C) C 0 E016 = = = C G G = G = A A = A G = A C = = A = = G = = = T = C = = = G A T = A = G G = G A = G A = = G = = C = = = C = T 0 E017 = (A) = = = = = = = = = = = = = = = = = = C = = A I A ? ? ? = (C) = = = = = = = = = = = = = = = = = = T = = G D G ? ? ? 0 E018 = = (C) C G G = G = A A = A G = A C = = A = C = = = = T = C = = (T) G A T = A = G G = G A = G A = = G = T = = = = C = T 0 E019 = = = = = = = = A = = = = = = = = = C = = = = G D G ? ? ? = = = = = = = = G = = = = = = = = = A = = = = A I A ? ? ? 0 E020 = (A) = = = = = = A = = = = = = = = = = = = C C = = = T (C) C = (C) = = = = = = G = = = = = = = = = = = = T G = = = C (G) T 0 E021 = = = = (A) (T) = = = = = = (G) = (T) = A = A G = = C A I A C = = = = = = (G) (G) = = = = = = (A) = (C) = C = C A = = G G D G T = = 0 E022 (A) = = = = = = = = = = = = = = = = = = = = = = = = = T C C (G) = = = = = = = = = = = = = = = = = = = = = = = = = C G T 0 E023 = = (C) C G G = = (G) = = = (A) (G) (C) = = = = = = = = (A) (I) (A) = (G) (T) = = (T) G A T = = (A) = = = (G) (A) (T) = = = = = = = = (G) (D) (G) = (C) (C) END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.51 = = 0.62 0.62 0.62 = = 0.56 = = = = = = = = = = = = 0.99 0.99 = 0.99 0.99 ? ? ? 0.59 = = = = 1.00 = = 0.99 ? = = = = = = 0.76 = = = = = = 0.96 0.96 = ? ? ? 0.62 = = 0.99 0.99 = = = = = = = = 0.99 0.99 = = = = = = = = = = = = = ? 0.69 = = = = = = = 0.95 = = = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 1.00 ? ? ? = = = 0.98 0.98 0.98 1.00 = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = 0.56 0.56 ? ? ? = = = 0.88 0.88 = = = 0.87 = = = = = = = 0.62 = = = = = = = = = ? ? ? 0.51 = = = = = = = 0.63 = = = = 0.90 = = 0.90 = = = = 0.95 0.95 = = = ? ? ? 0.58 = = 0.83 0.83 = = = = ? = = 0.88 = 0.88 0.82 0.82 = = = = 0.82 0.82 = = 0.52 ? ? ? = = 0.53 0.99 0.99 = = = 0.96 = = = 0.86 = 0.86 = = = = = = = = = = = = = = 0.78 = = 0.77 0.77 = = = = = = = = = = = = = = = = = = = 0.82 0.82 = = = = = = = = = = = = = = = 0.63 = = = = 1.00 = = = = = = = = = = = 0.51 = = = = = = = = = = = 0.72 = = = 0.67 = = = = 0.89 = = 0.96 0.96 = = 0.98 0.59 = = 0.99 0.99 = = = = = = = = 1.00 0.99 = = = = = = 0.61 = = = = = = = 0.61 0.66 = = = = = = = = = = = 0.95 = = 0.95 = = = = 1.00 1.00 = = = 0.98 = 0.98 0.64 = = 0.95 0.95 = = = = = = = = 0.97 = = = 0.98 = = = 1.00 1.00 = 1.00 1.00 = = 0.99 = 0.63 0.53 = = = = = 0.79 = = = = 0.56 = = 0.87 = = 0.95 = = 0.95 = = = = = = = = = = = = = = = = = = 0.91 = ? = 0.92 = = = = = = = = = = = 0.95 0.54 = = 1.00 1.00 1.00 0.98 = = = = 0.98 0.98 0.95 = = = = = = = 0.74 = = 0.73 0.73 = = 0.73 = = = 0.85 0.85 0.85 = = = = = 0.96 0.98 0.98 0.96 = = ? = = = 0.91 0.90 = = = = = = = = = 0.97 0.97 = = = = = = = = = 0.98 = 0.98 = = = = = = = = = 0.78 = 0.78 0.59 = 0.57 0.97 0.97 0.97 = = 0.98 = = = 0.94 0.94 0.94 = = = = = = 0.88 = = 0.80 = = 0.82 0.78 = = = = = 0.96 0.98 = = = = 0.98 = = = = 1.00 = = = = = = = 0.59 0.59 0.59 = = 0.60 = 0.58 = = = = = 0.89 = = = 1.00 1.00 1.00 = 0.71 = = = = 1.00 1.00 = = = = = 0.97 = 0.72 = 0.98 0.98 = = = = = = = 0.99 = 0.99 = = = = = = = = = = = 0.93 = = = = 0.68 = 0.84 = = = = = = = = = 0.88 1.00 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 = = 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 0.95 0.99 0.71 0.73 = 0.75 0.75 0.75 = = 0.72 = = = = 0.82 = = = = = = = 0.84 0.84 = = = 0.83 = 0.83 0.50 = = 0.69 0.69 0.70 = = 0.92 = = = 0.71 = 0.71 = = = 0.89 = = = = 0.89 0.89 0.89 0.90 = = = = 0.60 0.98 0.98 = = = = = = = = 0.99 0.99 = = = = = 0.99 0.99 0.99 = = = = = 0.98 0.58 = = = = = = = = = = = = = = = = = 0.99 = = = = 1.00 1.00 1.00 = = 0.99 = = = = = = = = 0.88 = = = = = = = = = 1.00 = = = = 1.00 1.00 1.00 = = 0.98 = 0.55 = = = = = = 0.54 = = = = 0.54 = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = 0.93 0.50 = 0.54 0.99 0.99 = = = 0.99 = = = = = = = = = = = = = = 0.99 0.99 0.99 = = = 0.55 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 = 0.62 0.55 = 0.87 0.87 = = = = = = = = 0.91 0.91 = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = 0.59 = = = = = = = = = 0.78 = = = = = = 0.98 = = = = = 0.98 0.74 = = = = = = = = = = = = = = 0.54 = = = = = = = 1.00 1.00 = = = = 0.73 0.98 = 0.70 0.66 0.97 0.97 = = 0.50 = = = = = 0.97 0.97 = = = = = 0.99 0.99 0.99 = = = = 0.68 0.99 = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 0.98 = 1.00 1.00 = = 1.00 = = 1.00 = = = 0.94 = 0.93 = 0.65 = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 ? ? ? = = 0.66 0.99 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 = = = = = = = = 0.91 = = = = = = = = = 1.00 = = = = 1.00 1.00 1.00 ? ? ? = 0.54 = = = = = = 0.91 = = = = = = = = = = = = 1.00 1.00 = = = 1.00 0.90 1.00 = = = = 0.52 0.52 = = = = = = 0.54 = 0.52 = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = 0.53 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 0.95 1.00 = = 0.50 0.92 0.92 0.92 = = 0.74 = = = 0.89 0.90 0.90 = = = = = = = = 0.62 0.62 0.62 = 0.60 0.69 END PHASEPROBS