************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 protz.phase.inp protz.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST protz.phase.out_freqs : haplotype frequency estimates protz.phase.out_pairs : most likely haplotype pairs for each individual protz.phase.out_recom : estimates of recombination parameters protz.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 44 Positions of loci: 274 557 737 1034 1882 2188 2241 2773 3145 3511 3759 4121 6621 7629 7739 7822 7924 7931 8435 8843 8870 9058 9823 9977 10109 10352 10399 10520 10699 10709 11060 11400 11403 11452 11511 11872 12108 13011 13187 13235 14522 15040 15375 15996 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file protz.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TTCAGAGAGDCTCATAGTGAGCGCCCAAGCITGCGGGCCAGCCG 1.000000 2 TTCAGAGAGDTCAATAGTATGCAACTCAAGIGACGCGCTGTTTG 1.000000 3 TTCAGAGAGDTCAATAGTGTGCAACTCAAGIGACGCGCTGTTTG 1.000000 4 TTCAGAGAGDTCAATAGTGTGCGCCCAAGCITACAGGCTAGCCG 1.000000 5 TTCAGAGAGDTCAATAGTGTGCGCTCAAGCITACAGGCTAGCCG 3.000000 6 TTCAGAGAGDTCATCGGTGTGCGCTCAAGCITACAGGCTAGCCG 1.000000 7 TTCGAAGAGDCCCACGGTGAGCGCCCAAGCDTGCGGGCCAGCCG 2.000000 8 TTCGAAGAGDCCCACGGAATACGCCTCGAGITATGCTGTGTCCA 3.000000 9 TTCGAAGAGDCCCTCAGTGAGCGCTCAAGCITACAGGCTAGCCG 1.000000 10 TTCGAAGAGDCCCTCGGTGAGCGCCCAAGCDTGCGGGCCAGCCG 36.000000 11 TTCGAAGAGDCCCTCGGTGAGCGCCCAAGCITACAGGCTAGCCG 2.000000 12 TTCGAAGAGDCCCTCGGTGAGTGCCCAAGCDTGCGGGCCAGCCG 18.000000 13 TTCGAAGAGDCTAATAGTGTGCAACTCAAGIGACGCGCTGTTTG 1.000000 14 TTCGAAGGGDCCCACGGTGAGCGCTCAAGCITACAGGCTAGCCG 1.000000 15 TTCGAAGGGDCCCTCGGTGAGCGCCCAAGCDTGCGGGCCAGCCG 1.000000 16 TTCGAGAGADCTCACGGAATACGCCTCGAGITATGCTGTGTCCA 1.000000 17 TTCGAGAGAICTCACGGAATACGCCTCGAGITATGCTGTGTCCA 6.000000 18 TTCGGAGAGDCCCACGGTATGCGCCTCAAGIGACGCGCTGTCCG 1.000000 19 TTCGGAGAGICCCACGGTATGCGCCTCGAGITACGCTCTGTCCA 1.000000 20 TTCGGGAGGICTCTCGGTGAGCGCCCAAGCITGCGGGCCAGCCG 2.000000 21 TTCGGGAGAICTCACGGAATACGCCTCGAGITATGCTGTGTCCA 4.000000 22 TTTGGAGGGDCTCATAGTGAGCGCTCAAGCITACAGGCTAGCCG 1.000000 23 TTTGGGGGGDCTCATGATGTGCGCTCAAGCITACAGGCTAGCCG 1.000000 24 TTTGGGGGGDCTCATGATGTGCGCTCAAGCITACAGGCTAGTCG 1.000000 25 GCCAAAGAGDCCCACGGTGAGCGCTCAAGCITACAGGCTAGCCG 2.000000 26 GCCAAAGAGDCCCTCGGTGAGCGCTCAAGCITACAGGCTAGCCG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (2,10) D002: (9,23) D003: (10,10) D004: (11,21) D005: (10,10) D006: (10,20) D007: (10,25) D008: (5,25) D009: (20,24) D010: (7,10) D011: (7,11) D012: (5,10) D013: (1,22) D014: (8,10) D015: (14,19) D016: (12,26) D033: (10,18) D034: (5,15) D035: (4,10) D036: (10,10) D037: (3,13) D038: (10,10) D039: (6,10) D040: (10,12) E001: (10,21) E002: (10,10) E003: (10,21) E004: (10,21) E005: (8,12) E006: (10,10) E007: (8,10) E008: (10,10) E009: (12,17) E010: (10,12) E011: (10,10) E012: (12,17) E013: (10,12) E014: (12,12) E015: (12,16) E016: (10,12) E017: (10,17) E018: (12,12) E019: (12,12) E020: (12,17) E021: (12,17) E022: (10,10) E023: (12,17) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T T C A G A G A G D T C A A T A G T A T G C A A C T C A A G I G A C G C G C T G T T T G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D002 T T C G A A G A G D C C C T C (A) G T G A G C G C T C A A G C I T A C A G G C T A G C C G T T T G G G G G G D C T C A T (G) A T G T G C G C T C A A G C I T A C A G G C T A G C C G 0 D003 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D004 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C I T A C A G G C T A G C C G T T C G G G A G A I C T C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A 0 D005 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D006 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G G G A G G I C T C T C G G T G A G C G C C C A A G C I T G C G G G C C A G C C G 0 D007 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G G C C A A A G A G D C C C A C G G T G A G C G C T C A A G C I T A C A G G C T A G C C G 0 D008 T T C A G A G A G D T C A A T A G T G T G C G C T C A A G C I T A C A G G C T A G C C G G C C A A A G A G D C C C A C G G T G A G C G C T C A A G C I T A C A G G C T A G C C G 0 D009 T T C G G G A G G I C T C T C G G T G A G C G C C C A A G C I T G C G G G C C A G (C) C G T T T G G G G G G D C T C A T G A T G T G C G C T C A A G C I T A C A G G C T A G (T) C G 0 D010 T T C G A A G A G D C C C A C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D011 T T C G A A G A G D C C C (A) C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C (T) C G G T G A G C G C C C A A G C I T A C A G G C T A G C C G 0 D012 T T C A G A G A G D T C A A T A G T G T G C G C T C A A G C I T A C A G G C T A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D013 T T (C) (A) G A G (A) G D C T C A T A G T G A G C G C C C A A G C I T G C G G G C C A G C C G T T (T) (G) G A G (G) G D C T C A T A G T G A G C G C T C A A G C I T A C A G G C T A G C C G 0 D014 T T C G A A G A G D C C C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D015 T T C G (A) A G (G) G (D) C C C A C [G] G T G A G C G C T C A A G C I T A C A G G C T A G C C G T T C G (G) A G (A) G (I) C C C A C G G [T] A T G C G C C T C G A G I T A C G C T C T G T C C A 0 D016 (T) (T) C [G] A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G (G) (C) C A A A G A G D C C C T C G G T G A G C G C T C A A G C I T A C A G G C T A G C C G 0 D033 T T C G (A) A G A G D C C C (T) C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G (G) A G A G D C C C (A) C G G T A T G C G C C T C A A G I [G] A C G C G C T G T C C G 0 D034 T T C A G A G (A) G D T C A A T A G T G T G C G C T C A A G C I T A C A G G C T A G C C G T T C G A A G (G) G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D035 T T C A G A G A G D T C A A T A G T G T G C G C C C A A G C (I) T (A) C (A) G G C [T] A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C (D) T (G) C (G) G G C C A G C C G 0 D036 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D037 T T C A G A G A G D T C A A T A G T G T G C A A C T C A A G I G A C G C G C T G T T T G T T C G A A G A G D C T A A T A G T G T G C A A C T C A A G I G A C G C G C T G T T T G 0 D038 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C [T] C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D039 T T C (A) (G) A G A G D (T) C (A) T C G G T G T G C G C T C A A G C I T A C A G G C T A G C C G T T C (G) (A) A G A G D (C) C (C) T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 D040 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E001 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G G G A G A I C T C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A 0 E002 T T C G A A G A G D C C C T C G G T G A G [C] G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E003 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G G G A G A I C T C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A 0 E004 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G G G A G A I C T C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A 0 E005 T T C G A A G A G D C C C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E006 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E007 T T C G A A G A G D C C C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E008 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E009 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A I C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A 0 E010 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E011 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E012 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A [I] C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A 0 E013 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E014 T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E015 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A D C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A 0 E016 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E017 T T C G A A G A G D C C C T C G G T G A G [C] G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A I C T C A C G G A A T A C G C C T C G A G I T A T G C T G T G T C C A 0 E018 T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E019 T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C T C G G T G A G T G C C C A A G C D T G C G G G C C A G C C G 0 E020 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A I C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A 0 E021 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A I C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A 0 E022 T T C G A A G A G D C C C T C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G T T C G A A G A G D C C C [T] C G G T G A G C G C C C A A G C D T G C G G G C C A G C C G 0 E023 T T C G A A G A G D C C C T C G G T G A G (T) G C C C A A G C D T G C G G G C C A G C C G T T C G A G A G A I C T C A C G G A A T A (C) G C C T C G A G I T A T G C T G T G T C C A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 D001 = = = A G = = = = = T = A A ? A ? = A T = = A A = T C = A G I G A = = C = = T G T T T = = = = G A = = = = = C = C T ? G ? = G A = = G C = C A = G C D T G = = G = = C A G C C = 0 D002 = = C = A A = A = = = C = T C (A) G = = A = ? = = = = = = = = = = = = = = = = = = = = = = = = T = G G = G = = = T = A T (G) A = = T = ? = = = = = = = = = = = = = = = = = = = = = = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = 0 D004 = = = = A A G A G D = C = T = = = T G A G = = = = C A A G C = = = C A G G C = A G = = G = = = = G G A G A I = T = A = = = A A T A = = = = T C G A G = = = T G C T G = G T = = A 0 D005 = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D006 = = = = A A G A = D = C = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = G G A G = I = T = = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = 0 D007 T T = G = = = = = = = = = ? ? ? ? ? = = = = = = C = = = = = D = G = G = = = C = = = = = G C = A = = = = = = = = = ? ? ? ? ? = = = = = = T = = = = = I = A = A = = = T = = = = = 0 D008 T T = = G = = = ? ? T = A = T A = = = T = = = = = = = = = = = = = = = = = = = = ? = = = G C = = A = = = ? ? C = C = C G = = = A = = = = = = = = = = = = = = = = = = = = ? = = = 0 D009 = = C = = ? ? = = I = = = T C = G = = A = = = = C = = = = = = = G = G = = = C = = (C) = = = = T = = ? ? = = D = = = A T = A = = T = = = = T = = = = = = = A = A = = = T = = (T) = = 0 D010 = = = = = = = = = = = = = A ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D011 = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = ? = G = G = = = C = ? = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = = = = = = ? = A = A = = = T = ? = = = 0 D012 = = = A G = = = = = T = A ? ? A = = = T = = = ? T = = = = = I = A = A = = = T = = = = = = = = G A = = = = = C = C ? ? G = = = A = = = ? C = = = = = D = G = G = = = C = = = = = 0 D013 = = (C) (A) = = = (A) = = = = = = = = = = = = = = = = C = = = = = = = G = G = = = C = = = = = = = (T) (G) = = = (G) = = = = = = = = = = = = = = = = T = = = = = = = A = A = = = T = = = = = 0 D014 = = = = = = = = = = = = = ? = = = A A T A = = = = T C G A G I = A T = C T G T G T = = A = = = = = = = = = = = = = ? = = = T G A G = = = = C A A G C D = G C = G G C C A G = = G 0 D015 = = = = (A) = = (G) = (D) = = ? = ? ? ? ? G A = = = = T C A A G C = = = = A G G = = A G = = G = = = = (G) = = (A) = (I) = = ? = ? ? ? ? A T = = = = C T C G A G = = = = G C T = = G T = = A 0 D016 (T) (T) = ? = = = = ? = = = ? = = = = = = = = T = = C = = = = = D = G = G = = = C = = = = = (G) (C) = ? = = = = ? = = = ? = = = = = = = = C = = T = = = = = I = A = A = = = T = = = = = 0 D033 = = = = (A) = = = = = = = = (T) = = = = G A = = = = = C A = G C ? ? ? ? ? G = = C A G = = = = = = = (G) = = = = = = = = (A) = = = = A T = = = = = T C = A G ? ? ? ? ? C = = T G T = = = 0 D034 = = = A G = = (A) = = ? = A A T A = = = T = = = = T = = = = = I ? ? ? ? = = ? ? ? = = = = = = = G A = = (G) = = ? = C T C G = = = A = = = = C = = = = = D ? ? ? ? = = ? ? ? = = = = 0 D035 = = = A G = = = = = T = A ? T A = = = T = = = = = = = = = = (I) = (A) = (A) = = ? ? ? = = = = = = = G A = = = = = C = C ? C G = = = A = = = = = = = = = = (D) = (G) = (G) = = ? ? ? = = = = 0 D036 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = 0 D037 = = = A G = = = = = T C = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G A = = = = = C T = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D038 = = = = = = = = = ? = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? 0 D039 = = = (A) (G) = = = = = (T) ? (A) = = = = = = T = = = = T = = = = = I = A = A = = = T = = = = = = = = (G) (A) = = = = = (C) ? (C) = = = = = = A = = = = C = = = = = D = G = G = = = C = = = = = 0 D040 = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = 0 E001 = = = = A A G A G D ? C = T = = = T G A G = = = = C A A G C D ? ? ? ? G G C C A G = = G = = = = G G A G A I ? T = A = = = A A T A = = = = T C G A G I ? ? ? ? C T G T G T = = A 0 E002 = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = 0 E003 = = = = A A G A G D = C = T = = = T G A G = = = = C A A G C D = G C = G G ? C A G = = G = = = = G G A G A I = T = A = = = A A T A = = = = T C G A G I = A T = C T ? T G T = = A 0 E004 = = = = A A G A G D ? C = T = = = T G A G = = = = C A A G C D = G C = G G C C A G = = G = = = = G G A G A I ? T = A = = = A A T A = = = = T C G A G I = A T = C T G T G T = = A 0 E005 = = = = = = = = = = = = = A = = = A A T A C = = = T C G A G I = A T = C T G T G ? = = A = = = = = = = = = = = = = T = = = T G A G T = = = C A A G C D = G C = G G C C A ? = = G 0 E006 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = 0 E007 = = = = = = = = = = = = = A = = = A A T A = = = = T C G A G I = A T = C T G T G T = = A = = = = = = = = = = = = = T = = = T G A G = = = = C A A G C D = G C = G G C C A G = = G 0 E008 = = = = = ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 E009 = = = = = A G A G D = C = T = = = T G A G (T) = = = C A A G C D = G C = G G C C A G = = G = = = = = G A G A I = T = A = = = A A T A (C) = = = T C G A G I = A T = C T G T G T = = A 0 E010 = = = = = = = = = = ? = = ? = = ? = = = = C = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? = = ? = = ? = = = = T = = = = = = = = = = = = = = = = = = = = = ? 0 E011 = = = = = = = = ? = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = 0 E012 = = = = = A G A G ? = C = T = = = T G A G (T) = = = C A A G C D = G C = G G C C A G = = G = = = = = G A G A ? = T = A = = = A A T A (C) = = = T C G A G I = A T = C T G T G T = = A 0 E013 = = = = = = = = = = ? = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = 0 E015 = = = = = A G A G = = C = T = = = T G A G (T) = = = C A A G C D = G C = G G C C A G = = G = = = = = G A G A = = T = A = = = A A T A (C) = = = T C G A G I = A T = C T G T G T = = A 0 E016 = = = = = = = = ? = = = = = = = = = = = = C = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = T = = = = = = = = = ? ? ? ? = = = = = = = = = 0 E017 = = = = = A G A G D = C ? T = = = T G ? ? ? = = = C A A G C ? = G C = G G C C A ? = = G = = = = = G A G A I = T ? A = = = A A ? ? ? = = = T C G A G ? = A T = C T G T G ? = = A 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? 0 E019 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0 E020 = = = = = A G A G D = C = T ? = = T G A G (T) = = = C A A G C D = G C = G G C C A G = = G = = = = = G A G A I = T = A ? = = A A T A (C) = = = T C G A G I = A T = C T G T G T = = A 0 E021 = = = = = A G A G D = C = T = = = T G ? ? (T) = = = C A A G C D = G C = G G C C A G = = G = = = = = G A G A I = T = A = = = A A ? ? (C) = = = T C G A G I = A T = C T G T G T = = A 0 E022 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E023 = = = = = A G A G D = C = T = = = T G A G (T) = = = C A A G C D = G C = G G C C A ? = = ? = = = = = G A G A I = T = A = = = A A T A (C) = = = T C G A G I = A T = C T G T G ? = = ? END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = 0.98 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 0.98 = 1.00 = = = 1.00 = 1.00 1.00 0.71 0.97 = = 0.95 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = ? = = = = = = = 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 = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = ? ? ? ? ? = = = = = = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = 1.00 1.00 = = 1.00 = = = ? ? 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 = = ? ? = = 1.00 = = = 1.00 1.00 = 1.00 = = 1.00 = = = = 1.00 = = = = = = = 1.00 = 1.00 = = = 1.00 = = 0.56 = = = = = = = = = = = = = = = 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 = 1.00 = = = 1.00 = = = = = = = 0.60 0.61 = = = 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 = = 1.00 = = = = 0.54 = = 0.64 = 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 0.87 0.87 = ? = = = = ? = = = ? = = = = = = = = 0.95 = = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = = = = = 0.73 = = = = = = = = 0.85 = = = = 0.99 0.99 = = = = = 1.00 1.00 = 1.00 1.00 ? ? ? ? ? 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = 0.51 = = ? = 1.00 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 = = = = = 1.00 ? ? ? ? = = ? ? ? = = = = = = = 1.00 1.00 = = = = = 1.00 = 1.00 ? 1.00 1.00 = = = 1.00 = = = = = = = = = = 0.80 = 0.80 = 0.80 = = ? ? ? = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = 0.94 0.94 = = = = = 1.00 1.00 = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = 0.54 0.54 = = = = = 0.54 ? 0.54 = = = = = = 0.93 = = = = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 1.00 1.00 1.00 1.00 1.00 ? 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = 0.97 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 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 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 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 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 0.79 = = = 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 1.00 ? = 1.00 = 1.00 = = = 1.00 1.00 1.00 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 1.00 1.00 = = 1.00 = = = = = = = = = = ? = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 0.79 = = = 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 1.00 1.00 = 1.00 ? 1.00 = = = 1.00 1.00 ? ? ? = = = 1.00 1.00 1.00 1.00 1.00 ? = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? = = 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 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 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 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 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 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? = = ? END PHASEPROBS