************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 tnr1a.phase.inp tnr1a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST tnr1a.phase.out_freqs : haplotype frequency estimates tnr1a.phase.out_pairs : most likely haplotype pairs for each individual tnr1a.phase.out_recom : estimates of recombination parameters tnr1a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 38 Positions of loci: 685 718 1596 1625 1823 2241 2547 2608 2991 3802 3975 3976 4071 4506 5664 5749 6196 6201 6247 6410 7205 7776 9375 10186 10841 11186 11678 11839 12502 13178 13899 13900 15042 15475 15536 15660 15799 16017 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file tnr1a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCGAAGAT 1 GGCAATGTGDTGCTCCACCAGGGGCDTAI 1.000000 2 CCGAAGAT 2 GGCAATGCADCGCTCCACGAAGGGCDTAI 2.000000 3 CCGAAGAT 2 GGCAATGTGDTGCTCCACCAGGGGCDTAI 23.000000 4 CCGAAGAT 2 GGCAATGTGDTGCTCCACCAGGGGCITAD 3.000000 5 CCGAAGAT 2 GGCAATGTGDTGCTCCGCCAGGGGCDTAI 2.000000 6 CCGAAGAT 2 GGCAATGTGDTGCTCCGCCAGGGGCDTGD 1.000000 7 CCGAAGAT 2 GGCAATGTGDTGCTCTACGAAGGGCITAD 1.000000 8 CCGAAGAT 2 GGCAACGTGDTGCTCCACCAGGGGCDTAI 1.000000 9 CGGAAGAT 2 GGCGACGCADCTCTCCACGAAGGGCDTGI 2.000000 10 CGGAAGAT 2 CAAGATACADCGCTCCACGAAGGGCDTAD 1.000000 11 CGGAAAAT 2 GGCGATGCADCGTTCCACGAATTGCDTGI 2.000000 12 CGGAAAAT 2 GGCGATGCADCGTTCCACGAATTGTDTAD 1.000000 13 CGGAAAAT 2 GGCGATGCADCGTTCCACGAATTGTDCAD 3.000000 14 CGGAAAAT 2 GGCGATACADCGCTCCGCCAAGGGTDTAD 1.000000 15 CGGAAAAT 2 GGCGACGCADCTCTCCACCAAGGGCDTAD 1.000000 16 CGGAAAAT 2 CAAGATACADCGCTCCACGAAGGGCDTAI 1.000000 17 CGGAAAAT 2 CAAGATACADCGCTCCACGAAGGGCDTAD 4.000000 18 CGGAAAAT 3 GGCGGTACADCTCGCCACGGAGGGCDTGI 2.000000 19 CGTAAAAT 2 GGCGACGCADCTCTCTACGAAGGGCDTAI 5.000000 20 CGTAAAAT 2 GGCGACGCADCTCTCTACGAAGGGCDTAD 1.000000 21 CGTAAAAT 2 GGCGACGCADCTCTCTACGAAGGGCITAD 13.000000 22 CGTAAAAT 3 GGCGGTACADCTCGCCACGGAGGGCDTGI 1.000000 23 TGGGAGGC 2 GGCGATGCAICGCGCCACCAGGGACDTAI 1.000000 24 TGGGAGGC 2 GGCGATGCAICGCGCCACCAGGGGCDTGD 2.000000 25 TGGGAGGC 2 GGCGATGCAICGCGTCACCAGGGACDTAI 3.000000 26 TGGGAGGC 2 GGCGATGCAICGCGTCACCAGGGGCDTAI 2.000000 27 TGGGAGGC 2 GGCGATGCAICGCGTCACCAGGGGCITAD 1.000000 28 TGGGAAGC 2 GGCGATGCAICGCGCCACCAGGGGCDTAD 1.000000 29 TGGGAAGC 2 GGCGATGCAICGCGCCATCAAGGGCDTAI 1.000000 30 TGGGAAGC 2 GGCGATGCAICGCGCCATCAAGGGCDTGI 1.000000 31 TGGGAAGC 2 GGCGATGCAICGCGCCATCAAGGGCDTGD 2.000000 32 TGGGAAGC 2 GGCGATGCAICGCGCCATCAAGGGCITAI 1.000000 33 TGGGAAGC 2 GGCGATGCAICGCGCCATCAAGGGTDTAD 2.000000 34 TGGGAAGC 2 GGCGATGCAICGCTCCATCAAGGGTDTAD 1.000000 35 TGGGAAAC 2 GGCGATGCADCTCGCCACGAAGGGCDTAD 1.000000 36 TGGGCAGC 2 GGCGATACADCGCTCCGCCAAGGATDTAD 1.000000 37 TGGGCAGC 2 GGCGATACADCGCTCCGCCAAGGGCDTAD 1.000000 38 TGGGCAGC 2 GGCGATACADCGCTCCGCCAAGGGCITAD 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (3,23) D002: (25,31) D003: (18,33) D004: (13,27) D005: (13,36) D006: (21,37) D007: (16,21) D008: (12,18) D009: (10,26) D010: (2,24) D011: (5,24) D012: (11,26) D013: (9,28) D014: (3,25) D015: (19,33) D016: (14,31) D033: (21,38) D034: (3,30) D035: (29,35) D036: (9,22) D037: (11,32) D038: (5,34) D039: (6,17) D040: (13,25) E001: (1,3) E002: (17,21) E003: (3,3) E004: (4,17) E005: (3,3) E006: (7,21) E007: (3,21) E008: (3,17) E009: (19,19) E010: (3,19) E011: (21,21) E012: (3,3) E013: (3,21) E014: (4,21) E015: (3,19) E016: (8,21) E017: (3,21) E018: (3,3) E019: (3,20) E020: (2,3) E021: (3,3) E022: (4,21) E023: (3,15) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G (G) C D T A I T G G G A G G C 2 G G C G A T G C A I C G C G C C A C C A G G G (A) C D T A I 0 D002 T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G A C D T A I T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G C D T G D 0 D003 C G G A A A A T 3 G G C G G T A C A D C T C G C C A C G G A G G G C D T G I T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G T D T A D 0 D004 