************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 il21r.phase.inp il21r.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il21r.phase.out_freqs : haplotype frequency estimates il21r.phase.out_pairs : most likely haplotype pairs for each individual il21r.phase.out_recom : estimates of recombination parameters il21r.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 65 Positions of loci: 811 1260 2276 2323 2324 2361 3367 3400 3535 3674 3677 3767 4127 5498 5518 5696 6348 6664 6875 6923 7246 7337 7556 7916 8033 8205 8346 8712 8713 8900 9042 10080 10150 11247 11905 12019 13547 13560 13787 14281 14464 14469 14473 15562 15614 17426 17547 17927 18020 19132 19479 20024 20384 20924 20941 20982 21766 22499 23303 23763 23934 24067 24387 24557 26314 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il21r.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 AICCCIGDCTCCGCGGTGTCGGTAAGIGTCCCGGCGCIICCAGCAATDACGTCGGACGGGGCCCC 1.000000 2 AICCCIADCCCTGCGGCAGCGACAAGIGTCCCGGTGCIICCAGCTGCICCCGCAAGTGGAGACGT 1.000000 3 AICCCIADCCTTGCGGCAGCGACCTGIGTCCCAACGAIDCAAGCAATDACGTCGGACGGGGCCCC 1.000000 4 AICCCIADCCTTGCGGCAGCGACAAGIGTCCCAACGAIDCCAGCAATDAAGTCGGACGGGGCCCC 1.000000 5 AICCCIAICCCTGCGGTAGCGACCACDGTCCCGACGCIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 6 AICCCIAICCCTGCGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 7 AICCCIAICCCTGCGGCAGCGACCACDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 8 AICCCIAICCCTGCGGCAGCGACCTGDGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAAACGT 1.000000 9 AICCCIAICCCTGCGGCAGCGACAAGIGTCCCGGTGCIICCAGCTGCICCCGCAAGTGGAGACGT 1.000000 10 AICCCIAICCCTGCGGCAGCGACAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 11 AICCCIAICCCTGCGGCAGCGACAAGIGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAGACGT 1.000000 12 AICCCIAICCCTGCGGCAGCGACAAGIGTTCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 13 AICCCIAICCCTGCGGCAGCAACCACDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 14 AICCCIAICCTTGCGGTAGCGACCACDGTCCCAACGCIDCCAGCAGTIACCGGAAGCGAAGACGT 1.000000 15 AICCCIAICCTTGCGGTGTCGGTAAGIGTCCCAACGAIDCCAGCAATDAAGTCGGACGGGGCCCC 1.000000 16 AICCCIAICCTTGCGGCAGCGACCAGIACCCCAACGCIDCCAGCAGTIACCGGAAGCAGAGACGT 1.000000 17 AICCCIAICCTTGCGGCAGCGACCACDGTCCCGACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 18 AICCCIAICCTTGCGGCAGCGACCACDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 3.000000 19 AICCCIAICCTTGCGGCAGCGACCACDGTCCCAACGAIDCCGGCAGTIACCGGAAGCAGAAACGT 1.000000 20 AICCCIAICCTTGCGGCAGCGACCACDGTCTCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 21 AICCCIAICCTTGCGGCAGCGACCACIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 22 AICCCIAICCTTGCGGCAGCGGTAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 23 AICCCIAICCTTGCGGCGGCGACCACDGTCCCAACAAIDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 24 AICCCIAICCTTGTGGTGTCGGTAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 25 AICTGDGDCCTCGCGGCGTCGGCCACDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 26 AICTGDGDCTCTACGACAGCGACCAGIGTCCCGACGAIDCAAGCAATDAAGTCGGACGGGGCCCC 1.000000 27 AICTGDGDCTCTACGACAGCGACCAGIGTCCCAACGCIDCCAGCAGTIACCGGAAGCGAAGACGT 1.000000 28 AICTGDGDCTCTACGACAGCGACCAGIGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAGACGT 1.000000 29 AICTGDGDCTCTACGACAGCGACCTGIGTCCCAACGAIICCAGCAATDACGTCAGACGGGGCCCC 1.000000 30 AICTGDGDCTCTACGGCAGCGACCAGIACCCCAACGCIDCCAGCAGTIACCGGAAGCGAAGACGT 1.000000 31 AICTGDGDCTCTACAACAGCGACCTGDGTCCCAACGADDCCAGCAATDACGTCAAGCGGGGCCCC 1.000000 32 AICTGDGDCTCTACAACAGCGACCTGDGTCCCAACGCIDCCGACAGTIACCGGAAGCGAAGACGT 1.000000 33 AICTGDGDCTCTACAGCAGCGACCAGDACCCCGACGCIDCCGACAATDACGTCGGACGGGGCCCC 1.000000 34 AICTGDGDCTCTATGGTGTCGGTCAGDGTCCCAACGAIDCCAGCAATDAAGTCAGACGGGGCCCC 1.000000 35 AICTGDGDCTCTATGGTGTCGGTCAGDGTCCCAACGAIDCCAGCAATDAAGTCGGACGGGGCCCC 1.000000 36 AICTGDGDCTCTATGGTGTCGGTCAGDGTCCCAACGCIDCCGACAGTIACCGGAAGCGAAGACGT 1.000000 37 AICTGDGDCTCTGCGACAGCGACCAGIGTTCCGGCGCIICCAGCTGCICCCGCAAGCGGAGACGT 1.000000 38 AICTGDGDCTCTGCGGTGTCGATAAGDGTCCCGGTGCIICCAGCTGCICCCGCAAGTGGAGACGT 1.000000 39 AICTGDGDCTCTGCGGCAGTGACCAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 40 AICTGDGDCTCCGCGGTGTCGGTCAGIGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAAACGT 1.000000 41 AICTGDGDCTCCGCGGTGTCGGTCTGDGTCCCAACGCIDCCGACAGTIACCGGAAGCAGAAACGT 1.000000 42 AICTGDGDCTCCGCGGTGTCGGTAAGDGTCCCAACGCIDCCGGTAGTIACCGGAAGCAGAAACGT 1.000000 43 AICTGDGDCTCCGCGGTGTCGGTAAGIGTCCCGGCGCIICAGGCAATDACGTCGGACGGGGCCCC 1.000000 44 AICTGDGDCTCCGCGGCAGCGACCAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 45 AICTGDGDCTCCGCGGCAGCGACCAGIACCCCAACGCIDCCAGCAGTIACCGGAAGCGAAGACGT 1.000000 46 AICTGDGDCTCCGCGGCAGTGACCAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGACCC 1.000000 47 AICTGDGDCTCCGCGGCAGTGACCAGIGTCCCAACGAIDTCAGCAATDACGTCGGACGGGGCCCC 1.000000 48 AICTGDGDCTCCGCGGCGTCGGTCAGIACTCCAACGCIDCCAGCAGTIACCGGAAGCGAAGACGT 1.000000 49 AICTGDGDCTCCGTGGTGTCGATCAGIGTCCCGACGAIDCCGGCAATDACGTCGGACGGGGCCCC 1.000000 50 AICTGDGDCTCCGTGGTGTCGATCAGIGTCCCGACAAIDCAGGCAATDACGTCGGACGGGGCCCC 1.000000 51 