************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 il1r1.phase.inp il1r1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST il1r1.phase.out_freqs : haplotype frequency estimates il1r1.phase.out_pairs : most likely haplotype pairs for each individual il1r1.phase.out_recom : estimates of recombination parameters il1r1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 82 Positions of loci: 31 196 267 680 1472 1632 2176 2187 2235 2749 2759 3162 3563 3977 4442 4893 4948 5162 5882 6049 6058 6345 6596 7413 7625 7750 7821 8350 8351 9259 9282 9356 9612 9714 9757 10087 10404 10515 10614 10839 11266 11548 11937 12061 12544 12751 12806 12974 13061 13328 13947 14250 16053 16266 16694 16749 16981 17419 18364 19020 19669 19734 20593 21077 21758 22164 22276 22449 23657 23772 24338 24430 24804 25179 25276 25438 25500 26760 27322 27323 27421 27680 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file il1r1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TGTCTATCCAGCGCTCGTAACGCGTTCAICCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGCTACCAGGATT 2.000000 2 TGTCTATCCAGCGCTCGTAACGCGTTCAICCCAAAGGTAATTGTCTGTGAGGICCAAACGAATGADGDAAGCTACCAGGATT 1.000000 3 TGTCTATCCAGCGCTCGTAACGCGTTGAICCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGGTACCAGGATT 7.000000 4 TGTCTATCCAGCGCTCGTAACGCGTTGAICCCAAAGGTAATTGTCTGTGAGGICCAAGGGAATGADGDAAGGTACCAGGATT 1.000000 5 TGTCTATCCAGCGCTCGTAACGCGTTGAICCCAAAGGTAATTGTCGGTGAGGICCAAGCGAATGADGDAAGCTACCAGGATT 1.000000 6 TGTCTATCCAGCGCTCGTAACGCGTTGAIGCCAGAGGTTATTGTGTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 4.000000 7 TGTCTATCCAGCGCTCGTGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCAAGCTGATGADGIGAGCTGCCAGGATT 1.000000 8 TGTCTATCCAGCGCTCGTGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDTTCGGCTGATGADGIGAGCTGCCAGGATT 1.000000 9 TGTCTATCCGGCGCCCGTGGCGCGTTGAIGCCAGAGGCTATTGTCTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 1.000000 10 TGTCTATCCGGCGCCCGTGGCGCGTTGADGCCAGAGGTTATTGTCTGCATGGICCAAGCGGATGCDGIACGCGGCTAGGATT 1.000000 11 TGTCTATTCAGCGCTCGTAACGCGTTGAICCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGGTACCAGGATT 1.000000 12 TGTCTATTCAGCGCTCGTAACGCGTTGAIGCCAGAGGTTATTGTGTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 1.000000 13 TATCTATCCAGCGCCCGTAACGCGTTCAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 14 TATCTATCCAGCGCCCGTAACGCGTTGAICCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGGTACCAGGATT 1.000000 15 TATCTATCCAGCGCCCGTAACGCGTTGAIGCCAAAGGTAATTGTCTGTGAGGICCAAGCGAGTGADGDAAACTGCCAGGAAT 2.000000 16 TATCTATCCAGCGTCCATGACGCATTGAIGCCAAAGGTAATTGTCTGTGAGGICCAAGCGAGTGADGDAAACTGCCAGGAAT 1.000000 17 TATCTATCCAGCGTCCATGACGCATTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 18 TATCTATCCAGCGTCCATGACAGGTTGAIGCCAGAGGTTATTGTGTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 1.000000 19 TATCTATCCGGCGCCCGTGGCGCGTTGAIGCTGGAGGTTGGTGTCTGCGTGTICCAAGCTGATGADGIGAGCTGCCAGGATT 1.000000 20 TATCTGTCCACCGTCCGTGACGCGTTGADGCCAGTGGTTATTGTCTGCATGGICCAAGCGGATGCDGIACGCGGCTAGGATT 1.000000 21 TATCTGTCCACCGTCCGTGACGCATTGAIGCTAGAAGTTATTGTCGGCGTGTICCAAGCGGGCGADGIAAGCTGCCAGGATT 2.000000 22 TATCTGTCCACCGTCCATGACGCGTTGAICCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGGTACCAGGATT 1.000000 23 TATCTGTCCACCGTCCATGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 24 TATCTGTCCACCGTCCATGACGCGTTGAIGCTAGAAGTTATTGTCGGCGTGTICCAAGCGGGTGADGIAAGCTGCCAGGATT 2.000000 25 TATCTGTCCACCGTCCATGACGCGATGTIGCCAAAGGTAATTGTCTGTGAGGICCAAAGGAATGAIGDAAACTGCCAGGAAT 1.000000 26 TATCTGTCCACCGTCCATGACGCATTCAIGTCAGAGATTATTTTCTGCGTGGICCAAGCGGATCADAIAAGCTGGCAGTTTA 1.000000 27 TATCTGTCCACCGTCCATGACGCATTGAIGCCAAAGGTAATTGTCTGTGAGGICCAAGCGAGTGADGDAAACTGCCAGGAAT 1.000000 28 TATCTGTCCACCGTCCATGACGCATTGAIGCCAGTGGTTATTGTCTGCATGGICCAAGCGGATGCDGIACGCGGCTAGGATT 2.000000 29 TATCTGTCCACCGTCCATGACGCATTGAIGCCAGTGGTTATTGTCTGCATGGICCAAGGGGATGCDGIACGCGGCTAGGATT 1.000000 30 TATCTGTCCACCGTCCATGACGCATTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 3.000000 31 TATCTGTCCACCGTCCATGACGCATTGAIGCTAGAAGTTATTGTCGGCGTGTICCAAGCGGGCGADGIAAGCTGCCAGGATT 2.000000 32 TATCTGTCCACCGTCCATGACGCATTGAIGCTAGAAGTTATTGTCGGCGTGTICCAAACGGGCGADGIAAGCTGCCAGGATT 1.000000 33 TATCTGTCCACTGTCCATGACAGGTTGAIGCCAGAGGCTATTGTCTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 2.000000 34 TAGCTATCCGGCCCCCGTGGTGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 35 TAGCTATCCGGCCCCCGTGGTGCGTCCAIGCTAGAGGTAATGGTCTGCGTAGICCAAGCGGATGADGDAAGCTGCCAGGAAT 3.000000 36 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCCAGAGGTAATTGTCTGCGTGGICCAAGCGGATGADGDAAGCTGCCAGGAAT 1.000000 37 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCCAGAGGTTATTGTCTGCGTGGICCAAGCGGATGADGDAAGCTGCCAGGAAT 1.000000 38 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTAATGGTCTGCGTGGICCAAGCGGATGADGDAAGCTGCCAGGAAT 2.000000 39 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTAATGGTCTGCGTAGICCAAGCGGATGADGDAAGCTGCCAGGATT 1.000000 40 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTAATGGTCTGCGTAGICCAAGCGGATGADGDAAGCTGCCAGGAAT 1.000000 41 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTAATGGTCTGCGTAGITCAAGCGGATGADGDAAGCTGCCAGGAAT 2.000000 42 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTAAGGGTCTGCGTGGICCAAGCGGATGADGDAAGCTGCCAGGAAT 