************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ifgr1.phase.inp ifgr1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ifgr1.phase.out_freqs : haplotype frequency estimates ifgr1.phase.out_pairs : most likely haplotype pairs for each individual ifgr1.phase.out_recom : estimates of recombination parameters ifgr1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 50 Positions of loci: 987 1433 1863 1972 1988 2138 2173 2698 2782 3004 3077 3238 6054 7231 8489 9303 9313 9663 9758 11317 11478 12582 12737 22729 22921 23840 24621 25018 25919 25920 25947 27276 27550 27719 28765 29791 29857 29863 30361 30999 31117 31617 31785 31786 31978 32050 32509 33218 33435 33485 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ifgr1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATAATGCAGCIGTACTG 3.000000 2 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATAGTGGCGCIGCACTG 7.000000 3 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATAGTGGCGCITCACTG 1.000000 4 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATAGTGGCACIGTGCTG 1.000000 5 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATAGCGCAGCIGTACTG 1.000000 6 TATCTTGCDGIACGACAGCAGGAATICTGCCAAATGGCGGCACIGTAAAA 1.000000 7 TATCTTGCDGIACGACAGCAGGAATICTGCCGAATAGTGCAGCIGTACTG 1.000000 8 TATCTTGCDGIACGACAGCAGGAATICTGCCGGATAGCGGCACIGTAAAA 1.000000 9 TATCTTGCDGIACGACAGCAGGAATICTGCCGGATAGCAGCACIGTAAAA 1.000000 10 TATCTTGCDGIACGACAGCAGGAATICTAACAAGGAGTGGCGCIGCACTG 2.000000 11 TATCTTGCDGIACGACAGCAGGAATICTAACAAGGAGTGGCGADGTACTG 1.000000 12 TATCTTGCDGIACGGCAGCAGGAATICTAACAAGGGGCGGCGCITCACTG 1.000000 13 TATCTTGCDGIACGGCAGCAGGAATICTAACAAGGGGCGGCACIGTAAAA 2.000000 14 TATCCTGTIGIACGACGGCAGGGATIATGCCGGATAGCGGCACIGTAAAA 1.000000 15 TATCCCGCDGIACGACAGCAGGAATICTGCCAAATGGCGGCACIGTAAAA 1.000000 16 TATCCCGCDGIGCCACACCAGGGATICTGCCAAATAGTGGCGCIGCACTG 2.000000 17 TATCCCGCDGIGCCACACCAGGGATICTGCCAAATAGTGGCACIGTAATG 1.000000 18 TATCCCGCDGIGCCACACCAGGGATICTGCCGAATAGTGGCGCIGCACTG 2.000000 19 TATCCCGCDCIACGACAGCAAGGATICAGCCAAATAGTGGCGCIGTACTG 1.000000 20 TATCCCGCDCDACGACAGTGAAGATDCAGCCAAATAGTGGCACIGTAAAA 1.000000 21 TATCCCGCDCDACGACAGTGAAGATDCAGCCAAATAGTGGCACIGTGCTG 1.000000 22 TATCCCGTDGIACGACAGCAGGGATIATGCCAAATAGTGGCGADGTACTG 3.000000 23 TATCCCGTDGIATGATAGCAGGGAGIATGCCGAATAGTGGCGADGTACTG 7.000000 24 TATCCCGTDGIATGATAGCAGGGAGIATGCGGAATAGTGGCGADGTACTG 1.000000 25 TATCCCGTDGIATGATAGCAGGGAGIATGCGGAATAGTGGCACIGTAATG 2.000000 26 TATCCCGTDGIATGATAGCAGGGAGIATGCGGAATAGTGGCACIGTAAAA 2.000000 27 TATCCCACDCDACGACAGTGAAGATICAGCCAAATAGTGGCGCITCACTG 1.000000 28 TATCCCACDCDACGACAGTGAAGATICAGCCAAATGGCGGCACIGTAAAA 3.000000 29 TATTCCACDCDACGACAGTGAAGGTICAGCCAAATAGTGGCACIGTAAAA 5.000000 30 TATTCCACDCDACGACAGTGAAGGTICAGCCAAGGGGCGGCACIGTAAAA 2.000000 31 TATTCCACDCDACGACAGTGAAGGTICAGCCGAATAGTGGCGADGTACTG 1.000000 32 TAGCCCGTDGIACGACGGCAGGGATIATGCCGGATAGTGGCGCIGCACTG 1.000000 33 TAGCCCGTIGIACGACGGCAGGGATIATGCCAAATAGTGCAGCIGTACTG 1.000000 34 TAGCCCGTIGIACGACGGCAGGGATIATGCCGGATAGCAGCACIGTAAAA 2.000000 35 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGAGTGCAGCIGTACTG 2.000000 36 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGAGTGGCGADGTACTG 1.000000 37 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGAGTGGCACIGTAAAA 1.000000 38 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGGGCGGCGCIGCACTG 2.000000 39 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGGGCGGCACIGTAAAA 15.000000 40 TGTCTTGCDGIACGACAGCAGGAATICTAACAAGGGGCAGCACIGTAAAA 1.000000 41 TGTCTTGCDGIACGACAGCAGGAATICTAACGAATAGTGGCGADGTACTG 1.000000 42 TGTCTTGCDGIACGACAGCAGGAATICTAACGAATAGCGGCACIGTAAAA 2.000000 43 TGTCTTGCDGIGCGACAGCAGGAATICTAACAAGGGGCGGCACIGTGCTG 