AICTGDGDCTCCGTGGTGTCGATCAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 52 AICTGDGDCTCCGTGGTGTCGGTCAGIGTCCCGACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 53 AICTGDGDCTCCGTGGTGTCGGTCAGIGTCCCGACGAIDCCGGCAATDACGTCGGACGGGGCCCC 1.000000 54 AICTGDGDCTCCGTGGTGTCGGTCAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 55 AICTGDGDCTCCGTGGTGTCGGTAAGDGTCCCGGTGCIICCGGCTGCIACCGCAAGCGGGGCCCC 1.000000 56 AICTGDGDCTCCGTGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 57 AICTGDGDCTCCGTGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCTCC 1.000000 58 AICTGDGDCTCCGTGGTGTCGGTAAGDGTCTCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 59 AICTGDGDCTCCGTGGTGTCGGTAAGIGTCCCGGTGCIICCAGCTGCICCCGCAAGCGGGGCCCC 1.000000 60 AICTGDGDCTCCGTGGTGTCGGTAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCTCC 2.000000 61 AICTGDGDCTCCGTGGTGTCAGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 62 AICTGDGDCTCCGTGGCGTCGGTAAGDGTCCCGGTGCIICCGGCTGCIACCGCAAGCGGGGCCCC 1.000000 63 AICTGIGDCTCCGTGGTGTCGGTAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCTCC 1.000000 64 AITCCIAICCTTGCGGCAGCGACCACDGTCCCGACGCIDCCGGCAATDAAGTCGGACGGGGCCCC 1.000000 65 AITTGDGDCTCCGCGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDAAGTCGGACGGGGCCCC 1.000000 66 AITTGDGDCTCCGCGGTGTCGGTAAGDGTCCCAACGAIDCCGGCAATDACGTCGGACGGGGCCCC 1.000000 67 ADCCCIGDCCTTGCGGCAGTGACCAGDGTCCCGGCGCIDCAAGCAATDACGTCGGACGGGGCCCC 2.000000 68 ADCCCIGDCCTTGCGGCAGTGACCAGIGTCCCAACGAIDTCAGCAATDACGTCGGACGGGGCCCC 1.000000 69 ADCCCIGDTCCTGTGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 70 ADCCCIGDTCCTGTGGTGTCGGTAAGDGTCCCAACGAIDCCGGCAATDACGTCGGACGGGGCCCC 1.000000 71 ADCCCIGDTCTTGCGACAGCGACCTGDGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAAACGT 1.000000 72 ADCCCIGDTCTTGTGGTGTCGGTAAGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 73 GICCCIGICCTTGCGGCGGCGACCACDGTCCTAACGCIDCCAGTAGTIACCGGAAGCAGAAACGT 1.000000 74 GICCCIGICCTTGCGGCGGCGACCACDGTCCTAACGCIDCCGGTAGTIACCGGAAGCAGAAACGT 1.000000 75 GICTGDGDCTCTACGACAGCGACCTGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 76 GICTGDGDCTCTACGACAGCGACCTGDGTCCCAACGADDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 77 GICTGDGDCTCTACGACAGCGACCTGDGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAAACGT 2.000000 78 GICTGDGDCTCTACGACAGCGACCTGDGTCCCAACGCIDCCGGTAGTIACCGGAAGCAGAAACGT 1.000000 79 GICTGDGDCTCTACGACAGCGACCTGDGTCCCAACAAIDCCAGCAATDACGTCGGACGGGGCCCC 1.000000 80 GICTGDGDCTCTATGGTGTCGGTAAGIGTCCCAACGCIDCCAGCAGTIACCGGAAGCAGAAACGT 1.000000 81 GICTGDGDCTCTATGGTGTCAGTAAGDGTCCTAACGCIDCCGGTAGTIACCGGAAGCAGAAACGC 1.000000 82 GICTGDGDCTCTATGGTGTCAGTAAGIGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 83 GICTGDGDCTCTGCGGCAGCGACCTGDGTCCCAACGAIDCCAGCAATDACGTCGGACGGGGCCCC 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (14,35) D002: (9,38) D003: (31,48) D004: (28,34) D005: (29,45) D006: (24,27) D007: (46,76) D008: (10,20) D009: (16,52) D010: (11,70) D011: (37,67) D012: (5,12) D013: (47,68) D014: (36,41) D015: (1,51) D016: (39,77) D033: (58,75) D034: (49,53) D035: (32,33) D036: (2,13) D037: (43,50) D038: (30,4) D039: (39,59) D040: (26,67) E001: (78,81) E002: (21,76) E003: (18,75) E004: (23,61) E005: (25,57) E006: (18,77) E007: (6,8) E008: (22,82) E009: (64,42) E010: (19,62) E011: (56,65) E012: (40,60) E013: (66,71) E014: (17,83) E015: (55,74) E016: (7,69) E017: (44,72) E018: (3,54) E019: (23,73) E020: (80,82) E021: (18,83) E022: (15,79) E023: (60,63) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 A I C C C I A I C C T T G C G G T A G C G A C C A [C] [D] G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C G A A G A C G T A I C T G D G D C T C T A T G G T G T C G G T C A G D G T C C C A A C G A I D C C A G C A A T D A A G T C G G A C G G G G C C C C 0 D002 A I C C C I A I C C C T G C G G (C) (A) (G) C G A (C) A A G (I) G T C C C G G T G C I I C C A G C T G C [I] C C C G C A A G T G G A G A C G T A I C T G D G D C T C T G C G [G] (T) (G) (T) C G A (T) A A G (D) G T C C C G G T G C I I C C A G C T G C [I] C C C G C A A G T G G A G A C G T 0 D003 A I C T G D G D C T C T A C A A C A G C G A C C [T] G D G T C C C A A C G A D D C C A G C A A T D A C G T C A A G C G G G G C C C C A I C T G D G D C T C C G C G G C G T C G G T C A G I A C T C C A A C G C I D C C A G C A G T I A C C G G A A G C G A A G A C G T 0 D004 A I C T G D G D C T C T A (C) G (A) (C) (A) (G) C G (A) (C) C [A] G [I] G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A G A C G T A I C T G D G D C T C T A (T) G (G) (T) (G) (T) C G (G) (T) C A G [D] G T C C C A A C G A I D C C A G C A A T D A A G T C A G A C G G G G C C C C 0 D005 A I C T G D G D C T C T A C [G] A C A G C G A C C T G I G T C C C A A C G A I I C C A G C A A T D A C G T C A G A C G G G G C C C C A I C T G D G D C T C C G C G G C A G C G A C C A G I [A] [C] C C C A A C G C I D C C A G C A G T I A C C G G A A G C G A A G A C G T 0 D006 A I C (C) (C) (I) (A) (I) C (C) (T) T (G) (T) G (G) (T) (G) (T) C G (G) (T) (A) A G I G T C C C A A C G (A) I D C C A G C A (A) T (D) A C (G) (T) (C) (G) (G) (A) C G (G) [G] G (C) C (C) (C) A I C (T) (G) (D) (G) (D) C (T) (C) T (A) (C) G (A) (C) (A) (G) C G (A) (C) (C) A G I G T C C C A A C G (C) I D C C A G C A (G) T (I) A C (C) (G) (G) (A) (A) (G) C G (A) [A] G (A) C (G) (T) 0 D007 A I C T G D G D C T C C G C G G C A G T G A C C A G D G T C C C A A C G A (I) D C C A G C A A T D A C G T C G G A C G G G G (A) C C C G I C T G D G D C T C T A C G A C A G C G A C C T G D G T C C C A A C G A (D) D C C A G C A A T D A C G T C G G A C G G G G (C) C C C 0 D008 A I C C C I A I C C C T G C G G C A G C G A C A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A I C C C I A I C C [T] T G C G G C A G C G A C C [A] [C] D G T C T C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D009 A I C (C) (C) (I) (A) (I) C (C) (T) (T) G (C) G G (C) (A) (G) C G (A) (C) C A G I (A) (C) C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A G A C G T A I C (T) (G) (D) (G) (D) C (T) (C) (C) G (T) G G (T) (G) (T) C G (G) (T) C A G I (G) (T) C C C G A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D010 A (I) C C C I (A) (I) (C) C C T G [C] G G (C) (A) (G) C G (A) (C) A A G (I) G T C C C A A C G C I D C C (A) G C A G T I A C C G G A A G C A G A G A C G T A (D) C C C I (G) (D) (T) C C T G [T] G G (T) (G) (T) C G (G) (T) A A G (D) G T C C C [A] A C G A I D C C (G) G C A A T D A C G T C G G A C G G G G C C C C 0 D011 A (I) C (T) (G) (D) G D C (T) (C) T G C G (A) C A G (C) G A C C A G I [G] [T] T C C G G C G C I I C C A G C T G C I C C C G C A A G C G G A G A C G T A (D) C (C) (C) (I) G D C (C) (T) T G C G (G) C A G (T) G A C C A G D G T C C C G G C G C I D C A A G C A A T D A C G T C G G A C G G G G C C C C 0 D012 A I C C C I A I C C C T G C G G (T) A G C G A C C A C D G T (C) C C (G) A C G (C) I D C C A G C A A T D A C G T C G G A C G G G G C C C C A I C C C I A I C C C T G C G G (C) A G C G A C A A G [I] G T (T) C C (A) A C G (A) I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D013 A I C T G D G D C T C C G C G G C A G T G A C C A G I G T C C C A A C G A I D T C A G C A A T D A C G T C G G A C G G G G C C C C A D C C C I G D C C T T G C G G C A G T G A C C A G I G T C C C A A C G A I D T C A G C A A T D A C G T C G G A C G G G G C C C C 0 D014 A I C T G D G D C T C (T) (A) (T) G G T G T C G G T C (A) G D G T C C C A A C G C I D C C G A C A G T I A C C G G A A G C (G) (A) A (G) A C G T A I C T G D G D C T C (C) (G) (C) G G T G T C G G T C (T) G D G T C C C A A C G C I D C C G A C A G T I A C C G G A A G C (A) (G) A (A) A C G T 0 D015 A I C (C) (C) (I) G D C T C C G (C) G G T G T C G (G) T (A) A G I G T C C C (G) (G) C G [C] I (I) C C A G C A A T D A C G T C G G A C G G G G C C C C A I C (T) (G) (D) G D C T C C G (T) G G T G T C G (A) T (C) A G I G T C C C (A) (A) C G A I (D) C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D016 (A) I C T G D G D C T C T (G) C G (G) C A G [T] G A C C (A) G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C (G) I C T G D G D C T C T (A) C G (A) C A G [C] G A C C (T) G D G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A A A C G T 0 D033 A I C T G D G D C T C C G T G G T G T C G G T [A] A G D G T C (T) C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T A C G A C A G C G A C C T G D G T C (C) C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D034 A I C T G D G D C T C C G T G G T G T C G A T C A G I G T C C C G A C G [A] I D C C G G C A A T D A C G T C G G A C G G G G C C C C A I C T G D G D C T C C G T G G T G T C G G T C A G I G T C C C G A C G [A] I D C C G G C A A T D A C G T C G G A C G G G G C C C C 0 D035 A I C T G D G D C T C T A C A (A) C A G C G A C C (T) G D (G) (T) C C C (A) A C G C I D C C G A C A G T I A C C G G A A G C G A A G A C G T A I C T G D G D C T C T A C A (G) C A G C G A C C (A) G D (A) (C) C C C (G) A C G C I D C C G A C A A T D A C G T C G G A C G G G G C C C C 0 D036 A I C C C I A (D) C C C T G C G G C A G C (G) A C A A G I G T C C C G G T G C I I C C A G C T G C [I] C C C G C A A G T G G A G A C G T A I C C C I A (I) C C C T G C G G C A G C (A) A C C A C D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 D037 A I C T G D G D C T C C G C G G T G T C G G T A A G I G T C C C G G C (G) C I (I) C A G G C A A T D A C G T C G G A C G G G G C C C C A I C T G D G D C T C C G T G G T G T C G A T C A G I G T C C C G A C (A) [A] I (D) C A G G C A A T D A C G T C G G A C G G G G C C C C 0 D038 A I C (T) (G) (D) (G) [D] C (T) (C) T (A) C G G C A G C G A C (C) A G I (A) (C) C C C A A C G C I D C C A G C A G T I A C C G G A A G C G A A G A C G T A I C (C) (C) (I) (A) [D] C (C) (T) T (G) C G G C A G C G A C (A) A G I (G) (T) C C C A A C G A I D C C A G C A A T D A A G T C G G A C G G G G C C C C 0 D039 A I C T G D G D C T C (T) G (C) G G (C) (A) (G) (T) G (A) (C) (C) A G (D) G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A I C T G D G D C T C (C) G (T) G G (T) (G) (T) (C) G (G) (T) (A) A G (I) G T C C C G G T G C I I C C A G C T G C I C C C G C A A G C G G G G C C C C 0 D040 A I C T G D G D