1.000000 43 TAGCTATCCGGCCCCCGTGGTGCGTCGAIGCTAGAGGTTAGTGTCTGCGTGTDCTCAGCTGATGADGIGAGCTGCCAGGATT 1.000000 44 GATTTGACCAGCGTCCATGACGCGTTGAIGCTAGAGGTTAGTGTCGGCGTGTDCCCAACTGATGADGIGAGCTGCCAGGATT 1.000000 45 GATTTGACTAGCGCCCGTGGCGCGTTGADGCCAGAGGTTATTGTCTGCATGGICCAAGCGGATGCDGIACGCTGCCAGGATT 1.000000 46 GATTTGACTAGCGCCCGCGACGCGTTCAIGCTGGAGGTTGGTGTCTGCGTGTICCAAGCTGATGADGIGAGCTGCCAGGATT 2.000000 47 GATTTGACTAGCGCCCGCGACGCGTTGAIGCTGGAGGTTGGTGTCTGCGTGTICCAAGCTGATGADGIGAGCTGCCAGGATT 1.000000 48 GATTTGACTAGCGTCCATGACGCGTTGAICCCAGAGGTAATTGTCTGTGAGGICCAAGCGAATGADGDAAGCTGCCAGGATT 1.000000 49 GATTTGACTAGCGTCCATGACGCGTTGAIGCCAGAGGTTATTGTGTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 1.000000 50 GATTTGACTAGCGTCCATGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 51 GATTTGACTAGCGTCCATGACGCGATGTIGCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGAIGDAAACTGCCAGGAAT 1.000000 52 GATTTGACTAGCGTCCATGACGCATTGAIGCCAGTGGTTATTGTCTGCATGGICCAAGGGGATGCDGIACGCGGCTAGGATT 1.000000 53 GATTTGACTAGCGTCCATGACGCATTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCGGGATT 1.000000 54 GATTTGACTAGCGTCTATGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAGCTGATGADGIGAGCTGCCAGGATT 2.000000 55 GATTTGACTAGCGTCTATGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDCCCAACTGATGADGIGAGCTGCCAGGATT 1.000000 56 GATTTGACTAGCGTCTATGACGCGTTGAIGCTAGAGGTTAGTGTCTGCGTGTDTTCGGCTGATGADGIGAGCTGCCAGGATT 1.000000 57 GATTTGACTAGCGTCTATGACGCGTTGAIGCTAGAGGTTAGTGACTGCGTGTDCCCAGCTGATGADGIGAGCTGCCAGGATT 6.000000 58 GATTTGACTAGTGTCCGTAACGCGTTGAICCCAGAGGTAATTGTCTGTGAGGICCAAGGGAATGADGDAAGGTACCAGGATT 1.000000 59 GATTTGACTAGTGTCCGTAACGCGTTGAIGTCAGAGATTATTTTCTTCGTGGICCAAGCGGATCADAIAAGCTGGCAGTTTA 3.000000 60 GATTTGACTAGTGTCCATGACGCATTGAIGCCAAAGGTAATTGTCGGCGTGGICCAAGCGGATGADGIAAGCTGCCAGGATT 1.000000 61 GATTCGACTAGCGTCCATGACGCGATGTIGCCAAAGGTAATTGTCTGTGAGGICCAAGCGAATGAIGDAAACTGCCAGGAAT 2.000000 62 GATTCGACTAGCGTCCATGACAGGTTGAIGCCAGAGGTTAGTGTCTTCGTGGICCAGGCGGATGADAIAAGCTGCCATTTTT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,9) D002: (17,18) D003: (5,21) D004: (30,46) D005: (31,44) D006: (35,37) D007: (50,57) D008: (36,53) D009: (27,62) D010: (45,48) D011: (16,33) D012: (46,61) D013: (13,51) D014: (21,60) D015: (19,25) D016: (14,31) D033: (20,55) D034: (26,32) D035: (24,30) D036: (42,59) D037: (49,59) D038: (30,47) D039: (33,61) D040: (10,24) E001: (38,52) E002: (35,41) E003: (2,58) E004: (38,40) E005: (3,59) E006: (11,34) E007: (3,35) E008: (3,57) E009: (6,29) E010: (22,41) E011: (6,8) E012: (1,23) E013: (15,15) E014: (3,6) E015: (12,56) E016: (6,57) E017: (3,7) E018: (28,54) E019: (28,57) E020: (3,57) E021: (39,57) E022: (3,43) E023: (4,54) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T G T C T A T C C A G C G C T C G T A A C G C G T T C A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G C T A C C A G G A T T T G T C T A T C C G G C G C C C G T G G C G C G T T G A I G C C A G A G G C T A T T G T C T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T 0 D002 T A T C T A T C C A G C G T C C A T G A C (G) (C) (A) T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T T A T C T A T C C A G C G T C C A T G A C (A) (G) (G) T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T 0 D003 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C G G T G A G G I C C A A G C G A A T G A D G D A A G C T A C C A G G A T T T A T C T G T C C A C C G T C C G T G A C G C A T T G A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A G C G G G C G A D G I A A G C T G C C A G G A T T 0 D004 T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T G A T T T G A C T A G C G C C C G C G A C G C G T T C A I G C T G G A G G T T G G T G T C T G C G T G T I C C A A G C T G A T G A D G I G A G C T G C C A G G A T T 0 D005 T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A (G) C G G G C G A D G I A A G C T G C C A G G A T T G A T T T G A C C A G C G T C C A T G A C G C G T T G A I G C T A G A G G T T A G T G T C G G C G T G T D C C C A (A) C T G A T G A D G I G A G C T G C C A G G A T T 0 D006 T A G C T A T C C G G C C C C C G T G G T G C G T C C A I G C T A G A G G T (A) A T G G T C T G C G T A G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C C A G A G G T (T) A T T G T C T G C G T G G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T 0 D007 G A T T T G A C T A G C G T C C A T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 D008 T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C C A G A G G T (A) A T T G T C T G C G T G G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T G A T T T G A C T A G C G T C C A T G A C G C A T T G A I G C T A G A G G T (T) A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T 0 D009 (T) A T (C) (T) G (T) C (C) A (C) C G T C C A T G A C G C A T T G A I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A G T G A D G D A A A C T G C C A G G A A T (G) A T (T) (C) G (A) C (T) A (G) C G T C C A T G A C A G G T T G A I G C C A G A G G T T A G T G T C T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T 0 D010 G A T T T G A C T [A] G C G C C C G T G G C G C G T T G A D G C C A G A G G T T A T T G T C T G C A T G G I C C A A G C G G A T G C D G I A C G C T G C C A G G A T T G A T T T G A C T A G C G T C C A T G A C G C G T T G A I C C C A G A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G C T G C C A G G A T T 0 D011 T A T C T A T C C A G C G T C C A T G A C G C A T T G A I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A G T G A D G D A A A C T G C C A G G A A T T A T C T G T C C A C T G T C C A T G A C A G G T T G A I G C C A G A G G C T A T T G T C T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T 0 D012 G A T T T G A C T A G C G C C C G C G A C G C G T T C A I G C T G G A G G T T G G T G T C T G C G T G T I C C A A G C T G A T G A D G I G A G C T G C C A G G A T T G A T T C G A C T A G C G T C C A T G A C G C G A T G T I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A I [G] D A A A C T G C C A G G A A T 0 D013 T A T C T A T C C A G C G C C C G T A A C G C G T T C A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T G A T T T G A C T A G C G T C [C] A T G A C G C G A T G T I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A I [G] D A A A C T G C C A G G A A T 0 D014 (T) A T (C) T G (T) C (C) A (C) (C) G T C C (G) T G A C G C A T T G A I G C (T) A (G) A (A) G T (T) A T T G T C G G C G T G (T) I C C A A G C G G (G) (C) G A D G I A A G C T G C C A G G A T T (G) A T (T) T G (A) C (T) A (G) (T) G T C C (A) T G A C G C A T T G A I G C (C) A (A) A (G) G T (A) A T T G T C G G C G T G (G) I C C A A G C G G (A) (T) G A D G I A A G C T G C C A G G A T T 0 D015 T A T C T A T C C G G C G C C C G T G G C G C G T T G A I G C T G G A G G T T G G T G T C T G C G T G T I C C A A G C T G A T G A D G I G A G C T G C C A G G A T T T A T C T G T C C A C C G T C C A T G A C G C G A T G T I G C C A A A G G T A A T T G T C T G T G A G G I C C A A A G G A A T G A I [G] D A A A C T G C C A G G A A T 0 D016 T A T C T (A) T C C A (G) C G (C) C C (G) T (A) A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T T A T C T (G) T C C A (C) C G (T) C C (A) T (G) A C G C A T T G A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A G C G G G C G A D G I A A G C T G C C A G G A T T 0 D033 (T) A T (C) T G (T) C (C) A (C) C G T C (C) (G) T G A C G C G T T G A (D) G C C A G (T) G G T T A T T G T C T G C A T G G I C C A A G C G G A T G C D G I A C G C G G C T A G G A T T (G) A T (T) T G (A) C (T) A (G) C G T C (T) (A) T G A C G C G T T G A (I) G C T A G (A) G G T T A G T G T C T G C G T G T D C C C A A C T G A T G A D G I G A G C T G C C A G G A T T 0 D034 T A T C T G T C C A C C G T C C A T G A C G C A T T (C) A I G T C A G A G A T T A T T T T C T G C G T G G I C C A A (G) C G G A T C A D A I A A G C T G G C A G T T T A T A T C T G T C C A C C G T C C A T G A C G C A T T (G) A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A (A) C G G G C G A D G I A A G C T G C C A G G A T T 0 D035 T A T C T G T C C A C C G T C C A T G A C G C G T T G A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A G C G G G T G A D G I A A G C T G C C A G G A T T T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T 0 D036 T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A (G) G G T C T G C G T G G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T G A T T T G A C T A G T G T C C G T A A C G C G T T G A I G T C A G A G A T T A (T) T T T C T T C G T G G I C C A A G C G G A T C A D A I A A G C T G G C A G T T T A 0 D037 G A T T T G A C T A G C G T C C A T G A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T G A T T T G A C T A G T G T C C G T A A C G C G T T G A I G T C A G A G A T T A T T T T C T T C G T G G I C C A A G C G G A T C A D A I A A G C T G G C A G T T T A 0 D038 T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T G A T T T G A C T A G C G C C C G C G A C G C G T T G A I G C T G G A G G T T G G T G T C T G C G T G T I C C A A G C T G A T G A D G I G A G C T G C C A G G A T T 0 D039 T A T C T G T C C A C T G T C C A T G A C A G G T T G A I G C C A G A G G C T A T T G T C T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T G A T T C G A C T A G C G T C C A T G A C G C G A T G T I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A I [G] D A A A C T G C C A G G A A T 0 D040 T G T C T A T C C G G C G C C C G T G G C G C G T T G A D G C C A G A G G T T A T T G T C T G C A T G G I C C A A G C G G A T G C D G I A C G C G G C T A G G A T T T A T C T G T C C A C C G T C C A T G A C G C G T T G A I G C T A G A A G T T A T T G T C G G C G T G T I C C A A G C G G G T G A D G I A A G C T G C C A G G A T T 0 E001 T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T G G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T G A T T T G A C T A G C G T C [C] A T G A C G C A T T G A I G C C A G T G G T T A T T G T C T G C A T G G I C C A A G G G G A T G C D G I A C G C G G C T A G G A T T 0 E002 T A G C T A T C C G G C C C C C G T G G T G C G T C C A I G C T A G A G G T A A T G G T C T G C G T A G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T A G I T C A A G C G G A T G A D G D A A G C T G C C A G G A A T 0 E003 T G T C T A T C C A G C G C T C G T A A C G C G T T (C) A I C C C A (A) A G G T A A T T G T C T G T G A G G I C C A A (A) (C) G A A T G A D G D A A G (C) T A C C A G G A T T G A T T T G A C T A G T G T C C G T A A C G C G T T (G) A I C C C A (G) A G G T A A T T G T C T G T G A G G I C C A A (G) (G) G A A T G A D G D A A G (G) T A C C A G G A T T 0 E004 T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T G G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T A G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T 0 E005 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T G A T T T G A C T A G T G T C C G T A A C G C G T T G A I G T C A G A G A T T A T T T T C T T C G T G G I C C A A G C G G A T C A D A I A A G C T G G C A G T T T A 0 E006 T (G) (T) C T A T (T) C (A) G C (G) C (T) C G T (A) (A) (C) G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T T (A) (G) C T A T (C) C (G) G C (C) C (C) C G T (G) (G) (T) G C G T T [G] A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T 0 E007 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T T A G C T A T C C G G C C C C C G T G G T G C G T C C A I G C T A G A G G T A A T G G T C T G C G T A G I C C A A G C G G A T G A D G D A A G C T G C C A G G A A T 0 E008 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E009 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C C A G T G G T T A T T G T C T G C A T G G I C C A A G G G G A T G C D G I A C G C G G C T A G G A T T 0 E010 T A T C T G T C C A C C G T C C A T G A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G [G] T A C C A G G A T T T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T A G I T C A A G C G G A T G A D G D A A G C T G C C A G G A A T 0 E011 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T T G T C T A T C C A G C G C T C G T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D T T C G G C T G A T G A D G I G A G C T G C C A G G A T T 0 E012 T (G) T C T (A) T C C A (G) C G (C) (T) C (G) T (A) A C G C G T T [C] A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G C T A C C A G G A T T T (A) T C T (G) T C C A (C) C G (T) (C) C (A) T (G) A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C G G G A T T 0 E013 T A T C T A T C C A G C G C C C G T A A C G C G T T G A I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A G T G A D G D A A A C T G C C A G G A A T T A T C T A T C C A G C G C C C G T A A C G C G T T G A I G C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A G T G A D G D A A A C T G C C A G G A A T 0 E014 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T T G T C T A T C C A G C G C T C G T A A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T 0 E015 T G T C T A T (T) C A G C G C T C G T A A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T G A T T T G A (C) T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D [T] T C [G] G C T G A T G A D G I G A G C T G C C A G G A T T 0 E016 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I G C C A G A G G T T A T T G T G T T C G T G G I C C A G G C G G A T G A D A I A A G C T G C C A T T T T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E017 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T T G T C T A T C C A G C G C T C G T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C A A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E018 T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C C A G T G G T T A T T G T C T G C A T G G I C C A A G C G G A T G C D G I A C G C G G C T A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E019 T A T C T G T C C A C C G T C C A T G A C G C A T T G A I G C C A G T G G T T A T T G T C T G C A T G G I C C A A G C G G A T G C D G I A C G C G G C T A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E020 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G C G A A T G A D G D A A G G T A C C A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E021 T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T A A T G G T C T G C G T A G I C C A A G C G G A T G A D G [D] A A G C T G C C A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G A C T G C G T G T D C C C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E022 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C (C) A A G C G A A T G A D G D A A G G T A C C A G G A T T T A G C T A T C C G G C C C C C G T G G T G C G T C G A I G C T A G A G G T T A G T G T C T G C G T G T D C (T) C A G C T G A T G A D G I G A G C T G C C A G G A T T 0 E023 T G T C T A T C C A G C G C T C G T A A C G C G T T G A I C C C A A A G G T A A T T G T C T G T G A G G I C C A A G (G) G A A T G A D G D A A G G T A C C A G G A T T G A T T T G A C T A G C G T C T A T G A C G C G T T G A I G C T A G A G G T T A G T G T C T G C G T G T D C C C A G (C) T G A T G A D G I G A G C T G C C A G G A T T 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 = = = = T = = = A A = = = = = = C = = C = = = A = = = T A = = = ? = = = G T = A = = ? = = = A ? = = A = = = = = G D = = = = ? A = = = G G A = = = = = = = = = = = G = = = = C = = = G G = = = = = = G = = G = = = G = = = C T = = = ? = = = T C = T = = ? = = = G ? = = G = = = = = A I = = = = ? G = = = T T T = = 0 D002 = = = = = = = = = = = = = = = = = = = = = (G) (C) (A) = = = = = = = T = = = = = = = = G = ? = C = G = = = = T D = = C A = = T = = = = = = G = G = = = = = = = G G G A = = = = = = = = = = = = = = = = = = = = = = = (A) (G) (G) = = = = = = = C = = = = = = = = T = ? = G = T = = = = G I = = A G = = G = = = = = = A = A = = = = = = = A T T T = = 0 D003 = G = = = A = = = = G = = C T = = = A = = = = G = = = = = C = C = A = G = = A = = = ? = = = = T = A = G = = = = = = = = A A T = = = = D = = = = = A = = = = = = = = = A = = = G = = = = C = = T C = = = G = = = = A = = = = = G = T = G = A = = T = = = ? = = = = C = T = T = = = = = = = = G G C = = = = I = = = = = G = = = = = = = = 0 D004 T = = C = = T = C = C = = T = = A T = = = = = A = = G = = = = = A = = = = = = A = = = = = = = = = = = = D = = C = = = = = = = ? = = = = = = = = = = = = G = = = = = G = = T = = A = T = G = = C = = G C = = = = = G = = C = = = = = G = = = = = = G = = = = = = = = = = = = I = = A = = = = = = = ? = = = = = = = = = = = = A = = = = = 0 D005 ? ? ? C = = T = = = C = = = = = = = = = = = = A = = = = = = = = = = = A = = = = T = = = = = = = = = = = I = = A = (G) = G = G C = = = = = A = = = = = = = = = = = = = ? ? ? T = = A = = = G = = = = = = = = = = = = G = = = = = = = = = = = G = = = = G = = = = = = = = = = = D = = C = (A) = T = A T = = = = = G = = = = = = = = = = = = = 0 D006 = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = T = = = = = = (A) = = G = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = C = = = = = = (T) = = T = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 D007 = = = = = = = = = ? ? ? = ? = C = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = G = = = = = = = = = = = = = = ? ? ? = ? = T = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = A = = = = = 0 D008 T = G C = A T = C G = = C ? = = G = = G T = = G = C = = = = = C = = = = = = (A) = T = = = = = = = = = = G I = = A = = = G = = = = = ? = D A = = = = = = = A ? = = A = G = T T = G A = T A = = G ? = = A = = A C = = A = T = = = = = T = = = = = = (T) = G = = = = = = = = = = T D = = C = = = T = = = = = ? = I G = = = = = = = G ? = = T = 0 D009 (T) = = (C) (T) = (T) = (C) = (C) = = = = = = = = = = G C A = = ? = = = = = = A = = = = A = T = = = = = G T = A = = ? ? ? = A = = = A G = = = = G D = = A = = = = = = G G A A = (G) = = (T) (C) = (A) = (T) = (G) = = = = = = = = = = A G G = = ? = = = = = = G = = = = T = G = = = = = T C = T = = ? ? ? = G = = = G A = = = = A I = = G = = = = = = T T T T = 0 D010 = = = = = = = = = ? ? ? = C = = G = = G = = = = = = = = D G = = = = = = = = T = = = = = = = = C A T = = = = = = = = = = G = = = C = = I = C = = = = = = = = = = = = = = = = = = = = = ? ? ? = T = = A = = A = = = = = = = = I C = = = = = = = = A = = = = = = = = T G A = = = = = = = = = = A = = = A = = D = A = = = = = = = = = = = = 0 D011 = = = = = A = = = = G C = = = = = = = = = G C A = = = = = = = = = A = = = T A = = = = = = = G T = A = = = = = = A = = = A G = = = = G D = = A = = = = = = G G A A = = = = = = G = = = = C T = = = = = = = = = A G G = = = = = = = = = G = = = C T = = = = = = = T C = T = = = = = = G = = = G A = = = = A I = = G = = = = = = T T T T = 0 D012 = = = = T = = = = = = = = C = = G C = = = = = = T = C A = = = T G G = = = = T G G = = = = = = C = T = T = = = = = = = T G = = = ? D ? ? G = G = = = = = = = = = T = = = = = C = = = = = = = = T = = A T = = = = = = A = G T = = = C A A = = = = A A T = = = = = = T = A = G = = = = = = = G A = = = ? I ? ? A = A = = = = = = = = = A = 0 D013 T = = C = A T = C ? ? ? = C = ? G = A = = = = = T = C A = = = T = G = = = = T = G = = = = = = C = T = T D = = C = = = T G = = = = D ? ? G = G = = = = = G = = = T = G = = T = G A = T ? ? ? = T = ? A = G = = = = = A = G T = = = C = A = = = = A = T = = = = = = T = A = G I = = A = = = G A = = = = I ? ? A = A = = = = = A = = = A = 0 D014 (T) = = (C) = = (T) = (C) = (C) (C) = = = = (G) = = = = = = = = = = = = = = (T) = (G) = (A) = = (T) = = = = = = = = = = = = (T) = = = = = = = = = (G) (C) = = = = = = = = = = = = = = = = = = = (G) = = (T) = = (A) = (T) = (G) (T) = = = = (A) = = = = = = = = = = = = = = (C) = (A) = (G) = = (A) = = = = = = = = = = = = (G) = = = = = = = = = (A) (T) = = = = = = = = = = = = = = = = = = = 0 D015 = = = = = A = = = G G = = C = = G = = G = = = = T = = A = = = T G G = = = = T G G = = = = ? ? ? = T = T = = = = = G C T G = = = = D ? ? G = G = = = = = = = = = T = = = = = = G = = = A C = = T = = A = = A = = = = A = = T = = = C A A = = = = A A T = = = = ? ? ? = A = G = = = = = A G G A = = = = I ? ? A = A = = = = = = = = = A = 0 D016 = = = = = (A) = = = = (G) = = (C) = = (G) = (A) = = = = G = = = = = C = C = A = G = = A = = = = = = T = T = A = G = = = = = = = = A A T = = = = D = = = G = A = = = ? = = = = = = = = = (G) = = = = (C) = = (T) = = (A) = (G) = = = = A = = = = = G = T = G = A = = T = = = = = = G = C = T = T = = = = = = = = G G C = = = = I = = = C = G = = = ? = = = = 0 D033 (T) = = (C) = = (T) = (C) = (C) = = ? = (C) (G) = = = = = = = = = ? = (D) = = C = = (T) = = = = = T = = = = = = = A = = G I ? = A = G = G = = = = C = = = A C = = G = = T = = = = = = (G) = = (T) = = (A) = (T) = (G) = = ? = (T) (A) = = = = = = = = = ? = (I) = = T = = (A) = = = = = G = = = = = = = G = = T D ? = C = A = T = = = = A = = = G A = = T = = C = = = = = = 0 D034 = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = = T C = = = G A = = = = = T = = T = = = = = G = = = = = (G) = = = A T C = = A = = = = = = = G = = = T T = A = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = C T = = = A G = = = = = G = = G = = = = = T = = = = = (A) = = = G C G = = G = = = = = = = C = = = G A = T 0 D035 = = = = = = = = = = = = = ? = = = = = = = = = G = = = = = = = = = = = A = = = = T = = = ? G = = = = = = I = = A = = = G = G = = = = = = A = = = = = = = A = = = = = = = = = = = = = = = = = = ? = = = = = = = = = A = = = = = = = = = = = G = = = = G = = = ? T = = = = = = D = = C = = = T = A = = = = = = G = = = = = = = G = = = = = 0 D036 T = G C = A T = C G = C C C = = = = G G T = = = = C = = = = C T = = = = G = A = (G) G G = ? ? G = = = = = = = = = = = = = = = = G = = G D = = = = = = C = = = G A A T G = T T = G A = T A = T G T = = = = A A C = = = = T = = = = T C = = = = A = T = (T) T T = ? ? T = = = = = = = = = = = = = = = = C = = A I = = = = = = G = = = T T T A 0 D037 = = = = = = = = = = = C = = = = A = G = = = = = = = = = = = C = = = = = G = = = = = G = G ? = = = = = = = = = = G = = = = = = G = = = = = = ? ? = = C = = T = = = T = = = = = = = = = = = T = = = = G = A = = = = = = = = = = = T = = = = = A = = = = = T = C ? = = = = = = = = = = A = = = = = = C = = = = = = ? ? = = G = = G = = = A 0 D038 T = = C = = T = C = C = = T = = A T = = = = = A = = = = = = = = A = = = = = = A = = = = = = = = = = = = D = = C = = = = = = = = = = = = = = = = = = = = G = = = = = G = = T = = A = T = G = = C = = G C = = = = = G = = = = = = = = G = = = = = = G = = = = = = = = = = = = I = = A = = = = = = = = = = = = = = = = = = = = A = = = = = 0 D039 T = = C T = ? ? C = C T = = = = = = = = = A G = T = = A = = = = = G = = = C T = = = = = = = T C = T = = = ? = = G = = = G = = = = D ? ? = = G = = = = = = T T T T = G = = T C = ? ? T = G C = = = = = = = = = G C = A = = T = = = = = A = = = T A = = = = = = = G T = A = = = ? = = A = = = A = = = = I ? ? = = A = = = = = = G G A A = 0 D040 = G = = = A = = = G G = = C = = G = = G = = = = = = = = D = = C = = = G = = = = = = = = = T = = A = = G = = = = = = = = = A = = C = = = = C = = G = = T = ? = = = = = A = = = G = = = A C = = T = = A = = A = = = = = = = = I = = T = = = A = = = = = = = = = G = = G = = T = = = = = = = = = G = = A = = = = A = = T = = C = ? = = = = 0 E001 T = G C = A T = C G = = C C = ? ? = = G T = = G = C = = = = = T = = A = = = A = = G = = = = = = G = = = = = = = = = C = = = = = A = = D ? A = = T = = C = = = = A = G = T T = G A = T A = = G T = ? ? = = A C = = A = T = = = = = C = = T = = = T = = T = = = = = = A = = = = = = = = = G = = = = = C = = I ? C = = G = = T = = = = T = 0 E002 = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E003 T G = C = A T = C = = C = C T = = = = = = = = = = = (C) = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = (A) (C) = = = = = = = = = = = = (C) = = = = = ? = = = = G A = T = G A = T = = T = T C = = = = = = = = = = = (G) = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = (G) (G) = = = = = = = = = = = = (G) = = = = = ? = = = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = ? = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = ? = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = 0 E005 T G = C = A T = C = = C = C T = = = = = = = = = = = = = = C C = = A = = G = A = = = G = = = G T = A = = = = = = = = ? = A = = G = = G D = = = G = A C = = = G A = T G A = T = G A = T = = T = T C = = = = = = = = = = = = = = G T = = G = = A = T = = = T = = = T C = T = = = = = = = = ? = G = = C = = A I = = = C = G G = = = T T = A 0 E006 = (G) (T) = = = = (T) = (A) = = (G) = (T) = = = (A) (A) (C) = = = = = ? = = C = C = A = = = = A = T = = = = = = T = A = G I = = A = = = G A = = = = = = D A = = G = A = = A = = = = = = (A) (G) = = = = (C) = (G) = = (C) = (C) = = = (G) (G) (T) = = = = = ? = = G = T = G = = = = T = G = = = = = = C = T = T D = = C = = = T G = = = = = = I G = = C = G = = G = = = = = 0 E007 = G T = = = = = = A = = G = T = = = A A C = = = = T G = = C = C = A = = = = = = = T = = ? = = T = A G = = ? = = = = = = A = = = = = = = = = = G = A = = = = = = T = = A G = = = = = = G = = C = C = = = G G T = = = = C C = = G = T = G = = = = = = = G = = ? = = C = T A = = ? = = = = = = G = = = = = = = = = = C = G = = = = = = A = 0 E008 T G = C = A ? ? C = = = = C T C G = A = = = = = = = = = = C = C = A = = = = A = T = = T = = = T = A = G I = = A = = = G A = = = = = = D A = ? G = A = = = = = = = = G A = T = G ? ? T = = = = T C T A = G = = = = = = = = = = G = T = G = = = = T = G = = A = = = C = T = T D = = C = = = T G = = = = = = I G = ? C = G = = = = = = = = 0 E009 = G = = = A = = = = G = = C T = G = A = = = = G = = ? = = = = = = = A = = = = = = = = = G = T = G = = = = ? ? ? G = C = = = = = A = A = = A = = T = = C = T T T = = = A = = = G = = = = C = = T C = A = G = = = = A = = ? = = = = = = = T = = = = = = = = = C = G = A = = = = ? ? ? A = G = = = = = C = G = = C = = G = = T = G G A = = 0 E010 = = T = = G = = = A C = G T = = ? = = A C = = = = T = = = ? ? C ? ? ? = = = = = = T = = = = = T = A G = = C = = = = = = A = = = = = = = = ? ? ? ? A = = = = = = T = = = G = = A = = = G G = C C = = ? = = G T = = = = C = = = ? ? T ? ? ? = = = = = = G = = = = = C = T A = = T = = = = = = G = = = = = = = = ? ? ? ? G = = = = = = A = 0 E011 = = = = = = ? ? = = = = = = = = = = A = = = = = = = = = = = = C = = = = = = = = T = = = G = T = = = = G I C C A = ? = G = = = = = = A = A = = = = = = = = T T T = = = = = = = = ? ? = = = = = = = = = = G = = = = = = = = = = = = T = = = = = = = = G = = = C = G = = = = T D T T C = ? = T = = = = = = G = G = = = = = = = = G G A = = 0 E012 = (G) = = = (A) = = = = (G) = = (C) (T) = (G) = (A) = = = = = = ? ? = = C = C = A = = = = A = T = = = = = = T = A = G I = = A = = = G A = = = = ? = D A = = = = A = = A = = = = = = (A) = = = (G) = = = = (C) = = (T) (C) = (A) = (G) = = = = = = ? ? = = G = T = G = = = = T = G = = = = = = C = T = T D = = C = = = T G = = = = ? = I G = = = = G = = G = = = = = 0 E013 ? = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = ? = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = 0 E014 ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = C = = = A = = ? ? A = = = = = C = G T = A = = = = = = A = = = A = = ? = = G D = = = G = A = = = G G A = = ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = G = = = G = = ? ? T = = = = = G = T C = T = = = = = = G = = = G = = ? = = A I = = = C = G = = = T T T = = 0 E015 T G = C = A T (T) C = = = = C T C G = A = = = = = = = = = = = = C = = = = = = = = T = = = G = T = = = = G I ? C A ? ? = G = = = = = = A = A = = = = = = = = T T T = = G A = T = G A (C) T = = = = T C T A = G = = = = = = = = = = = = T = = = = = = = = G = = = C = G = = = = T D ? T C ? ? = T = = = = = = G = G = = = = = = = = G G A = = 0 E016 T G = C = A ? ? C = = = = C T C G = A = = = = = = = = = = = = C = = = = = = = = T = = T G = T = = = = G I = = A G = = ? = = = ? = = A = A = ? ? = = = = = ? T T = ? G A = T = G ? ? T = = = = T C T A = G = = = = = = = = = = = = T = = = = = = = = G = = A C = G = = = = T D = = C A = = ? = = = ? = = G = G = ? ? = = = = = ? G A = ? 0 E017 = = = = = = ? ? = = = = = = = = = = A = = = = = = = = = = C = C = A = = = = A = T = = = = = = T = A = G I = ? = = ? = G A = = ? = = = D A = ? ? = A = = = = ? ? ? ? = = = = = = ? ? = = = = = = = = = = G = = = = = = = = = = G = T = G = = = = T = G = = = = = = C = T = T D = ? = = ? = T G = = ? = = = I G = ? ? = G = = = = ? ? ? ? 0 E018 ? = = C = = T = C = C = = = = C = = = = = = = A = = = = = = = C = = T = = = = = T = = = = = = = A = = G I = = A = = = G = = = = C = = = A C = = G = = T = = = = = = ? = = T = = A = T = G = = = = T = = = = = = = G = = = = = = = T = = A = = = = = G = = = = = = = G = = T D = = C = = = T = = = = A = = = G A = = T = = C = = = = = = 0 E019 T = = C = = ? ? C = C = = = = C = = = = = = = A = = = = = = = C = = T = = = = = T = = T = = = = A = = G I = = A = = = G = = = = C = = = A C = = G = = T = = = = = ? G = = T = = ? ? T = G = = = = T = = = = = = = G = = = = = = = T = = A = = = = = G = = A = = = = G = = T D = = C = = = T = = = = A = = = G A = = T = = C = = = = = ? 0 E020 T G = C = A T = C = = = = C T C G = A = = = = = = = = = = C = C = A = = = = A = T = = T = = = T = A = G I = = A = = = G A = = = = = = ? A = = G ? A = = = = = = = = G A = T = G A = T = = = = T C T A = G = = = = = = = = = = G = T = G = = = = T = G = = A = = = C = T = T D = = C = = = T G = = = = = = ? G = = C ? G = = = = = = = = 0 E021 T = G C = A ? ? C G = = C C = C G = = G T = = = = C = = = = = = = = = = = = A = T G = T = = = = = = A G I = = A = ? = G = = = ? = = ? ? A = = = = = = = = = = = = = G = T T = G ? ? T A = = G T = T A = = A C = = = = T = = = = = = = = = = = = T = G T = A = = = = = = G T D = = C = ? = T = = = ? = = ? ? G = = = = = = = = = = = = = 0 E022 = G T = = = = = = A = = G = T = = = A A C = = = = T = = = C = C = A = = = = A = T = = = = = = T = A = G I = (C) A = ? = G A = = = = = = D A = = G = A = = = = = = = = = A G = = = = = = G = = C = C = = = G G T = = = = C = = = G = T = G = = = = T = G = = = = = = C = T = T D = (T) C = ? = T G = = = = = = I G = = C = G = = = = = = = = 0 E023 T G = C = A T = C = = = = C T C G = A = = = = = = = = = = C = C = A = = = = A = T = = = = = = T = A = G I = = A = = (G) G A = = = = = = D A = = G = A = = = = = = = = G A = T = G A = T = = = = T C T A = G = = = = = = = = = = G = T = G = = = = T = G = = = = = = C = T = T D = = C = = (C) T G = = = = = = I G = = C = G = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = = = 0.64 0.64 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 = = = 0.93 = = = 0.93 = = = = 0.93 = = 0.93 0.93 = = = 0.93 = = = = 0.98 = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = = = ? = = = = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 1.00 1.00 = = = = 1.00 = = = = = 1.00 = = = = = = = = 1.00 = = 1.00 = = 1.00 = 1.00 = 1.00 = = 1.00 = = 1.00 1.00 = = = = = 1.00 = = 1.00 = = = = = 1.00 = = = = = = 1.00 = = = = = = = = = = = = 1.00 = = 1.00 = = = = = = = ? = = = = = = = = = = = = 1.00 = = = = = ? ? ? 0.94 = = 0.94 = = = 0.94 = = = = = = = = = = = = 0.95 = = = = = = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = 1.00 = = 1.00 = 0.66 = 1.00 = 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 = = = = = = 0.72 = = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? ? ? = ? = 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 = = = = = = 0.62 = 1.00 = = = = = = = = = = 1.00 1.00 = = 1.00 = = = 1.00 = = = = = ? = 1.00 1.00 = = = = = = = 1.00 ? = = 1.00 = 0.66 = = 0.66 0.66 = 0.66 = 0.66 = 0.66 = = = = = = = = = = 0.93 0.93 0.93 = = ? = = = = = = 1.00 = = = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 = = ? ? ? = 1.00 = = = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = = = = = = = = = = ? ? ? = 1.00 = = 1.00 = = 1.00 = = = = = = = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = 1.00 = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = 0.97 = = = = 0.97 1.00 = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = 1.00 = = = 1.00 1.00 = = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 1.00 = = = ? 1.00 ? ? 1.00 = 1.00 = = = = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 1.00 = 1.00 ? ? ? = 1.00 = ? 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 = = = = 1.00 ? ? 1.00 = 1.00 = = = = = 1.00 = = = 1.00 = 0.77 = = 0.77 = = 0.77 = 0.77 = 0.77 0.75 = = = = 0.56 = = = = = = = = = = = = = = 0.88 = 0.88 = 0.88 = = 0.88 = = = = = = = = = = = = 0.89 = = = = = = = = = 0.89 0.89 = = = = = = = = = = = = = = = = = = = = = = = = 0.92 = = = 0.92 0.92 = = 0.92 = = 0.92 = = 0.92 = = = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = = = ? ? ? = 1.00 = 1.00 = = = = = 1.00 1.00 1.00 1.00 = = = = 1.00 ? ? 1.00 = 1.00 = = = = = = = = = 1.00 = = = = = = 0.86 = = = = 0.86 = = 0.86 = = 0.86 = 0.86 = = = = 1.00 = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 1.00 1.00 = = = = 1.00 = = = 1.00 = 1.00 = = = ? = = = = 0.84 = = 0.84 = = 0.84 = 0.84 = 0.84 = = ? = 0.84 0.84 = = = = = = = = = ? = 0.78 = = 1.00 = = 0.80 = = = = = 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 = = = = = 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 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 = = = = = 0.96 = = = = = = = = 0.93 = = = = = = 0.93 = = = = = = = = = = = = 0.93 = = 0.93 = = = = = = = = = = = = = = = = = = = = 0.93 = = = = = 1.00 = = 1.00 1.00 = ? ? 1.00 = 1.00 1.00 = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 = = = = = 1.00 = = = 1.00 1.00 = = = = = = = 1.00 1.00 = 1.00 = = = ? = = 1.00 = = = 1.00 = = = = 1.00 ? ? = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = = 1.00 1.00 = = 1.00 = = 1.00 = = 1.00 = = = = = = = = 1.00 = = 1.00 = = = 1.00 = = = = = = = = = 1.00 = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = 1.00 = = = = 1.00 = = 1.00 = = 1.00 = ? = = = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = ? ? = = 1.00 1.00 = = 1.00 = 1.00 = = = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = 1.00 = = 1.00 ? 1.00 = = 1.00 = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.93 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = 0.78 = = = = = = 0.62 = = = = = = = = = = = = = = = = = = = = = = = 0.50 0.71 = = = = = = = = = = = = 0.78 = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = ? = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = = = 1.00 = = = 1.00 1.00 = 1.00 = = = = = = = = ? = 1.00 = = 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 = 0.71 0.71 = = = = 0.53 = 0.71 = = 0.71 = 0.71 = = = 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 0.98 = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = ? = = 1.00 = 1.00 1.00 = = ? = = = = = = 1.00 = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 ? ? 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 = = = = = = 1.00 1.00 = ? 1.00 = 1.00 = = = = = = = = = 1.00 = = = 1.00 = = = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = = = = 1.00 = = ? = = = = = = = 1.00 = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = ? ? ? 1.00 = 1.00 = = = = = 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = ? = = 1.00 1.00 = = = = 1.00 = = = ? ? 1.00 ? ? ? = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 = = = = = = 1.00 = = = = = = = = ? ? ? ? 1.00 = = = = = = 1.00 = = = = = = = ? ? = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = = 1.00 = 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 = 1.00 = = = 1.00 1.00 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 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 1.00 = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 = = = = 1.00 1.00 = = 1.00 1.00 = = ? = = = ? = = 1.00 = 1.00 = ? ? = = = = = ? 1.00 1.00 = ? = = = = = = ? ? = = = = = = = = = = 1.00 = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = ? = = ? = 1.00 1.00 = = ? = = = 1.00 1.00 = ? ? = 1.00 = = = = ? ? ? ? ? = = 0.94 = = 0.94 = 0.94 = 0.94 = = = = 0.94 = = = = = = = 0.94 = = = = = = = 1.00 = = 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 = = ? ? 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 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 = = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 1.00 = = = = = = ? 1.00 = = 1.00 ? 1.00 = = = = = = = = 1.00 = 1.00 1.00 = 1.00 ? ? 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = = = = 1.00 = = = = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 = = = = = = 1.00 1.00 1.00 = = 1.00 = ? = 1.00 = = = ? = = ? ? 1.00 = = = = = = = = = = = = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 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 1.00 = ? = 1.00 1.00 = = = = = = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 = 1.00 = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 0.64 1.00 1.00 = = = = = = 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = END PHASEPROBS