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T G T D C A D T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G G C I T A D 0 D005 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T (G) T D C A D T G G G C A G C 2 G G C G A T A C A D C G C T C C G C C A A G G (A) T D T A D 0 D006 C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D T G G G C A G C 2 G G C G A T A C A D C G C T C C G C C A A G G [G] [C] [D] T A D 0 D007 C G G A A A A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 D008 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T G (T) D T (A) (D) C G G A A A A T 3 G G C G G T A C A D C T C G C C A C G G A G G G (C) D T (G) (I) 0 D009 C G G A A G A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A D T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G G C D T A I 0 D010 C C G A A G A T 2 G G C A A T G C A D C G C T C C A C G A A G G G C D T (A) (I) T G G G A G G C 2 G G C G A T G C A I C G C G [C] C A C C A G G G G C D T (G) (D) 0 D011 C C G A A G A T 2 G G C A A T G T G D T G C T C C (G) C C A G G G G C D T (A) (I) T G G G A G G C 2 G G C G A T G C A I C G C G C C (A) C C A G G G G C D T (G) (D) 0 D012 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T G C D T (G) I T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G G C D T (A) I 0 D013 C G G A A (G) A T 2 G G C G A C G C A D C T C T C C A C G A A G G G C D T (G) (I) T G G G A (A) G C 2 G G C G A T G C A I C G C G C C A C C A G G G G C D T (A) (D) 0 D014 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G A C D T A I 0 D015 C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A I T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G T D T A D 0 D016 C G G A A A A T 2 G G C G A T A C A D C G C T C C G C C A A G G G (T) D T (A) D T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G (C) D T (G) D 0 D033 C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D T G G G C A G C 2 G G C G A T A C A D C G C T C C G C C A A G G G C I T A D 0 D034 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T (A) I T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G C D T (G) I 0 D035 T G G G A A (G) C 2 G G C G A T G C A I C G C G C C A T C A A G G G C D T A (I) T G G G A A (A) C 2 G G C G A T G C A D C T C G C C A C G A A G G G C D T A (D) 0 D036 C G G A A G A T 2 G G C G A C G C A D C T C T C C A C G A A G G G C D T G I C G T A A A A T 3 G G C G G T A C A D C T C G C C A C G G A G G G C D T G I 0 D037 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T G C (D) T (G) I T G G G A A G C 2 G G C G A T G C A I C G C G C C A T C A A G G G C (I) T (A) I 0 D038 C C G A A G A T 2 G G C A A T G T G D T G C T C C (G) C C A G G G G C D T A I T G G G A A G C 2 G G C G A T G C A I C G C T C C (A) T C A A G G G T D T A D 0 D039 C C G A A G A T 2 G G C A A T G T G D T G C T C C G C C A G G G G C D T G D C G G A A A A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A D 0 D040 C G G A A A A T 2 G G C G A T G C A D C G T T C C A C G A A T T (G) T D C A D T G G G A G G C 2 G G C G A T G C A I C G C G T C A C C A G G G (A) C D T A I 0 E001 C C G A A G A T 1 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E002 C G G A A A A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A D C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E003 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E004 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C I T A D C G G A A A A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A D 0 E005 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E006 C C G A A G A T 2 G G C A A T G T G D T G C T C T A C G A A G G G C I T A D C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E007 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E008 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G G A A A A T 2 C A A G A T A C A D C G C T C C A C G A A G G G C D T A D 0 E009 C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A I 0 E010 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A I 0 E011 C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E012 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E013 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E014 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C I T A D C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E015 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A I 0 E016 C C G A A G A T 2 G G C A A C G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E017 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E018 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E019 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A (I) C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C D T A (D) 0 E020 C C G A A G A T 2 G G C A A T G C A D C G C T C C A C G A A G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E021 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C D T A I 0 E022 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A G G G G C I T A D C G T A A A A T 2 G G C G A C G C A D C T C T C T A C G A A G G G C I T A D 0 E023 C C G A A G A T 2 G G C A A T G T G D T G C T C C A C C A (G) G G G C D T A (I) C G G A A A A T 2 G G C G A C G C A D C T C T C C A C C A (A) G G G C D T A (D) 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 = A = = ? T = = = = A = = = ? ? D T = = T = = = = = = = = = (G) = = = = = T G = G = = ? C = = = = G = = = ? ? I C = = G = = = = = = = = = (A) = = = = = 0 D002 = = = = = G = = ? = = = = = = = = = = = = = = T = = C = = G = = A = = = A I = = = = = A = = ? = = = = = = = = = = = = = = C = = T = = A = = G = = = G D 0 D003 C = = A = = A T 3 = = = = G = A = = D = T = = = = = C G G ? = = = C = = G I T = = G = = G C 2 = = = = A = G = = I = G = = = = = T C A ? = = = T = = A D 0 D004 C = = A = A A T = = = = = = = = = = D = = ? T C = = = G = A T T = T D C = = T = = G = G G C = = = = = = = = = = I = = ? G T = = = C = G G G = C I T = = 0 D005 C = = A A = ? ? = = = = = = = G = = = = = T = = = A = G = = T T (G) = = C = = T = = G C = ? ? = = = = = = = A = = = = = C = = = G = C = = G G (A) = = T = = 0 D006 C = T A A = A T ? = = = = = C G = = = = T = = = T A = G = = = = ? ? ? = = = T = G G C = G C ? = = = = = T A = = = = G = = = C G = C = = = = ? ? ? = = = 0 D007 = = G = = = = = = C A A = = T A = = = = G ? = = C = = = = = = = ? = D = = I = = T = = = = = = G G C = = C G = = = = T ? = = T = = = = = = = ? = I = = D 0 D008 = = = = = = = = 2 = = = = A = G = = = = G ? T = = = = = A = T T = (T) = = (A) (D) = = = = = = = = 3 = = = = G = A = = = = T ? G = = = = = G = G G = (C) = = (G) (I) 0 D009 C = = A = = A T = C A A = = = A = = D = = = T C = = = G = A = = = = = = = D T = = G = = G C = G G C = = = G = = I = = = G T = = = C = G = = = = = = = I 0 D010 C C = A = = ? T = = = = A = = = = = D = = = T ? = = = G = A = = = = = = (A) (I) T G = G = = ? C = = = = G = = = = = I = = = G ? = = = C = G = = = = = = (G) (D) 0 D011 C C = A = = A T = = = = A = = = T G D T = = T = = (G) = = = = = = = = = = (A) (I) T G = G = = G C = = = = G = = = C A I C = = G = = (A) = = = = = = = = = = (G) (D) 0 D012 C = = A = A A T = = = = = = = = = = D = = T T C = = = G = A T T = = = = (G) = T = = G = G G C = = = = = = = = = = I = = C G T = = = C = G G G = = = = (A) = 0 D013 C = = A = (G) A T = = = = = = C = = = D = T = T = = = = G = A = = = = = = (G) (I) T = = G = (A) G C = = = = = = T = = = I = G = G = = = = C = G = = = = = = (A) (D) 0 D014 C C = A = = A T = = = = A = = = T G D T = = T C = = = = = = = = G = = = = = T G = G = = G C = = = = G = = = C A I C = = G T = = = = = = = = A = = = = = 0 D015 C = T A = = A T = = = = = = C = ? ? D = T = T = T = C G = = = = ? C = = = I T = G G = = G C = = = = = = T = ? ? I = G = G = C = T C = = = = ? T = = = D 0 D016 C = = A = = A T = = = = = = = A = = D = = = T = = G C = = = = = = (T) = = (A) = T = = G = = G C = = = = = = = G = = I = = = G = = A T = = = = = = (C) = = (G) = 0 D033 C = T A A = A T = = = = = = C G = = = = T = = = T A ? G = ? = = = = = = = = T = G G C = G C = = = = = = T A = = = = G = = = C G ? C = ? = = = = = = = = 0 D034 C C = A = G A T = = = = A = = = T G D T = = T = = = C = = G = = ? = = = (A) = T G = G = A G C = = = = G = = = C A I C = = G = = = T = = A = = ? = = = (G) = 0 D035 = = = = = = (G) = = = = = = = = = = = I = G = = = = = T C = = = = = = = = = (I) = = = = = = (A) = = = = = = = = = = = D = T = = = = = C G = = = = = = = = = (D) 0 D036 = = G = = G = = 2 = = = = A C G = = = = = = T ? = = = = A = = = = = = = = = = = T = = A = = 3 = = = = G T A = = = = = = G ? = = = = G = = = = = = = = = 0 D037 C = = A = = A T = = = = = = = = = = D = = T T = = = C G = = T T = = (D) = (G) = T = = G = = G C = = = = = = = = = = I = = C G = = = T C = = G G = = (I) = (A) = 0 D038 C C = A = G A T = = = = A = = = T G D T = = = = = (G) C = = G = = = C = = = I T G = G = A G C = = = = G = = = C A I C = = = = = (A) T = = A = = = T = = = D 0 D039 = C = = = G = = = G G C A = = G T G = T = = = = = G = C = G = = = = = = G = = G = = = A = = = C A A G = = A C A = C = = = = = A = G = A = = = = = = A = 0 D040 C = = A = A A ? = = = = = = = = = = D ? = T T C = = = G = A T T (G) T = C = D T = = G = G G ? = = = = = = = = = = I ? = C G T = = = C = G G G (A) C = T = I 0 E001 = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 2 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = = G = = = = = = C A A = = T A = = = = G = = ? C = = = = = = = = = D = = = = = T = = = = = = G G C = = C G = = = = T = = ? T = = = = = = = = = I = = = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = C = = = G = = = G G C A = = G T G = T = = = = = = = C = G = = = = I = = = = G = = = A = = = C A A G = = A C A = C = = = = = = = G = A = = = = D = = = 0 E005 = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 E006 = C G = = G = = = = = = A = T = T G = T G = = = = = = = = = = = = = = = = = = G T = = A = = = = = = G = C = C A = C T = = = = = = = = = = = = = = = = = 0 E007 = C G = = G = = = = = = A = T = T G = T G = = = C = = C = G = = = = D = = I = G T = = A = = = = = = G = C = C A = C T = = = T = = G = A = = = = I = = D 0 E008 = C = = = G ? = = G G C A = = G T G = T = = = = = = = C = G = = = = = = = I = G = = = A ? = = C A A G = = A C A = C = = = = = = = G = A = = = = = = = D 0 E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = C G = ? G = = = = = = A = T = T G = T G = = = C = = C = G = = = = = = = = = G T = ? A = = = = = = G = C = C A = C T = = = T = = G = A = = = = = = = = 0 E011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E013 = C ? = = G = = = = = = A = T = T G = T G = = = C = = C = G = = = = D = = I = G ? = = A = = = = = = G = C = C A = C T = = = T = = G = A = = = = I = = D 0 E014 = C G = = G = = = = = = A = ? ? ? G = T G = = = C = = C = ? = = = = = = = ? = G T = = A = = = = = = G = ? ? ? A = C T = = = T = = G = ? = = = = = = = ? 0 E015 = C G = = ? = = = = = = A = T = T G = T G = = = C = = C = G = = = = = = = = = G T = = ? = = = = = = G = C = C A = C T = = = T = = G = A = = = = = = = = 0 E016 = C G = = ? = = = = = = A = = = T G = T G = = = C = = C = G = = = = D = = I = G T = = ? = = = = = = G = = = C A = C T = = = T = = G = A = = = = I = = D 0 E017 = C G = = G = = = = = = A = T = T G = T G = = = C = = C = G = = = = D = = I = G T = = A = = = = = = G = C = C A = C T = = = T = = G = A = = = = I = = D 0 E018 = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 E019 = C G = = G = = = = = = A = T = T G = T G = = = C = = C = G = = = = = = = (I) = G T = = A = = = = = = G = C = C A = C T = = = T = = G = A = = = = = = = (D) 0 E020 = = = = = ? = = = = = = = = = = C A = C = = = = = = = G = A = = = = = = = = = = = = = ? = = = = = = = = = = T G = T = = = = = = = C = G = = = = = = = = 0 E021 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E022 = C G = = G = = = = = = A = T = T G = T G = = = C = = C = G = = = ? = = = = = G T = = A = = = = = = G = C = C A = C T = = = T = = G = A = = = ? = = = = 0 E023 = C = = = G = = = = = = A = T = T G = T G = = = = = = = = (G) = = = = = = = (I) = G = = = A = = = = = = G = C = C A = C T = = = = = = = = (A) = = = = = = = (D) 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 = = = = = = = = = 0.77 = = = = = = = = = = 1.00 = = ? = = = = = = = = = = = = = = 1.00 = = 1.00 = = 1.00 = = 1.00 = = = 1.00 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 = = 1.00 1.00 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 0.97 = = 1.00 = = 1.00 1.00 = ? ? = = = = = = = 0.99 = = = = = 0.99 = = = 0.99 = 0.99 = = 0.99 0.99 0.63 = = 0.99 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 ? = = = = = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 = 1.00 = = = = ? ? ? = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = 1.00 ? = = 1.00 = = = = = = = ? = 1.00 = = 1.00 = = = = = = = = 1.00 = = = = 1.00 = 1.00 = = = = 1.00 ? 1.00 = = = = = 1.00 = 1.00 1.00 = 0.75 = = 0.75 0.75 1.00 = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = = 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 = = = = = = = 0.97 1.00 1.00 = 1.00 = = ? 1.00 = = = = 1.00 = = = = = 1.00 = = = 1.00 ? = = = 0.99 = 0.99 = = = = = = 0.84 0.81 1.00 1.00 = 1.00 = = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 = = 0.89 = = = = = = = = = = 0.53 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 = = = = 0.85 = 1.00 = = 1.00 = 0.51 1.00 1.00 = = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = = = = 0.98 = 0.98 = = = = = = 0.52 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 = = = = = = = = 0.97 = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = 1.00 = ? ? 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = ? 0.96 = = = 0.96 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = 1.00 = = 1.00 = = = 1.00 = = 1.00 1.00 = = = = = = 0.60 = = 0.60 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 ? 1.00 = ? = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 = = 1.00 = = ? = = = 0.83 = = = = = = = 0.51 = = = = = = = = = = = 0.95 = 0.95 = = = = = 1.00 1.00 = = = = = = = = = 0.79 = = 1.00 = = 1.00 = = 1.00 = = = = 1.00 1.00 1.00 = = = = = = 1.00 ? = = = = 1.00 = = = = = = = = = 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 = = 0.74 = 0.80 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = 0.69 0.95 = = 1.00 = = = 0.98 = = = 0.98 = 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 0.81 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = 1.00 = = ? 1.00 = = = = = = = = = 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = = = = 0.98 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 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 = = = = 0.90 = = 0.90 = 1.00 = = = 1.00 ? = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = = = = = = = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = ? 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 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 = 1.00 1.00 = = 1.00 = = = = = = 1.00 = ? ? ? 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = ? = = = = = = = ? = 1.00 1.00 = = ? = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = = = = = = = 1.00 1.00 = = ? = = = = = = 1.00 = = = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = = 0.90 = = 0.90 = 1.00 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = = 0.91 = = 0.91 = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = = = = = 0.68 = = = = = ? = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 = = = ? = = = = = 1.00 = = = 0.96 = = = = = = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = 0.74 = = = = = = = 0.60 END PHASEPROBS