C T C T A C G A C A G C G A C C A G (I) G T C C C G (A) C G [A] I D C A A G C A A T D A A G T C G G A C G G G G C C C C A D C C C I G D C C T T G C G G C A G T G A C C A G (D) G T C C C G (G) C G [C] I D C A A G C A A T D A C G T C G G A C G G G G C C C C 0 E001 G I C T G D G D C T C T A C G A C A G C G A C C T G D G T C C (C) A A C G C I D C C G G T A G T I A C C G G A A G C A G A A A C G (T) G I C T G D G D C T C T A T G G T G T C A G T A A G D G T C C (T) A A C G C I D C C G G T A G T I A C C G G A A G C A G A A A C G (C) 0 E002 A I C C C I A I C C T T G C G G C A G C G A C C A C (I) G T C C C A A C G A (I) D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T A C G A C A G C G A C C T G (D) G T C C C A A C G A (D) D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E003 A I C C C I A I C C T T G C G G C A G C G A C C A C D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T A C G A C A G C G A C C T G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E004 A I C C C I A I C C T T G C G G C G G C (G) A C C A C D G T C C C A A C A A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A I C T G D G D C T C C G T G G T G T C (A) G T A A G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E005 A I C T G D G D C (C) (T) C G (C) G G (C) G T C G G C C A C D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C (C) C C A I C T G D G D C (T) (C) C G (T) G G (T) G T C G G T A A G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C (T) C C 0 E006 (A) I C (C) (C) (I) (A) (I) C (C) (T) T (G) C G [G] C A G C G A C C (A) (C) D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C (G) I C (T) (G) (D) (G) (D) C (T) (C) T (A) C G [A] C A G C G A C C (T) (G) D G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A A A C G T 0 E007 A I C C C I A I C C C T G C G G (T) (G) (T) C G (G) (T) (A) (A) G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A I C C C I A I C C C T G C G G (C) (A) (G) C G (A) (C) (C) (T) G D G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A A A C G T 0 E008 A I C C C I A I C C T T G C G G C A G C (G) G T A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T A T G G T G T C (A) G T A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E009 A I (T) (C) (C) (I) (A) (I) C (C) (T) (T) G C G G (C) (A) (G) C G (A) (C) (C) A (C) D G T C C C (G) A C G C I D C C G G C A A T D A (A) G T C G G A C G G G G C C C C A I (C) (T) (G) (D) (G) (D) C (T) (C) (C) G C G G (T) (G) (T) C G (G) (T) (A) A (G) D G T C C C (A) A C G C I D C C G G T A G T I A (C) C G G A A G C A G A A A C G T 0 E010 A I C (C) (C) (I) (A) (I) C (C) (T) (T) G (C) G G C (A) (G) C G (A) (C) (C) A (C) D G T C C C A A C G A I D C C G G C A G T I A C C G G A A G C A G A A A C G T A I C (T) (G) (D) (G) (D) C (T) (C) (C) G (T) G G C (G) (T) C G (G) (T) (A) A (G) D G T C C C G G T G C I I C C G G C T G C I A C C G C A A G C G G G G C C C C 0 E011 A I C T G D G D C T C C G T G G T G T C G G T A A G D G T C C C A A C G A I D C C A G C A A T D A (C) G T C G G A C G G G G C C C C A I T T G D G D C T C C G C G G T G T C G G T A A G D G T C C C A A C G A I D C C A G C A A T D A (A) G T C G G A C G G G G C C C C 0 E012 A I C T G D G D C T C C G (C) G G T G T C G G T (C) A G I G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A A A C G T A I C T G D G D C T C C G (T) G G T G T C G G T (A) A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C T C C 0 E013 A (I) (T) (T) (G) (D) G D (C) (T) (C) (C) G C G G T G T C G G T A A G D G T C C C A A C G A I D C C (G) G C A A T D A C G T C G G A C G G G G C C C C A (D) (C) (C) (C) (I) G D (T) (C) (T) (T) G C G A C A G C G A C C T G D G T C C C A A C G C I D C C (A) G C A G T I A C C G G A A G C A G A A A C G T 0 E014 A I C C C I A I C C T T G C G G C A G C G A C C A C D G T C C C (G) A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T G C G G C A G C G A C C T G D G T C C C (A) A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E015 (A) I C (T) (G) (D) G (D) C (T) (C) (C) G (T) G G (T) G (T) C G (G) (T) (A) A (G) D G T C C C G G T G C I I C C G G C T G C I A C C G C A A G C G G G G C C C C (G) I C (C) (C) (I) G (I) C (C) (T) (T) G (C) G G (C) G (G) C G (A) (C) (C) A (C) D G T C C T A A C G C I D C C G G T A G T I A C C G G A A G C A G A A A C G T 0 E016 A I C C C I A I C C C T G C G G C A G C G A C C A C D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A D C C C I G D T C C T G T G G T G T C G G T A A G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E017 A (I) C (T) (G) (D) G D (C) (T) (C) (C) G (C) G G C (A) (G) C G (A) (C) (C) A G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C A (D) C (C) (C) (I) G D (T) (C) (T) (T) G (T) G G T (G) (T) C G (G) (T) (A) A G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E018 A I C C C I A D C C T T G C G G C A G C G A C C T G I G T C C C A A C G A I D C (A) A G C A A T D A C G T C G G A C G G G G C C C C A I C T G D G D C T C C G T G G T G T C G G T C A G I G T C C C A A C G A I D C (C) A G C A A T D A C G T C G G A C G G G G C C C C 0 E019 (A) I C C C I (A) I C C T T G C G G C G G C G A C C A C D G T C C C A A C A A I D C C A G C A A T D A C G T C G G A C G G G G C C C C (G) I C C C I (G) I C C T T G C G G C G G C G A C C A C D G T C C T A A C G C I D C C A G T A G T I A C C G G A A G C A G A A A C G T 0 E020 G I C T G D G D C T C T A T G G T G T C (G) G T A A G I G T C C C A A C G C I D C C A G C A G T I A C C G G A A G C A G A A A C G T G I C T G D G D C T C T A T G G T G T C (A) G T A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E021 A I C C C I A I C C T T G C G G C A G C G A C C A C D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C G I C T G D G D C T C T G C G G C A G C G A C C T G D G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C C C C 0 E022 A I C C C I A I C C T T G C G G T G T C G G T A A G (I) G T C C C A A C (G) A I D C C A G C A A T D A (A) G T C G G A C G G G G C C C C G I C T G D G D C T C T A C G A C A G C G A C C T G (D) G T C C C A A C (A) A I D C C A G C A A T D A (C) G T C G G A C G G G G C C C C 0 E023 A I C T G D G D C T C C G T G G T G T C G G T A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C T C C A I C T G I G D C T C C G T G G T G T C G G T A A G I G T C C C A A C G A I D C C A G C A A T D A C G T C G G A C G G G G C T 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 = = = C C I ? ? = C T = G C = ? = A G = = A C = ? ? ? ? ? ? ? ? ? = = ? C = = ? = = = ? ? G = I = C C G G A A G = = A ? = A = G ? = = = T G D ? ? = T C = A T = ? = G T = = G T = ? ? ? ? ? ? ? ? ? = = ? A = = ? = = = ? ? A = D = A G T C G G A = = G ? = C = C ? 0 D002 = = = C ? I ? I = C = = = = = ? (C) (A) (G) = = = (C) = ? ? (I) = = = = = = = = = = = = ? ? ? ? = = = = ? ? = = = = = = = = = = = = = = = ? = = = T ? D ? D = T = = = = = ? (T) (G) (T) = = = (T) = ? ? (D) = = = = = = = = = = = = ? ? ? ? = = = = ? ? = = = = = = = = = = = = = = = ? 0 D003 = = = = = = ? ? = = = T A = A A = A G = = A C = ? ? D G T C = = = = = = A D = = = = = = = A = D = = G T C = = ? = = G ? = C = C C = = = = = = ? ? = = = C G = G G = G T = = G T = ? ? I A C T = = = = = = C I = = = = = = = G = I = = C G G = = ? = = A ? = A = G T 0 D004 = = = = = = = = = = = = = (C) = (A) (C) (A) (G) = = (A) (C) = ? ? ? = = = = = = = = = C = = = = = = = = G = ? ? C C G G = A G = A = ? = A = G T = = = = = = = = = = = = = (T) = (G) (T) (G) (T) = = (G) (T) = ? ? ? = = = = = = = = = A = = = = = = = = A = ? ? A G T C = G A = G = ? = C = C C 0 D005 = = = = = = = = = = = T A = ? A = = = = = = = = T = = ? ? = = = = = = = A = I = = = = = = A = D = = G T C = ? A = = G ? = C = C C = = = = = = = = = = = C G = ? G = = = = = = = = A = = ? ? = = = = = = = C = D = = = = = = G = I = = C G G = ? G = = A ? = A = G T 0 D006 = = = (C) (C) (I) (A) (I) = (C) (T) = (G) (T) = (G) (T) (G) (T) = = (G) (T) (A) = = = = = = ? = = = = = (A) = = = = = = = = (A) = (D) = = (G) (T) (C) (G) (G) (A) = = (G) ? = (C) = (C) (C) = = = (T) (G) (D) (G) (D) = (T) (C) = (A) (C) = (A) (C) (A) (G) = = (A) (C) (C) = = = = = = ? = = = = = (C) = = = = = = = = (G) = (I) = = (C) (G) (G) (A) (A) (G) = = (A) ? = (A) = (G) (T) 0 D007 A = = = = = = = = = = C G = = G = = = T = = = = ? = = = = = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = = (A) = = = G = = = = = = = = = = T A = = A = = = C = = = = ? = = = = = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = = (C) = = = 0 D008 = = = = = = ? ? = = ? = = = = = = = = = = = = A ? ? I = = = C = = = = ? = = = = ? ? ? = = = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = ? ? = = ? = = = = = = = = = = = = C ? ? D = = = T = = = = ? = = = = ? ? ? = = = ? = = = = = = = = = = = = ? ? ? = = = 0 D009 = = = (C) (C) (I) (A) (I) = (C) (T) (T) ? (C) ? = (C) (A) (G) = = (A) (C) = = = = (A) (C) = ? = A = ? = C = = = = = = = = G ? I = ? C G G A A G = A ? A = A = G ? = = = (T) (G) (D) (G) (D) = (T) (C) (C) ? (T) ? = (T) (G) (T) = = (G) (T) = = = = (G) (T) = ? = G = ? = A = = = = = = = = A ? D = ? G T C G G A = G ? G = C = C ? 0 D010 = (I) = = = = (A) (I) (C) = = = = ? ? = (C) (A) (G) = = (A) (C) = = = (I) = = = = = ? = = = C = = = = (A) = = = G = I = = C G G A A G = A = ? = A = G ? = (D) = = = = (G) (D) (T) = = = = ? ? = (T) (G) (T) = = (G) (T) = = = (D) = = = = = ? = = = A = = = = (G) = = = A = D = = G T C G G A = G = ? = C = C ? 0 D011 = (I) = (T) (G) (D) = = = (T) (C) = = = = (A) = = = (C) = = = = = = I ? ? T = = = = = = = = I ? ? ? ? = T G C I C = C G = A A G = = = A = A = G T = (D) = (C) (C) (I) = = = (C) (T) = = = = (G) = = = (T) = = = = = = D ? ? C = = = = = = = = D ? ? ? ? = A A T D A = G T = G G A = = = G = C = C C 0 D012 = = = = = = = = = = = = = = = = (T) = = = = = = C = C ? = = (C) = = (G) = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = A = G ? = = (T) = = (A) = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D013 = I = T G D = = = T C C = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D = C C I = = = C T T = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D014 = ? = = = = = = = = = (T) (A) (T) = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) (A) = (G) = = = = = ? = = = = = = = = = (C) (G) (C) = = = = = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) (G) = (A) = = = = 0 D015 = = = (C) (C) (I) = = = = = = = (C) = = = = = = = (G) = (A) = = = = = = = = (G) (G) = = ? ? (I) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) (G) (D) = = = = = = = (T) = = = = = = = (A) = (C) = = = = = = = = (A) (A) = = ? ? (D) = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D016 (A) = = = = = = = = = = = (G) = = (G) = ? ? ? = = = = (A) = = = = = = = = = = = A = = ? = = = = = A = D = = G T C G G A = G = G G C = C C (G) = = = = = = = = = = = (A) = = (A) = ? ? ? = = = = (T) = = = = = = = = = = = C = = ? = = = = = G = I = = C G G A A G = A = A A A = G T 0 D033 A = = = = = = = = = = C G T = ? ? ? T = ? G ? ? A = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? G = = = = = = = = = = T A C = ? ? ? G = ? A ? ? T = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 D034 = = = = = = = = = = = = = = = = = = = = = A ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = G ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = ? 0 D035 = = = = = = = = = = = = = = = (A) = = = = = = = = (T) = = (G) (T) = ? = (A) = = = = = = = = = = = = G = I = = C G G A A G = = A A = A = G T = = = = = = = = = = = = = = = (G) = = = = = = = = (A) = = (A) (C) = ? = (G) = = = = = = = = = = = = A = D = = G T C G G A = = G G = C = C C 0 D036 = = = = = = = (D) = = = = = = = = = = = = (G) = = A = G I = = = = = G G T = ? ? I = = = = = T G C ? C = C G = A A G T = = A = A = G T = = = = = = = (I) = = = = = = = = = = = = (A) = = C = C D = = = = = A A C = ? ? D = = = = = A A T ? A = G T = G G A C = = G = C = C C 0 D037 = = = = = = = = = = = = = C = = = = = = = G = A = = = = = ? ? = = G = (G) ? ? (I) ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = A = C = = = = = ? ? = = A = (A) ? ? (D) ? = = = = = = = ? ? = = = = = = = = = = = = = = = = 0 D038 = = = (T) (G) (D) (G) ? = (T) (C) = (A) = = = = = = = = = = (C) = = = (A) (C) = = = = = = = ? = = = = = = = = G = I = C C G G A A G = = A A = A = G T = = = (C) (C) (I) (A) ? = (C) (T) = (G) = = = = = = = = = = (A) = = = (G) (T) = = = = = = = ? = = = = = = = = A = D = A G T C G G A = = G G = C = C C 0 D039 = = = = = = = = = = = (T) = (C) = = (C) (A) (G) (T) = (A) (C) (C) = ? (D) = = = = = A A C = A = D = = = = = A A T D A = G T = G G A = = = = = = = = = = = = = = = = = = = = (C) = (T) = = (T) (G) (T) (C) = (G) (T) (A) = ? (I) = = = = = G G T = C = I = = = = = T G C I C = C G = A A G = = = = = = = = = 0 D040 = I = T G D = = = T C = A ? ? A = = = C = = = = = = (I) = = = = = = (A) = = ? ? = ? = = = = = = = = = A = = = = = = = = = = = = = = = = D = C C I = = = C T = G ? ? G = = = T = = = = = = (D) = = = = = = (G) = = ? ? = ? = = = = = = = = = C = = = = = = = = = = = = = = = 0 E001 = = = = = = = = = = = = = C = ? C A G = G A C C T = = = = = = (C) = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = T = ? T G T = A G T A A = = = = = = (T) = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = (C) 0 E002 A = = C ? I A I = C T = G = = G = = = = = = = = A C (I) = = = = = = = = = = (I) = ? = = = = = ? ? = = = = = = = = = = = = = = = = = ? G = = T ? D G D = T C = A = = A = = = = = = = = T G (D) = = = = = = = = = = (D) = ? = = = = = ? ? = = = = = = = = = = = = = = = = = ? 0 E003 A = = C C I A I = C T = G = = G = = = = = = = = A C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? G = = T G D G D = T C = A = = A = = = = = = = = T G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 E004 = = = C C I A I = C T T = C = = C = G = (G) A C C = C = = = = = = = = = A = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = T G D G D = T C C = T = = T = T = (A) G T A = G = = = = = = = = = G = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0 E005 = = = = = = = = = (C) (T) = = (C) = = (C) = = = = = C C = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = (T) (C) = = (T) = = (T) = = = = = T A = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = 0 E006 (A) = = (C) (C) (I) (A) (I) = (C) (T) = (G) = = ? ? = = = = = = = (A) (C) = = = = = = = = = = A = = = = = = = = ? ? ? = = G T C G G A = G = ? G C = C C (G) = = (T) (G) (D) (G) (D) = (T) (C) = (A) = = ? ? = = = = = = = (T) (G) = = = = = = = = = = C = = = = = = = = ? ? ? = = C G G A A G = A = ? A A = G T 0 E007 = = = = = = = = = = = = = = = = (T) (G) (T) = = (G) (T) (A) (A) = = = = = = = = = = = A = = = = = = = = A = D = = G T C G G A = ? = G G C = C C = = = = = = = = = = = = = = = = (C) (A) (G) = = (A) (C) (C) (T) = = = = = = = = = = = C = = = = = = = = G = I = = C G G A A G = ? = A A A = G T 0 E008 A = = C C I A I = C T = G ? ? = C A G = (G) = = = = = = = = = = = = = = = = = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = G = = T G D G D = T C = A ? ? = T G T = (A) = = = = = = = = = = = = = = = = = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = 0 E009 = = (T) (C) (C) (I) (A) (I) = (C) (T) (T) = = = = (C) (A) (G) = = (A) (C) (C) = (C) = ? ? ? ? = (G) = = = = = = = = = = C = A ? ? = (A) G T C G G A = G = G G C = C C = = (C) (T) (G) (D) (G) (D) = (T) (C) (C) = = = = (T) (G) (T) = = (G) (T) (A) = (G) = ? ? ? ? = (A) = = = = = = = = = = T = G ? ? = (C) C G G A A G = A = A A A = G T 0 E010 = = = (C) (C) (I) (A) (I) = (C) (T) (T) = (C) = = = (A) (G) = = (A) (C) (C) = (C) = ? ? = = = A A C = A = D ? = = = = A = T = ? = = = G = = = = A = A A A = G ? = = = (T) (G) (D) (G) (D) = (T) (C) (C) = (T) = = = (G) (T) = = (G) (T) (A) = (G) = ? ? = = = G G T = C = I ? = = = = T = C = ? = = = C = = = = G = G G C = C ? 