************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 stat4.phase.inp stat4.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST stat4.phase.out_freqs : haplotype frequency estimates stat4.phase.out_pairs : most likely haplotype pairs for each individual stat4.phase.out_recom : estimates of recombination parameters stat4.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 49 Positions of loci: 446 891 2278 5595 8686 8888 9623 12255 13429 13529 14441 14897 15099 15513 17679 18043 18295 18330 19113 19306 20176 20655 20693 20878 38580 38701 38829 39162 43269 44769 44790 45686 46178 46881 47002 47154 47673 47677 48111 48516 48548 49577 49847 50342 50631 51649 51955 52147 52404 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file stat4.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TICTCGATAACATAGGGGATCGACAAACT 3 ACACGCCGGAGAATGCTCT 2.000000 2 TICTCGATAACATAGGGGATCGACAAGCC 3 ACACGGAAATGGATTCCAT 5.000000 3 TICTCGATAACATAGGGGATCGACAAGCC 3 ACACACCGGAGAATGCTCT 1.000000 4 TICTCGATAACATAGGGGATCGACAAGCC 3 ACGCGCAGGAGAATTCTCT 1.000000 5 TICTCGATAACATAGGGGATCGACAAGTC 3 ACACGCCGGAGAATGCTCT 1.000000 6 TICTCGATAACATAGGGGATCGGCAAGCC 3 ACACGGAAATGGATTCCAT 1.000000 7 TICTTGATAACTTAGGGGATCGGCAAACC 3 ACGCGCAGGAGAATTCCAT 2.000000 8 TICTTGATAACTTAGGGGTTGGGTAAACC 1 ACGGGCAGGAAAACTCCAT 1.000000 9 TICTTGATAACTTAGGGGTTGGGTAAGTC 3 ACACGCCGGAGAATGCTCT 2.000000 10 TICTTGATAACTTAGGAGATCGACAAACT 1 ACGCGCAGGAGAATTCCAT 1.000000 11 TICTTGATAACTTAGGAGATCGACAAACT 3 ACACACCGGAGAATGCTCT 5.000000 12 TICTTGATAACTTAGGAGATCGACAAACT 3 ACGCGCAGGAGAATTCCAT 1.000000 13 TICTTGATAACTTAGGAGATCGACAAACT 3 ACGCGGAAATGGATGCTCT 2.000000 14 TICTTGATAACTTAGGAGATCGACAAGTC 3 ATGCGCAGGAGAATTCCAT 1.000000 15 TICTTGATAACTTAGAGGACCAACAAGTC 3 GCGGGCAGGAAAACTCCAT 1.000000 16 TICTTGATAGCATAGGGGATCGACAAACC 1 ACGCGCCGGAGAATTCTCT 2.000000 17 TICTTGAGAACTTAGGAGATCGACAAACT 3 ACACACCGGAGAATGCTCT 2.000000 18 TICTTGAGTACTTAGGGGATCGGTAAACT 1 ACGCGCAGGAGAATTCTCT 1.000000 19 TICTTGAGTACTTAGGGGATCGGTAAGCC 1 ACGCGCAGGAGAATTCTCT 1.000000 20 TICTTGAGTACTTAGGGGTTCGGTAAACC 3 ACGCGCAGGAGAATTCCAT 1.000000 21 TICTTGAGTACTTAGGGGTTCGGTAAGCC 1 ACACACCGGAGAATGCTCT 1.000000 22 TICTTGAGTACTTAGGGGTTCGGTAAGCC 1 ACGCGCAGGAGAATTCTCT 18.000000 23 TICTTGAGTACTTAGGGGTTCGGTAAGCC 3 ACACGGAAATGGATTCCAT 1.000000 24 TICTTGAGTACTTAGGGGTTCGGTAAGCC 3 ACACACCGGAGAATGCTCT 4.000000 25 TICTTGAGTACTTAGGGGTTCGGTAAGCC 3 ACGCGCAGGAGAATTCTCT 2.000000 26 TICTTGAGTAGTTAGGGGTTCGGTAAGCC 1 ACGCGCAGGAGAATTCTCT 1.000000 27 TICATGATAACTTAGAGGACCAACGAGTC 3 ACGCGCAGGAGAATTCTCC 1.000000 28 TDCTTGATAACTTAGGGGATCGACAAACC 4 ACGCGCAGGAGAATTCTCT 2.000000 29 TDCTTGATAACTTAGGGGATCGACAAACT 3 ACACGCCGGAGAATGCTCT 3.000000 30 TDCTTGATAACTTAGGGGATCGACAAGTC 3 GCGGGCAGGAAAATTCCAT 1.000000 31 TDCTTGATAACTTAGGGGATCGACAAGTC 3 GTGCGCAGGAGATTTCTCT 1.000000 32 TDCTTGATAACTTAGGGGTTGGGTAAACC 3 ACGCGCAGGAGAATTCCAT 1.000000 33 TDCTTGATAACTTAGGGGTTGGGTAAGTC 3 ACACGCCGGAGAATGCTCT 2.000000 34 TDCTTGATAACTTAGAGGACCAACAAGTC 3 GCGGGCAGGAAAATTCCAT 1.000000 35 TDCTTGATAACTTAGAGGACCAACAAGTC 3 GCGGGCAGGAAAACTCCAT 2.000000 36 TDCTTGATAACTTAGAGGACCAACAAGTC 3 GTGCGCAGGAGATTTCTCT 1.000000 37 TDCTTGATAACTTAGAGGACCAACGAGTC 3 ATGCGCAGGAGAATTCTCC 1.000000 38 TDCTTGATAACTTAGAGGACCAGCAAGTC 3 ACGCGCAGGAGAATTCTCC 1.000000 39 TDCTTGGTAACTTGGGGAATCGGCAGACC 3 ACGCGCCGGAGAATGGTCT 4.000000 40 TDCTTAATAACTCAAAGGATCGACAAGTC 3 ACGCGCCGGAGAATGCTCT 1.000000 41 TDCTTAATAACTCAAAGGATCGACAAGTC 3 GTGCGCAGGAGATTTCTCT 1.000000 42 TDTTTGATAGCATAGGGGATCGACAAGCC 3 ACACGGAAATGGATTCCAT 1.000000 43 TDTATGATAACTTAGAGGACCAACGAGTC 3 ACGCGCAGGAGAATTCTCC 4.000000 44 TDTATAATAACTCAAAGGATCGACAAGTC 3 GTGCGCAGGAGATTTCTCT 1.000000 45 AICTTGAGTAGTTAGGGGTTCGGTAAGCC 1 ACGCGCAGGAGAATTCTCT 4.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,8) D002: (29,39) D003: (14,43) D004: (4,11) D005: (37,39) D006: (16,34) D007: (33,35) D008: (16,22) D009: (43,44) D010: (2,41) D011: (2,9) D012: (22,43) D013: (28,40) D014: (2,35) D015: (36,42) D016: (1,29) D033: (7,18) D034: (38,39) D035: (15,29) D036: (19,43) D037: (27,28) D038: (22,30) D039: (5,33) D040: (31,39) E001: (7,17) E002: (13,22) E003: (11,22) E004: (22,24) E005: (6,21) E006: (2,10) E007: (12,22) E008: (22,22) E009: (22,22) E010: (45,45) E011: (22,45) E012: (25,45) E013: (13,23) E014: (26,32) E015: (22,24) E016: (11,22) E017: (9,22) E018: (22,24) E019: (24,25) E020: (11,20) E021: (2,11) E022: (3,22) E023: (17,22) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T I C T C G A T A A C A T A G G G G A T C G A C A A A C T 3 A C A C G C C G G A G A A T G C T C T T I C T T G A T A A C T T A G G G G T T G G G T A A A C C 1 A C G G G C A G G A A A A [C] T C C A T 0 D002 T D C T T G A T A A C T T A G G G G A T C G A C A A A C T 3 A C A C G C C G G A G A A T G C T C T T D C T T G G T A A C T T G G G G A A T C G G C A G A C C 3 A C G C G C C G G A G A A T G G T C T 0 D003 T I C T T G A T A A C T T A G G A G A T C G A C A A G T C 3 A (T) G C G C A G G A G A A T T C C A T T D T A T G A T A A C T T A G A G G A C C A A C G A G T C 3 A (C) G C G C A G G A G A A T T C T C C 0 D004 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C 3 A C (G) C (G) C (A) G G A G A A T (T) C T C T T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C (A) C (A) C (C) G G A G A A T (G) C T C T 0 D005 T D C T T G A T A A C T T A G A G G A C C A A C G A G T C 3 A T G C G C A G G A G A A T T C T C C T D C T T G G T A A C T T G G G G A A T C G G C A G A C C 3 A C G C G C C G G A G A A T G G T C T 0 D006 T I C T T G A T A G C A T A G G G G A T C G A C A A A C C 1 A C G C G C C G G A G A A T T C T C T T D C T T G A T A A C T T A G A G G A C C A A C A A G T C 3 G C G G G C A G G A A A A T T C C A T 0 D007 T D C T T G A T A A C T T A G G G G T T G G G T A A G T C 3 A C A C G C C G G A G A A T G C T C T T D C T T G A T A A C T T A G A G G A C C A A C A A G T C 3 G C G G G C A G G A A A A C T C C A T 0 D008 T I C T T G A T A G C A T A G G G G A T C G A C A A A C C 1 A C G C G C C G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 D009 T D T A T G A T A A C T T A G A G G A C C A A C G A G T C 3 A C G C G C A G G A G A A T T C T C C T D T A T A A T A A C T C A A A G G A T C G A C A A G T C 3 G T G C G C A G G A G A T T T C T C T 0 D010 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C 3 A C A C G G A A A T G G A T T C C A T T D C T T A A T A A C T C A A A G G A T C G A C A A G T C 3 G T G C G C A G G A G A T T T C T C T 0 D011 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C 3 A C A C G G A A A T G G A T T C C A T T I C T T G A T A A C T T A G G G G T T G G G T A A G T C 3 A C A C G C C G G A G A A T G C T C T 0 D012 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T D T A T G A T A A C T T A G A G G A C C A A C G A G T C 3 A C G C G C A G G A G A A T T C T C C 0 D013 T D C T T G A T A A C T T A G G G G A T C G A C A A A C C 4 A C G C G C A G G A G A A T T C T C T T D C T T A A T A A C T C A A A G G A T C G A C A A G T C 3 A C G C G C C G G A G A A T G C T C T 0 D014 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C 3 A C A C G G A A A T G G A T T C C A T T [D] C T T G A T A A C T T A G A G G A C C A A C A A G T C 3 G C G G G C A G G A A A A C T C C A T 0 D015 T D (C) T T G A T A A C T T A G A G G A C C A A C A A G T C 3 G T G C G C A G G A G A T T T C T C T T D (T) T T G A T A G C A T A G G G G A T C G A C A A G C C 3 A C A C G G A A A T G G A T T C C A T 0 D016 T I C T C G A T A A C A T A G G G G A T C G A C A A A C T 3 A C A C G C C G G A G A A T G C T C T T D C T T G A T A A C T T A G G G G A T C G A C A A A C T 3 A C A C G C C G G A G A A T G C T C T 0 D033 T I C T T G A T A A C T T A G G G G A T C G G C A A A C C 3 A C G C G C A G G A G A A T T C (C) (A) T T I C T T G A G T A C T T A G G G G A T C G G T A A A C T 1 A C G C G C A G G A G A A T T C (T) (C) T 0 D034 T D C T T G A T A A C T T A G A G G A C C A G C A A G T C 3 A C G C G C A G G A G A A T T C T C [C] T D C T T G G T A A C T T G G G G A A T C G G C A G A C C 3 A C G C G C C G G A G A A T G G T C T 0 D035 T (I) C T T G A T A A C T T A G A G G A C C A A C A A G T C 3 G C G G G C A G G A A A A [C] T C C A T T (D) C T T G A T A A C T T A G G G G A T C G A C A A A C T 3 A C A C G C C G G A G A A T G C T C T 0 D036 T I C T T G A G T A C T T A G G G G A T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T D T A T G A T A A C T T A G A G G A C C A A C G A G T C 3 A C G C G C A G G A G A A T T C T C C 0 D037 T I C A T G A T A A C T T A G A G G A C C A A C G A G T C 3 A C G C G C A G G A G A A T T C T C C T D C T T G A T A A C T T A G G G G A T C G A C A A A C C 4 A C G C G C A G G A G A A T T C T C T 0 D038 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T D C T T G A T A A C T T A G G G G A T C G A C A A G T C 3 G C G G G C A G G A A A A T T C C A T 0 D039 T I C T C G A T A A C A T A G G G G A T C G A C A A G T C 3 A C A C G C C G G A G A A T G C T C T T D C T T G A T A A C T T A G G G G T T G G G T A A G T C 3 A C A C G C C G G A G A A T G C T C T 0 D040 T [D] C T T G A T A A C T T A G G G G A T C G A C A A G T C 3 G T G C G C A G G A G A T T T C T C T T D C T T G G T A A C T T G G G G A A T C G G C A G A C C 3 A C G C G C C G G A G A A T G G T C T 0 E001 T I C T T G A T A A C T T A G G G G A T C G G C A A A C C 3 A C G C G C A G G A G A A T T C C A T T I C T T G A G A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T 0 E002 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C G C G G A A A T G G A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E003 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E004 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C A C A C C G G A G A A T G C T C T 0 E005 T I C T C G A T A A C A T A G G G G A T C G G C A A G C C (3) A C A C G G A A A T G G A T T C C A T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C (1) A C A C A C C G G A G A A T G C T C T 0 E006 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C (3) A C A C G G A A A T G G A T T C C A T T I C T T G A T A A C T T A G G A G A T C G A C A A A C T (1) A C G C G C A G G A G A A T T C C A T 0 E007 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T (3) A C G C G C A G G A G A A T T C C A T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C (1) A C G C G C A G G A G A A T T C T C T 0 E008 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E009 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E010 A I C T T G A G T A G T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T A I C T T G A G T A G T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E011 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T A I C T T G A G T A G T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E012 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C G C G C A G G A G A A T T C T C T A I C T T G A G T A G T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E013 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C G C G G A A A T G G A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C A C G G A A A T G G A T T C C A T 0 E014 T (I) C T T G A G T A G T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T (D) C T T G A T A A C T T A G G G G T T G G G T A A A C C 3 A C G C G C A G G A G A A T T C C A T 0 E015 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C A C A C C G G A G A A T G C T C T 0 E016 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E017 T I C T T G A T A A C T T A G G G G T T G G G T A A G T C 3 A C A C G C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T 0 E018 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C A C A C C G G A G A A T G C T C T 0 E019 T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C A C A C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 3 A C G C G C A G G A G A A T T C T C T 0 E020 T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A A C C 3 A C G C G C A G G A G A A T T C C A T 0 E021 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C 3 A C A C G G A A A T G G A T T C C A T T I C T T G A T A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T 0 E022 T I C T C G A T A A C A T A G G G G A T C G A C A A G C C (3) A C (A) C (A) C (C) G G A G A A T (G) C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C (1) A C (G) C (G) C (A) G G A G A A T (T) C T C T 0 E023 T I C T T G A G A A C T T A G G A G A T C G A C A A A C T 3 A C A C A C C G G A G A A T G C T C T T I C T T G A G T A C T T A G G G G T T C G G T A A G C C 1 A C G C G C A G G A G A A T T C T C 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 = = = = C = = = = = = A = = = ? ? ? A = ? ? ? C = = = = T 3 = = A C = = C = = = G = = ? G = T C ? = = = = T = = = = = = T = = = ? ? ? T = ? ? ? T = = = = C 1 = = G G = = A = = = A = = ? T = C A ? 0 D002 = = = = = = A = = = = = = A = = = G = = = = A = = A = = T = = = A = = = = = = = = = = = = C = = = = = = = = = G = = = = = = G = = = A = = = = G = = G = = C = = = G = = = = = = = = = = = = G = = = 0 D003 = I C T = = = = = = = = = = = G A = = T = G = = A = = = = = = (T) = = = ? = = = = = ? ? = = = C A T = D T A = = = = = = = = = = = A G = = C = A = = G = = = = = = (C) = = = ? = = = = = ? ? = = = T C C 0 D004 = = = = C = = = = = ? A = = = = G = = = ? = = = = = G = C = = = (G) = (G) = (A) = = = = = = = (T) = = = = = = = = T = = = = = ? T = = = = A = = = ? = = = = = A = T = = = (A) = (A) = (C) = = = = = = = (G) = = = = 0 D005 = = = = = = A = = = = = = A = A = G = C = A A = G A G T = = = T ? = = = A = = = = = = = T C = = C = = = = = = G = = = = = = G = G = A = T = G G = A G A C = = = C ? = = = C = = = = = = = G G = = T 0 D006 = I = = = = = = = G = A = = = G ? = = T = G = = = = A C = 1 A = = C = = C = = = G = = = = = T C = = D = = = = = = = A = T = = = A ? = = C = A = = = = G T = 3 G = = G = = A = = = A = = = = = C A = 0 D007 = = = = = = = = = = = = = = = G ? ? T T G G G T = = = = = = A = A C = = C = = = G = = T ? = T C = = = = = = = = = = = = = = = = A ? ? A C C A A C = = = = = = G = G G = = A = = = A = = C ? = C A = 0 D008 = = = ? = = = T A G = A = = = = ? ? A = = = A C = = A = = = = = = ? = ? ? ? ? = = = = = = = = = = = = = ? = = = G T A = T = = = = ? ? T = = = G T = = G = = = = = = ? = ? ? ? ? = = = = = = = = = = 0 D009 = = = = = G = = = = = = T = G ? ? ? ? C = A = = G = = = = = A C = = = = = = = = = = A = = = = = C = = = = = A = = = = = = C = A ? ? ? ? T = G = = A = = = = = G T = = = = = = = = = = T = = = = = T 0 D010 = I = = C G = = = = = A T = G G = = = = ? = = = = = = C = = A C A = = G = A A T = G A = = = C A = = D = = T A = = = = = T C = A A = = = = ? = = = = = = T = = G T G = = C = G G A = A T = = = T C = 0 D011 = = = = C = = = = = = A = = = = = = A = C = A C = = = C = = = = = = = G A A A T = G = = T ? C A = = = = = T = = = = = = T = = = = = = T = G = G T = = = T = = = = = = = C C G G A = A = = G ? T C = 0 D012 = I C T = = = G ? ? = = = = = G = = T T = G G T A = = C = 1 = = = = = = = = = = = = = = = = = = T = D T A = = = T ? ? = = = = = A = = A C = A A C G = = T = 3 = = = = = = = = = = = = = = = = = = C 0 D013 = = = = = G = = = = = = T = G G = = = = ? = = = = = A C = 4 = = = = = = A = = = = = = = T = = = = = = = = = A = = = = = = C = A A = = = = ? = = = = = G T = 3 = = = = = = C = = = = = = = G = = = = 0 D014 = ? = = C = = = = = = A = = = G = = = T = G = = = = = C = = A = A C = G = A A T G G = T = = = = = = ? = = T = = = = = = T = = = A = = = C = A = = = = = T = = G = G G = C = G G A A A = C = = = = = 0 D015 = = (C) = = = = = = A = T = = = A = = = C = A = = = = = T = = G ? G = = C = G G A = ? T = ? = T C = = = (T) = = = = = = G = A = = = G = = = T = G = = = = = C = = A ? A = = G = A A T = ? A = ? = C A = 0 D016 = I = = C = = = ? ? = A = = = = = = = = ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = D = = T = = = ? ? = T = = = = = = = = ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = 0 D033 = = = = ? ? = T A = = = = = = ? ? ? = ? = = = C = = = = C 3 = = = = = = = = = = = = = = = = (C) (A) = = = = = ? ? = G T = = = = = = ? ? ? = ? = = = T = = = = T 1 = = = = = = = = = = = = = = = = (T) (C) = 0 D034 = = = = = = A = = = = = = A = A = G = C = ? = = = A G T = = = = = = = = ? = = = = ? = = T C = = ? = = = = = = G = = = = = = G = G = A = T = ? = = = G A C = = = = = = = = ? = = = = ? = = G G = = ? 0 D035 = (I) = = = = = = = = = = = = = A = = = C = A = = = = G T C = G = G G = = A = = = A = = ? ? = C A = = (D) = = = = = = = = = = = = = G = = = T = G = = = = A C T = A = A C = = C = = = G = = ? ? = T C = 0 D036 = I C T = = = G ? ? = = = = = G = = = T = G G T A = = C = 1 = ? = = = = = = = = = = = = = = = = T = D T A = = = T ? ? = = = = = A = = = C = A A C G = = T = 3 = ? = = = = = = = = = = = = = = = = C 0 D037 = I = A = = = ? = = = = = = = A = = = C = ? ? ? G = G T = 3 = = = = = = = = = = = = = ? = = = ? C = D = T = = = ? = = = = = = = G = = = T = ? ? ? A = A C = 4 = = = = = = = = = = = = = ? = = = ? T 0 D038 = I = = = = = G T = = = = = = = = = T = ? = G T = = = C = 1 A = = C = = = = = = G = = = = = T C = = D = = = = = T A = = = = = = = = = A = ? = A C = = = T = 3 G = = G = = = = = = A = = = = = C A = 0 D039 = I = ? C = = = = = = A = = = = = = A = ? ? ? C = = = = = = = ? = = = = = = = = = = = ? = = = = = = D = ? T = = = = = = T = = = = = = T = ? ? ? T = = = = = = = ? = = = = = = = = = = = ? = = = = = 0 D040 = ? = = = = A = = = = = = A = = = G = = = = A = = A G T = = G ? = = = = A = = = = = T = ? C = = = = ? = = = = G = = = = = = G = = = A = = = = G = = G A C = = A ? = = = = C = = = = = A = ? G = = = 0 E001 ? = = = ? ? = T = = = = = = = = G = = = ? = G = = = = = C = = = G = G = ? = = = = = = = T = C A = ? = = = ? ? = G = = = = = = = = A = = = ? = A = = = = = T = = = A = A = ? = = = = = = = G = T C = 0 E002 = = = = = = = T A = = = = = = = A = A = = = A C = = A = T 3 = = = = = G = A A T = G = ? G = = = = = = = = = = = G T = = = = = = = G = T = = = G T = = G = C 1 = = = = = C = G G A = A = ? T = = = = 0 E003 = ? = = = = = T A = = = = = = = A = A = = = A C = = A = T 3 = = A = A = C = = = = = = = G = = = = = ? = = = = = G T = = = = = = = G = T = = = G T = = G = C 1 = = G = G = A = = = = = = = T = = = = 0 E004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = G = G = ? ? ? = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 3 = = A = A = ? ? ? = = = = = G = = = = 0 E005 = = = = C = = T A = = A = = = = = = A = = = = C = = = = = (3) = = = = G G A A A T = G = = ? = C A = = = = = T = = G T = = T = = = = = = T = = = = T = = = = = (1) = = = = A C C G G A = A = = ? = T C = 0 E006 = = = = C = = = = ? = A = = = = G = = = = = = = = = G = C (3) = = A = = G = A A T = ? = = = = = = = = = = = T = = = = ? = T = = = = A = = = = = = = = = A = T (1) = = G = = C = G G A = ? = = = = = = = 0 E007 = = = = = = ? T A = = = = = = = A = A = = = A C = = A = T (3) = = = = = = = = = = = ? = = ? = C A = = = = = = = ? G T = = = = = = = G = T = = = G T = = G = C (1) = = = = = = = = = = = ? = = ? = T C = 0 E008 = = = = = = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E011 T = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = A = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0 E012 T = = = = = = = = = C = = = = = = = = = = = = = = = = = = 3 = = = = = = = = = = = = = = = = = = = A = = = = = = = = = G = = = = = = = = = = = = = = = = = = 1 = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = = = T A = = = = = = = ? ? A = = ? ? C = = A = T = = = G = = = = = = = = = = = G = T C = = = = = = = = G T = = = = = = = ? ? T = = ? ? T = = G = C = = = A = = = = = = = = = = = T = C A = 0 E014 = (I) = = = = = G T = G = = = = = = = = = C = = = = = G = = 1 = = = = = = = = ? = = = = = = = T C = = (D) = = = = = T A = C = = = = = = = = = G = = = = = A = = 3 = = = = = = = = ? = = = = = = = C A = 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = G = G = A = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 3 = = A = A = C = = = = = = = G = = = = 0 E016 = = = = = = ? T A = = = = = = = A = A = = = A C = = A = T 3 = = A = A = C = = = = ? = = G = = = = = = = = = = ? G T = = = = = = = G = T = = = G T = = G = C 1 = = G = G = A = = = = ? = = T = = = = 0 E017 = = = = = = = T A = = = = ? = = = = = = G = = = = = = T = 3 = = A = = = ? = = = = = = = G ? = = = = = = = = = = G T = = = = ? = = = = = = C = = = = = = C = 1 = = G = = = ? = = = = = = = T ? = = = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1 = = G = G = A = = = = ? = = T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 3 = = A = A = C = = = = ? = = G = = ? = 0 E019 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = A = A = C = = = = = = = G = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = G = G = A = = = = = = = T = = = ? 0 E020 = = = = = = = T A = ? = = = = = A = A = = = A C = = = = T = = = A = A = C = ? = = = = = G = T C = = = = = = = = G T = ? = = = = = G = T = = = G T = = = = C = = = G = G = A = ? = = = = = T = C A = 0 E021 = = = = C = = = = = = A = = = = G = = = = = = = = = G = C = = = = = G G ? ? ? T = G = = T = C A = = = = = T = = = = = = T = = = = A = = = = = = = = = A = T = = = = = A C ? ? ? A = A = = G = T C = 0 E022 = = = = C = = T A = = A = = = = = = A = = ? ? C = = = = = (3) = = (A) = (A) = (C) = = = = = = = (G) = = = = = = = = T = = G T = = T = = = = = = T = = ? ? T = = = = = (1) = = (G) = (G) = (A) = = = = = = = (T) = = = = 0 E023 = = = = = = = = A = = = = = = = A = A = = = A C = = A = T 3 = = A = A = C = = = = = = = G = = = = = = = = = = = = T = = = = = = = G = T = = = G T = = G = C 1 = = G = G = A = = = = = = = T = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = 1.00 = = = = = = 1.00 = = = ? ? ? 1.00 = ? ? ? 1.00 = = = = 1.00 1.00 = = 1.00 1.00 = = 1.00 = = = 1.00 = = ? 1.00 = 1.00 1.00 ? = = = = = = 1.00 = = = = = = 1.00 = = = 1.00 = = = = 1.00 = = 1.00 = = 1.00 = = = 1.00 = = = = = = = = = = = = 1.00 = = = = 0.99 0.99 0.99 = = = = = = = = = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 = = = = = = 0.54 = = = ? = = = = = ? ? = = = 1.00 1.00 1.00 = = = = 1.00 = = = = = ? 1.00 = = = = 1.00 = = = ? = = = = = 1.00 = 1.00 = = = 0.85 = 0.85 = 0.85 = = = = = = = 0.85 = = = = = = = = = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 ? = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = 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 = 0.95 = = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 1.00 = = = = ? = = = = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = = = 1.00 = = = = = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 ? 1.00 1.00 = = 1.00 1.00 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 = = = = = = 0.98 = 0.98 0.98 = = = = ? = = = = = 1.00 1.00 = 1.00 = = = = = = 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 = = = = = = = 0.90 = = = = = = 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 = = 0.99 = = 1.00 = = = ? ? = 1.00 = = = = = = = = ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = ? ? = 1.00 1.00 = = = = = = ? ? ? = ? = = = 1.00 = = = = 0.92 0.93 = = = = = = = = = = = = = = = = 0.81 0.81 = = = = = = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = 1.00 = ? = = = 1.00 1.00 1.00 = = = = = = = = ? = = = = ? = = 1.00 1.00 = = ? = 0.72 = = = = = = = = = = = = = 1.00 = = = 1.00 = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = 1.00 = = ? ? = 1.00 1.00 = = 1.00 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 = 0.95 = = = = = 0.96 0.96 = = = = = = = = = 0.96 = ? = 0.96 0.96 = = = 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 = ? 1.00 = = = ? = = = ? ? = 0.97 = = = = = = = = 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 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.95 = = 1.00 = 1.00 = ? ? ? = = = = = 1.00 = = = = = = = = 0.92 = = 0.92 0.92 = = 0.92 = = = = = = 0.92 = = = = 0.92 = = = = = 0.54 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = ? = 1.00 1.00 = = = = = 1.00 = = = = ? = 1.00 = = = = 1.00 = = = = = = = = = 1.00 = 1.00 0.62 = = 1.00 = = 1.00 = 1.00 1.00 1.00 = ? = = = = = = = = = = = = = ? 1.00 1.00 = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 0.51 = = = = = = = = = = = ? = = ? = 1.00 1.00 = = = = = = = = = = = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = 0.91 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = ? ? 1.00 = = ? ? 1.00 = = 0.99 = 0.99 = = = 0.99 = = = = = = = = = = = 0.99 = 0.99 0.99 = = 0.73 = = = = = 0.99 0.99 = 0.99 = = = = = = = = = 0.99 = = = = = 0.94 = = 0.94 = = = = = = = = ? = = = = = = = 0.94 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.95 = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = = = = = = = = = ? 1.00 1.00 = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = 1.00 = 1.00 = = = = ? = = 1.00 = = = = = = = = = = = 1.00 1.00 = = = = ? = = = = = = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 = = = ? = = = = = = = 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.95 = = 1.00 = 1.00 = 1.00 = = = = ? = = 1.00 = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 1.00 = 1.00 = 1.00 = = = = = = = 1.00 = = = ? = = = = = = = 0.98 0.98 = ? = = = = = 0.98 = 0.98 = = = 0.98 0.98 = = = = 1.00 = = = 0.95 = 0.95 = 0.95 = ? = = = = = 0.95 = 0.95 0.95 = = = = = 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 ? ? ? 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 = = 1.00 = = = = = = 1.00 = = ? ? 1.00 = = = = = 0.70 = = 0.56 = 0.56 = 0.56 = = = = = = = 0.56 = = = = = = = = = = = = 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