1.000000 44 TGTCTTGCDCDACGACAGTGAAGGTICAGCCAAATAGTGGCACIGTAAAA 1.000000 45 AATCCCGTDGIATGATAGCAGGGAGIATGCCGAATAGTGGCGADGTACTG 2.000000 46 AATCCCGTDGIATGATAGCAGGGAGIATGCCGAATGGCGGCACIGTAAAA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,1) D002: (11,14) D003: (39,44) D004: (2,18) D005: (4,43) D006: (17,33) D007: (10,42) D008: (32,34) D009: (2,10) D010: (19,35) D011: (2,34) D012: (2,21) D013: (8,20) D014: (2,39) D015: (5,23) D016: (7,22) D033: (39,39) D034: (1,23) D035: (9,22) D036: (6,29) D037: (16,42) D038: (16,39) D039: (35,36) D040: (15,18) E001: (23,39) E002: (28,39) E003: (28,30) E004: (2,45) E005: (12,27) E006: (25,29) E007: (3,45) E008: (37,39) E009: (23,39) E010: (30,38) E011: (23,31) E012: (29,39) E013: (29,46) E014: (2,40) E015: (23,41) E016: (13,39) E017: (29,39) E018: (26,26) E019: (22,38) E020: (13,28) E021: (39,39) E022: (24,25) E023: (23,39) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A A T G C A G C I G T A C T G T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A A T G C A G C I G T A C T G 0 D002 T A T C (T) T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G A G T G G C (G) (A) (D) G T A (C) (T) (G) T A T C (C) T G T I G I A C G A C G G C A G G G A T I A T G C C G G A T A G C G G C (A) (C) (I) G T A (A) (A) (A) 0 D003 T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A T G T C T T G C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A 0 D004 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A [G] T G [G] [C] G C I G [C] A C T G T A T C C C G C D G I G C C A C A C C A G G G A T I C T G C C G A A T A G T G G C G C I G C A C T G 0 D005 T A T C T T G C D G I (A) C G A C A G C A G G A A T I C T G C C A A A T A G T G G C A C I G T G C T G T G T C T T G C D G I (G) C G A C A G C A G G A A T I C T A A C A A [G] [G] [G] G [C] G G C A C I G T G [C] [T] [G] 0 D006 T A T C C C G C D G I G C C A C A C C A G G G A T I C T G C C A A A T A G T G (G) (C) [A] C I G T A (A) T G T A G C C C G T I G I A C G A C G G C A G G G A T I A T G C C A A A T A G T G (C) (A) [G] C I G T A (C) T G 0 D007 T (A) T C T T G C D G I A C G A C A G C A G G A A T I C T A A C (A) A [G] (G) A G T G G C G C I G C A C T G T (G) T C T T G C D G I A C G A C A G C A G G A A T I C T A A C (G) A A (T) A G [C] G G C A C I G T A A A A 0 D008 T A G C C C G T (D) G I A C G A C G G C A G G G A T I A T G C C G G A T A G T G G C G C I G C A C T G T A G C C C G T (I) G I A C G A C G G C A G G G A T I A T G C C G G A T A G C A G C A C I G T A A A A 0 D009 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T G G C G C I G C A C T G T A T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G A G T G G C G C I G C A C T G 0 D010 T A T C C C [G] C D (C) I A C G A C A G C A (A) G (G) A T I C A G C C A A A T A G T G (G) (C) G C I G T A C T G T [G] T C T T G C D (G) I A C G A C A G C A (G) G (A) A T I C T A A C A A G G A G T G (C) (A) G C I G T A C T G 0 D011 T A (T) C (T) (T) G (C) (D) G I A C G A C (A) G C A G G (A) A T I (C) T G C C A A A T A G T G G C G C I G C A C T G T A (G) C (C) (C) G (T) (I) G I A C G A C (G) G C A G G (G) A T I (A) T G C C G G A T A G C A G C A C I G T A A A A 0 D012 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T G G C (G) C I G (C) (A) C T G T A T C C C G C D C D A C G A C A G T G A A G A T D C A G C C A A A T A G T G G C (A) C I G (T) (G) C T G 0 D013 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C G G A T A G C G G C A C I G T A A A A T A T C C C G C D C D A C G A C A G T G A A G A T D C A G C C A A A T A G T G G C A C I G T A A A A 0 D014 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T G G C G C I G C A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 D015 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G (C) G C A G C I G T A C T G T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G (T) G G C G A D G T A C T G 0 D016 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C (G) A A T A G T G (C) (A) G (C) (I) G T A C T G T A T C C C G T D G I A C G A C A G C A G G G A T I A T G C C (A) A A T A G T G (G) (C) G (A) (D) G T A C T G 0 D033 T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 D034 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A A T G C A G C I G T A C T G T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G 0 D035 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C G G A T A G C A G C A C I G T A A A A T A T C C C G T D G I A C G A C A G C A G G G A T I A T G C C A A A T A G T G G C G A D G T A C T G 0 D036 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T G G C G G C A C I G T A A A A T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A 0 D037 T A T C C C G C D G I G C C A C A C C A G G G A T I C T G C C A A A T A G T G G C (G) C I G (C) A (C) (T) (G) T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C G A A T A G C G G C (A) C I G (T) A (A) (A) (A) 0 D038 T A T C C C G C D G I G C C A C A C C A G G G A T I C T G C C A A A T A G T G G C G C I G C A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 D039 T [G] T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G A G T G C A G C I G T A C T G T [G] T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G A G T G G C G A D G T A C T G 0 D040 T A T C C C G C D G I A C G A C A G C A G G A A T I C T G C C A A A T [G] G [C] G G C A C I G T A [A] [A] [A] T A T C C C G C D G I G C C A C A C C A G G G A T I C T G C C G A A T A G T G G C G C I G C A C T G 0 E001 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E002 T A T C C C A C D C D A C G A C A G T G A A G A T I C A G C C A A A T G G C G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E003 T A T C C C A C D C D A C G A C A G T G A A G A T I C A G C C A A A T G G C G G C A C I G T A A A A T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A G G G G C G G C A C I G T A A A A 0 E004 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T G G C G C I G C A C T G A A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G 0 E005 T A T C T T G C D G I A C G G C A G C A G G A A T I C T A A C A A G G G G C G G C G C I T C A C T G T A T C C C A C D C D A C G A C A G T G A A G A T I C A G C C A A A T A G T G G C G C I T C A C T G 0 E006 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C G G A A T A G T G G C A C I G T A A T G T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A 0 E007 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T G G C G C I (T) C A C T G A A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D (G) T A C T G 0 E008 T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G A G T G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E009 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E010 T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A G G G G C G G C (A) C I G (T) A (A) (A) (A) T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C (G) C I G (C) A (C) (T) (G) 0 E011 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C G A A T A G T G G C G A D G T A C T G 0 E012 T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E013 T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A A A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T G G C G G C A C I G T A A A A 0 E014 T A T C T T G C D G I A C G A C A G C A G G A A T I C T G C C A A A T A G T (G) G C G C I G C A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C (A) G C A C I G T A A A A 0 E015 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C G A A T A G T G G C G A D G T A C T G 0 E016 T A T C T T G C D G I A C G G C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E017 T A T T C C A C D C D A C G A C A G T G A A G G T I C A G C C A A A T A G T G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A 0 E018 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C G G A A T A G T G G C A C I G T A A A A T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C G G A A T A G T G G C A C I G T A A A A 0 E019 T A T C C C G T D G I A C G A C A G C A G G G A T I A T G C C A A A T A G T G G C G A D G T A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C G C I G C A C T G 0 E020 T A T C T T G C D G I A C G G C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A T A T C C C A C D C D A C G A C A G T G A A G A T I C A G C C A A A T G G C G G C A C I G T A A A A 0 E021 T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A A T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G [G] G [C] G [G] [C] [A] C I G T A [A] [A] [A] 0 E022 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C G G A A T A G T G G C G A D G T A C T G T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C G G A A T A G T G G C A C I G T A A T G 0 E023 T A T C C C G T D G I A T G A T A G C A G G G A G I A T G C C G A A T A G T G G C G A D G T A C T G T G T C T T G C D G I A C G A C A G C A G G A A T I C T A A C A A G G G G C G G C A C I G T A A A 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 = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = 0 D002 = = = = (T) = = C D = = = = = = = A = = = = = ? = = = C = A A = A A ? G = = T = = = (G) (A) (D) = = = (C) (T) (G) = = = = (C) = = T I = = = = = = = G = = = = = ? = = = A = G C = G G ? T = = C = = = (A) (C) (I) = = = (A) (A) (A) 0 D003 = = = = = = = = = G I = = = = = = = C A G G ? A = = = T A A = = = G G G = C = = = = = = = = = = = = = = = = = = = = = C D = = = = = = = T G A A ? G = = = A G C = = = A T A = T = = = = = = = = = = = = 0 D004 ? ? = = T T = = = = = ? = G ? ? ? G = = = = ? ? = ? = = = = = A = = ? ? ? ? = ? ? ? = = = ? = = = = ? ? = = C C = = = = = ? = C ? ? ? C = = = = ? ? = ? = = = = = G = = ? ? ? ? = ? ? ? = = = ? = = = = 0 D005 ? ? = = = = = = = = = (A) ? ? ? ? ? = = = = = = = = ? ? ? G C = ? ? ? ? ? ? ? = ? ? = = = = = = ? ? ? ? ? = = = = = = = = = (G) ? ? ? ? ? = = = = = = = = ? ? ? A A = ? ? ? ? ? ? ? = ? ? = = = = = = ? ? ? 0 D006 = = T = = ? = C D = = G = C = = A C = = = = = = = = C = = = = = = = = = = = = (G) (C) ? = = = = = (A) = = = = G = = ? = T I = = A = G = = G G = = = = = = = = A = = = = = = = = = = = = (C) (A) ? = = = = = (C) = = 0 D007 = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = ? (G) ? ? ? = = = ? = = = C = C T G = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = ? (T) ? ? ? = = = ? = = = T = A A A 0 D008 = = = = = = = = (D) = = = = = = = ? = = = = ? ? = = = = = = = = = = = = = = T G = = G = = = C = C T G = = = = = = = = (I) = = = = = = = ? = = = = ? ? = = = = = = = = = = = = = = C A = = A = = = T = A A A 0 D009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = A T = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A = = = G G = = = = = = ? = = = = ? = = = 0 D010 = ? = = C C ? = = (C) = ? = = = = = = = = (A) = (G) = = = = A G C = ? = A T = = = = (G) (C) = = = = = = = = = = ? = = T T ? = = (G) = ? = = = = = = = = (G) = (A) = = = = T A A = ? = G G = = = = (C) (A) = = = = = = = = = 0 D011 = = (T) = (T) (T) = (C) (D) = = = = = = = (A) = = = = = (A) = = = (C) = = = = A A = = = = T G = = G = = = C = C T G = = (G) = (C) (C) = (T) (I) = = = = = = = (G) = = = = = (G) = = = (A) = = = = G G = = = = C A = = A = = = T = A A A 0 D012 = = = = T T = = = G I = = = = = ? = C A G G A = = I = T ? ? = = = ? = = = = = = = (G) = = = (C) (A) = = = = = = = C C = = = C D = = = = = ? = T G A A G = = D = A ? ? = = = ? = = = = = = = (A) = = = (T) (G) = = = 0 D013 = = = = T T = = = G I = = = = = = = C A G G A = = I = T = = = G G = = = = C = = = = = = = = = = = = = = = = C C = = = C D = = = = = = = T G A A G = = D = A = = = A A = = = = T = = = = = = = = = = = = 0 D014 = A = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = A T A = T = = = G = = = C = C T G = G = = = = = = = = = = = = = = = = = = = = = = = = = = A A = = = G G G = C = = = A = = = T = A A A 0 D015 = = = = T T = C = = = = C = = C = = = = = = A = T = C = = = = A = = = = = (C) = C A = C I = = = = = = = = = = C C = T = = = = T = = T = = = = = = G = G = A = = = = G = = = = = (T) = G C = A D = = = = = = 0 D016 = = = = T T = C = = = = = = = = = = = = = = A = = = C = = = = (G) = = = = = = = (C) (A) = (C) (I) = = = = = = = = = = C C = T = = = = = = = = = = = = = = G = = = A = = = = (A) = = = = = = = (G) (C) = (A) (D) = = = = = = 0 D033 = = = = = = = = = = = ? = = = = ? ? ? = = = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = ? ? ? = = = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = 0 D034 ? ? = = T T = ? ? ? = = C ? = C = = = = = = A ? ? ? C = = = = ? = = ? = A = ? C A = ? ? = = = = = = ? ? = = C C = ? ? ? = = T ? = T = = = = = = G ? ? ? A = = = = ? = = ? = G = ? G C = ? ? = = = = = = 0 D035 = = = = T T = C = = = = = = = = = = = = = = A = = = C = = = = G G = = = = C A = = A C I = = = A A A = = = = C C = T = = = = = = = = = = = = = = G = = = A = = = = A A = = = = T G = = G A D = = = C T G 0 D036 = = = C T T G = = G I = = = = = = = C A G G A A = = = T = = = = = = = G = C = = = = = = = = = = = = = = = T C C A = = C D = = = = = = = T G A A G G = = = A = = = = = = = A = T = = = = = = = = = = = = 0 D037 = A = = C C = = = = = G = C = = = C = = = = G = = = = = G C = A = = = = = T = ? = (G) = = = (C) = (C) (T) (G) = G = = T T = = = = = A = G = = = G = = = = A = = = = = A A = G = = = = = C = ? = (A) = = = (T) = (A) (A) (A) 0 D038 = A = = C C = = = = = ? = C = = = C = = = = G = = = = = G C = = = A T A = T = = = ? = = = C = C T G = G = = T T = = = = = ? = G = = = G = = = = A = = = = = A A = = = G G G = C = = = ? = = = T = A A A 0 D039 ? ? = = = = = ? ? ? = = = ? = = = = = = ? ? ? ? ? ? = = = = ? = = ? ? = = = ? C A = C I = = ? = ? = ? ? = = = = = ? ? ? = = = ? = = = = = = ? ? ? ? ? ? = = = = ? = = ? ? = = = ? G C = A D = = ? = ? = 0 D040 ? ? = = = = = = = = = ? ? ? ? ? ? G = = = ? ? = = = ? ? = ? = A = = = ? ? ? = ? ? A = = = T ? ? ? ? ? ? = = = = = = = = = ? ? ? ? ? ? C = = = ? ? = = = ? ? = ? = G = = = ? ? ? = ? ? G = = = C ? ? ? ? 0 E001 = A = = C C = T = = = = T = = T = = = = = = G = G = A = G C = G = A T A = T = = = G A D = = = C T G = G = = T T = C = = = = C = = C = = = = = = A = T = C = A A = A = G G G = C = = = A C I = = = A A A 0 E002 = A = = C C A = = C D = = = = = = = T G A A G = = = = A G C = = ? A T = = = = = = = = = = = = = = = = G = = T T G = = G I = = = = = = = C A G G A = = = = T A A = = ? G G = = = = = = = = = = = = = = = 0 E003 = = = C = = = = = = = = = = = = = = = = = = = A = = = = = = = = = ? T = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = G = = = = = = = = = ? G = = = = = = = = = = = = = = = 0 E004 T = = = T T = C = = = = C = = ? ? = = = = = A = T = C = = = = A = = = = = = = = = = C I = C = = = = A = = = C C = T = = = = T = = ? ? = = = = = G = G = A = = = = G = = = = = = = = = = A D = T = = = = 0 E005 = = = = T T G = = G I = = = G = = = C A G G A = = = = T A A = = = G G G = C = = = ? ? ? = = = = = = = = = = C C A = = C D = = = A = = = T G A A G = = = = A G C = = = A T A = T = = = ? ? ? = = = = = = 0 E006 ? ? = C = = G T = G I = T = = T = = C A G G = A G = A T = = G G = = = = = = = = = ? = = = = = = T G ? ? = T = = A C = C D = C = = C = = T G A A = G T = C A = = C A = = = = = = = = = ? = = = = = = A A 0 E007 T = = = T T = C = = = = C = = C = = = = = = A = T = ? = = = = A = = = = = = = = = = C I (T) C = = = = A = = = C C = T = = = = T = = T = = = = = = G = G = ? = = = = G = = = = = = = = = = A D (G) T = = = = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = C = = = = = = = = = = = = 0 E009 = A = = C C = T = = = = T = = T = = = = = = G = G = A = ? ? ? ? ? ? T A = T = = = G A D = = = C T G = G = = T T = C = = = = C = = C = = = = = = A = T = C = ? ? ? ? ? ? G G = C = = = A C I = = = A A A 0 E010 = A = T C C A = = C D = = = = = = = T G A A G G = = = A G C = = = = = = = = = = = (A) = = = (T) = (A) (A) (A) = G = C T T G = = G I = = = = = = = C A G G A A = = = T A A = = = = = = = = = = = (G) = = = (C) = (C) (T) (G) 0 E011 = = = C = = G T = G I = T = = T = = C A G G = A G = A T = = = = = = = = = = = = = = = = = = = = = = = = = T = = A C = C D = C = = C = = T G A A = G T = C A = = = = = = = = = = = = = = = = = = = = = = 0 E012 = A = T C C A = = C D = = = = ? ? = T G A A G G = = = A ? ? ? = = ? T A = T = = = = = = = = = = = = = G = C T T G = = G I = = = = ? ? = C A G G A A = = = T ? ? ? = = ? G G = C = = = = = = = = = = = = 0 E013 T = = T = = A C = C D = C = = C = = T G A A = G T = C A = = = A = = = A = T = = = = = = = = = = = = A = = C = = G T = G I = T = = T = = C A G G = A G = A T = = = G = = = G = C = = = = = = = = = = = = 0 E014 = A = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = A T A = T (G) = = G = = = C = C T G = G = = = = = = = = = = = = = = = = = = = = = = = = = = A A = = = G G G = C (A) = = A = = = T = A A A 0 E015 = A = = C C = T = = = = T = = T = = = = = = G = G = A = G C = = = = = = = = = = = = = = = = = = = = = G = = T T = C = = = = C = = C = = = = = = A = T = C = A A = = = = = = = = = = = = = = = = = = = = 0 E016 = A = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E017 = A = T C C A = = C D = = = = = = = T G A A G G = = = A G C = ? ? ? T A = T = = = = = = = = = = = = = G = C T T G = = G I = = = = = = = C A G G A A = = = T A A = ? ? ? G G = C = = = = = = = = = = = = 0 E018 = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 E019 = A = = C C = T = = = = = = = = = = = = = = G = = = A = G C = = = A T A = T = = = = A D = T = = = = = G = = T T = C = = = = = = = = = = = = = = A = = = C = A A = = = G G G = C = = = = C I = C = = = = 0 E020 = = ? ? ? ? ? = ? G I = = = G = = = C A G G A = = = = T A A = = = G G = = = = = = = = = = = = = = = = = ? ? ? ? ? = ? C D = = = A = = = T G A A G = = = = A G C = = = A T = = = = = = = = = = = = = = = 0 E021 = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = ? ? ? = ? ? ? ? ? ? ? = ? ? ? = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = ? ? ? = ? ? ? ? ? ? ? = ? ? ? 0 E022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G A D = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A C I = = = A = = 0 E023 = A = = C C = T = = = = T = = T = = = = = = G = G = A = G C = G = ? ? A = T = = = G A D = = = C T G = G = = T T = C = = = = C = = C = = = = = = A = T = C = A A = A = ? ? G = C = = = A C I = = = A A A END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = 0.63 = = 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 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 0.98 = 0.98 = = = = = = = = = = = = ? ? = = 1.00 1.00 = = = = = ? = 1.00 ? ? ? 1.00 = = = = ? ? = ? = = = = = 1.00 = = ? ? ? ? = ? ? ? = = = ? = = = = ? ? = = = = = = = = = 0.58 ? ? ? ? ? = = = = = = = = ? ? ? 1.00 1.00 = ? ? ? ? ? ? ? = ? ? = = = = = = ? ? ? = = 1.00 = = ? = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = = = = = = 1.00 = = = = = = = = = = = = 0.64 0.64 ? = = = = = 0.64 = = = 0.85 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.80 = ? 0.80 ? ? ? = = = ? = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = 0.52 = = = = = = = ? = = = = ? ? = = = = = = = = = = = = = = 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 1.00 = = = = = = ? = = = = ? = = = = ? = = 0.95 0.95 ? = = 0.78 = ? = = = = = = = = 0.67 = 0.89 = = = = 0.95 0.98 0.98 = ? = 0.98 0.98 = = = = 0.89 0.89 = = = = = = = = = = = 0.75 = 0.75 0.75 = 0.75 0.75 = = = = = = = 0.75 = = = = = 0.75 = = = 0.75 = = = = 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 ? ? = = = ? = = = = = = = 0.78 = = = 0.78 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 = = = = = = = = = = = = = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 0.99 = = = 0.99 0.99 1.00 = 1.00 = = = 0.98 = = = 0.98 = 0.98 0.98 0.98 = = = = 1.00 1.00 = 1.00 = = = = 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = 1.00 = = = = 1.00 = = = = = 0.60 = 0.94 0.94 = 0.94 0.94 = = = = = = = = = = 0.99 0.99 = 0.99 = = = = = = = = = = = = = = 0.99 = = = 0.99 = = = = 0.65 = = = = = = = 0.84 0.84 = 0.84 0.84 = = = = = = = = = = = = = = = = = ? = = = = ? ? ? = = = = = = ? = = = = = = = = ? = = = = = = = = = = = = = = = ? ? = = 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 = = = = 1.00 1.00 = = = = 1.00 1.00 = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = = = = 0.92 = 0.92 = = = = = = = = = = = = = 0.98 = = 1.00 1.00 = = = = = 1.00 = 1.00 = = = 1.00 = = = = 1.00 = = = = = 1.00 1.00 = 0.98 = = = = = 0.91 = ? = 0.86 = = = 0.86 = 0.86 0.86 0.86 = 0.99 = = 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 ? ? = = = = = ? ? ? = = = ? = = = = = = ? ? ? ? ? ? = = = = ? = = ? ? = = = ? 1.00 1.00 = 1.00 1.00 = = ? = ? = ? ? = = = = = = = = = ? ? ? ? ? ? 1.00 = = = ? ? = = = ? ? = ? = 1.00 = = = ? ? ? = ? ? 1.00 = = = 1.00 ? ? ? ? = 1.00 = = 1.00 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 0.99 0.99 = = = 0.99 0.99 0.99 = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = ? 1.00 1.00 = = = = = = = = = = = = = = = = = = 0.99 = = = = = = = = = = = = = = = = = = = 0.99 = = = = = = = = = ? 1.00 = = = = = = = = = = = = = = = 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 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = ? ? ? = = = = = = ? ? = 1.00 = = 1.00 1.00 = 1.00 1.00 = 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 0.91 = = = 1.00 1.00 = 1.00 = = = = 1.00 = = 1.00 = = = = = = 1.00 = 1.00 = ? = = = = 1.00 = = = = = = = = = = 0.96 0.96 0.78 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 0.99 = 0.99 = = = 0.99 0.99 0.99 = = = 0.99 0.99 0.99 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = = = 0.81 = = = 0.81 = 0.81 0.81 0.81 = = = 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 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 = = = = = = = = = = = = 0.96 = = 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 = = = 0.91 = 0.91 = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 0.52 = = 0.97 = = = 0.97 = 0.97 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 0.99 = 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 = = = 1.00 1.00 0.99 = 0.99 = = = = 0.97 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 = ? ? 0.99 = 0.99 = = = 0.99 0.99 0.99 = = = 0.99 0.99 0.99 END PHASEPROBS