0 E011 = = C = = = = = = = = = = T = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = = = = = ? = = = = = = = = = T = = = = = = = = = = C = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = ? = = = = = = = 0 E012 = = = = = = = = = = = = = (C) = = = = = = = = = (C) = = = = = = = = = = = = C = = = = = = = = G = ? = = C G G A A G = A = A A A C G T = = = = = = = = = = = = = (T) = = = = = = = = = (A) = = = = = = = = = = = = A = = = = = = = = A = ? = = G T C G G A = G = G G C T C C 0 E013 = (I) (T) (T) (G) (D) = = (C) (T) (C) (C) = ? ? G T G T = = G T A A = = = = = = = = = = = A = = = = (G) = = = A = D = = G T C G G A = G = ? G C = C C = (D) (C) (C) (C) (I) = = (T) (C) (T) (T) = ? ? A C A G = = A C C T = = = = = = = = = = = C = = = = (A) = = = G = I = = C G G A A G = A = ? A A = G T 0 E014 A = = C C I A I = C T = = ? ? = = = = = = = ? = A C = = = = = = (G) = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = G = = T G D G D = T C = = ? ? = = = = = = = ? = T G = = = = = = (A) = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = 0 E015 (A) = = (T) (G) (D) = (D) = (T) (C) (C) = (T) = = (T) = (T) = = (G) (T) (A) = (G) = = = = = C G G T = = = I = ? = = C T = C = = = = = C = = = = G = G G C = C C (G) = = (C) (C) (I) = (I) = (C) (T) (T) = (C) = = (C) = (G) = = (A) (C) (C) = (C) = = = = = T A A C = = = D = ? = = T A = T = = = = = G = = = = A = A A A = G T 0 E016 = I = = = = A I C = = = = C = = C ? G = = A C C = C = = = = = = = = = = = = = ? = = = ? ? ? ? = = = ? = = = = = = = = = = = = = = = D = = = = G D T = = = = T = = T ? T = = G T A = G = = = = = = = = = = = = = ? = = = ? ? ? ? = = = ? = = = = = = = = = = = = = = 0 E017 = (I) = (T) (G) (D) = = (C) (T) (C) (C) ? (C) = = ? (A) (G) = = (A) (C) (C) = = = ? ? ? ? = = = ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = (D) = (C) (C) (I) = = (T) (C) (T) (T) ? (T) = = ? (G) (T) = = (G) (T) (A) = = = ? ? ? ? = = = ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = 0 E018 = = = C C I A = = C T T = C = = C A G = = A C = T = = = = = = = = = = = = = = = (A) = = ? ? = = = = = = = = = = = = ? = = = = ? ? ? = = = T G D G = = T C C = T = = T G T = = G T = A = = = = = = = = = = = = = = = (C) = = ? ? = = = = = = = = = = = = ? = = = = ? ? ? 0 E019 (A) = = = = = (A) = = = ? = = = = = = = = = = = = = = = = = = = = C = = = A A = = = = = = C = A = D = = G T C G G A = ? = ? G C = C C (G) = = = = = (G) = = = ? = = = = = = = = = = = = = = = = = = = = T = = = G C = = = = = = T = G = I = = C G G A A G = ? = ? A A = G T 0 E020 = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = C = = = = = = = = G = I = = C G G A A G = A = ? A A = G T = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = A = = = = = = = = A = D = = G T C G G A = G = ? G C = C C 0 E021 A = = C C I A I = C T = = = ? = = = = = = = = = A C = = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = ? = = = = = G = = T G D G D = T C = = = ? = = = = = = = = = T G = = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = ? = = = = = 0 E022 A = = C C I A I = C T = G = = G T G T = = G T A A = (I) = = = = = = = = (G) = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = G = = T G D G D = T C = A = = A C A G = = A C C T = (D) = = = = = = = = (A) = = = = = = = = = = = = = (C) = = = = = = = = = = = = = = = 0 E023 = = = = = D = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = 1.00 1.00 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 0.61 = = = 0.61 = ? ? 0.61 = = = = = = = = = = = = ? ? ? ? = = = = ? ? = = = = = = = = = = = = = = = ? = = = = = = ? ? = = = 1.00 1.00 = 0.97 1.00 = 1.00 1.00 = = 1.00 1.00 = ? ? 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = ? = = 1.00 ? = 1.00 = 1.00 1.00 = = = = = = = = = = = = = 0.76 = 0.76 0.76 0.76 0.76 = = 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 = = 1.00 1.00 1.00 = ? 1.00 = = 1.00 ? = 1.00 = 1.00 1.00 = = = 0.85 0.85 0.85 0.85 0.85 = 0.85 0.85 = 0.85 0.85 = 0.86 0.86 0.86 0.86 = = 0.86 0.86 0.87 = = = = = = ? = = = = = 0.70 = = = = = = = = 0.70 = 0.70 = = 0.70 0.70 0.70 0.70 0.70 0.70 = = 0.70 ? = 0.70 = 0.70 0.70 1.00 = = = = = = = = = = 0.99 1.00 = = 1.00 = = = 1.00 = = = = ? = = = = = = = = = = = = 0.58 = = = = = = = = = = = = = = = = = = = = = = = 0.50 = = = = = = = = = ? ? = = ? = = = = = = = = = = = = 1.00 ? ? 1.00 = = = 1.00 = = = = ? = = = = ? ? ? = = = ? = = = = = = = = = = = = ? ? ? = = = = = = 0.64 0.64 0.64 0.64 0.64 = 0.64 0.64 0.64 ? 0.59 ? = 0.59 0.59 0.59 = = 0.59 0.59 = = = = 0.59 0.59 = ? = 0.94 = ? = 0.99 = = = = = = = = 0.99 ? 0.99 = ? 0.99 0.99 0.99 0.99 0.99 0.99 = 0.99 ? 0.99 = 0.99 = 0.99 ? = 0.52 = = = = 0.52 0.52 0.52 = = = = ? ? = 0.52 0.52 0.52 = = 0.52 0.52 = = = 0.52 = = = = = ? = = = 1.00 = = = = 0.75 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? = 1.00 = 1.00 ? = 0.81 = 0.81 0.81 0.81 = = = 0.81 0.81 = = = = 0.85 = = = 0.85 = = = = = = 1.00 ? ? 1.00 = = = = = = = = 1.00 ? ? ? ? = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = 0.76 = = = = = = 0.96 = 0.96 ? = = 0.50 = = 0.52 = = = 0.76 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 0.99 = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0.81 0.81 0.81 = = = = = = = = = = 0.82 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.71 0.71 = 0.71 = = = = = = = 0.69 0.69 0.69 = = = = = = = 0.84 = = = = = = = 0.84 = 0.84 = = = = = = = = 0.81 0.81 = = ? ? 0.81 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.61 = = = = = = = = = = = 0.62 = = 0.62 = ? ? ? = = = = 0.62 = = = = = = = = = = = 1.00 = = ? = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 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 ? = = = = = = = = = = = = = ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0.53 = = = = = = = = 0.50 = = 0.54 0.54 = ? = 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 = = = = = = = 0.51 = = = = = = = = = = = = 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 = = = = = = = = = = = = = 0.91 = = = = = = = 0.91 = 0.91 = = = = = ? ? = = 1.00 = 0.53 ? ? 0.88 ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = 0.57 0.57 0.57 0.57 ? = 0.57 0.57 = 0.57 = = = = = = = = = = 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 = = = = = = = = = = = 0.55 = 0.57 = = 0.57 0.57 0.57 0.57 = 0.57 0.57 0.57 = ? 0.64 = = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 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 = = = = = = 0.83 = = ? ? = ? = = = = = = = = = 0.91 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = ? 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = = 0.56 = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 0.50 0.99 = = 1.00 ? 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = = = = = = = 1.00 1.00 0.55 = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0.95 0.95 0.95 0.95 0.95 = 0.95 0.95 0.95 = 1.00 = = 1.00 = 1.00 = 0.86 1.00 1.00 1.00 = 1.00 = = = = = = = = = 0.93 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.57 0.57 = = 0.88 = = 0.53 = = = = = 0.96 0.96 = 0.96 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.57 = = 0.65 = = 0.65 0.65 0.65 0.65 0.65 = 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 = = = = = = = = = = = = = = = = 0.63 0.63 0.63 = = 0.63 0.63 0.63 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 1.00 = 1.00 1.00 = 1.00 ? ? = 1.00 1.00 1.00 = 0.89 = = = = = = = = = = = = = = = = = = = = = = = = ? ? = ? = = = = = = = = = = = = = = = = = = 0.50 0.50 0.50 0.50 0.50 0.50 = 0.50 0.50 0.50 = = = = 0.50 0.50 0.50 = = 0.50 0.50 0.50 = 0.50 = ? ? ? ? = 0.82 = = = = = = = = = = 1.00 = 1.00 ? ? = 0.84 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 0.69 = 0.69 = = = 0.69 0.69 = = 0.69 0.69 0.69 = 0.69 = ? ? = = = 0.98 0.98 0.98 = 0.98 = 0.98 ? = = = = 0.98 = 0.98 = ? = = = 0.98 = = = = 0.98 = 0.98 0.98 0.98 = 0.98 ? = = 0.99 = = = = = = = = = = 0.99 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0.57 = = = = = = = = = 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 = 0.78 0.78 0.78 0.78 0.78 = = 0.78 0.78 0.78 0.78 = ? ? 0.95 0.95 0.95 0.95 = = 0.95 0.95 0.95 0.95 = = = = = = = = = = = 1.00 = = = = 0.66 = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? 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 0.95 = = = = = = 0.59 = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = 0.72 = = 0.72 0.72 0.72 = 0.72 = 0.72 0.72 0.72 = 0.72 = = 0.72 = 0.72 = = 0.72 0.72 0.72 = 0.72 = = = = = 1.00 0.99 0.99 0.99 = = = 0.99 = ? = = 0.99 0.99 = 0.99 = = = = = 0.99 = = = = 0.99 = 0.99 0.99 0.99 = 0.99 0.99 = 0.99 = = = = 0.99 0.99 0.99 = = = = 0.99 = = 1.00 ? 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = ? = = = ? ? ? ? = = = ? = = = = = = = = = = = = = = = 0.56 = 0.56 0.56 0.56 = = 0.57 0.56 0.56 0.56 ? 0.86 = = ? 0.86 0.86 = = 0.86 0.86 0.86 = = = ? ? ? ? = = = ? ? = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = 0.98 0.98 0.98 0.98 = = 0.98 0.98 0.98 = 0.98 = = 0.98 0.98 0.98 = = 0.98 0.98 = 0.92 = = = = = = = = = = = = = = = 0.50 = = ? ? = = = = = = = = = = = = ? = = = = ? ? ? 0.90 = = = = = 0.90 = = = ? = = = = = = = = = = = = = = = = = = = = 0.97 = = = 0.98 0.98 = = = = = = 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 = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = ? 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = ? = = = = = = = = = 0.97 0.97 = = = = = = = = = = = = = = = = = ? ? = = = ? = = = = = = = = = = ? = = = = = 0.99 = = 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 = 0.75 = = = = = = = = 0.55 = = = = = = = = = = = = = 0.56 = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS