************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 c26b1.phase.inp c26b1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST c26b1.phase.out_freqs : haplotype frequency estimates c26b1.phase.out_pairs : most likely haplotype pairs for each individual c26b1.phase.out_recom : estimates of recombination parameters c26b1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 94 Number of Loci: 23 Positions of loci: 5663 14204 14299 14465 14660 14726 15370 16647 16853 17206 18710 18829 19188 19425 19545 19723 19802 19821 19869 19908 19977 20654 20702 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file c26b1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACTCCTTCCTGGDICACCTGCAG 1.000000 2 ACTCCTTCCTGAIDCACGCCCAG 1.000000 3 ACTCTCCCCTGAIDCACGTGCAG 1.000000 4 ACTCTCCCTGCGDICACGTGCAG 1.000000 5 ATGCCTCTTGCGDDCCCCTGTAG 1.000000 6 ATGCCTCTTGCGIICACGTGCGG 1.000000 7 ATGCCTTCCTCGDDAACGCGCAG 1.000000 8 ATGCCTTTTGCGDDCACGCCCAG 1.000000 9 ATGCCTTTTGCGIDCACCTGCGG 1.000000 10 CCTCCTCCCTGADDCATCCGCGG 2.000000 11 CCTCTCCCCTGAIDCACGCGCAG 1.000000 12 CCTCTCCCCTGAIDCACGCGTGG 1.000000 13 CCTCTCCCCTGAIDCACGTGCAG 1.000000 14 CCTCTCCCCTGAIDCATCTGCAG 1.000000 15 CCTCTCCTCTGAIICACCTGCAG 1.000000 16 CCTCTCCTCTGAIICACCTGCGG 3.000000 17 CCTCTCCTCTGAIICCCCTCCGG 4.000000 18 CCTCTCCTCTGAIDCACGCGTGG 1.000000 19 CCTTCTTCCTCGDDACCGTGTGG 2.000000 20 CCTTCTTCCTGADICACCCCCAG 1.000000 21 CCTTCTTCCTGAIICATCTGCAA 13.000000 22 CCTTCTTTTGCGIDCACGCCCAG 1.000000 23 CTGCCTCTCGCGDICACGTGCAG 1.000000 24 CTGCCTCTCTGAIICACGTGCAG 1.000000 25 CTGCCTCTTGCGDICACCCGCGG 1.000000 26 CTGCCTCTTGCGDICACCTGCAG 29.000000 27 CTGCCTCTTGCGDICACCTGCGG 6.000000 28 CTGCCTCTTGCGDICACGTGCAG 2.000000 29 CTGCCTCTTGCGDICACGTGCGG 1.000000 30 CTGCCTCTTGCGDICCCGTGCGG 1.000000 31 CTGCCTCTTGCGDIACCGTGCGG 1.000000 32 CTGCCTCTTGCGDDCACGCCCAG 2.000000 33 CTGCCTCTTGCGDDAACCTGCAG 1.000000 34 CTGCCTCTTGCGDDAACGTGCAG 4.000000 35 CTGCCTCTTGCGDDAACGTGCAA 2.000000 36 CTGCCTCTTGCGDDAACGTGCGG 2.000000 37 CTGCCTCTTGCGDDACCCTCCGG 2.000000 38 CTGCCTCTTGCGDDACCCTGTAG 1.000000 39 CTGCCTCTTGCGDDACCCTGTGG 4.000000 40 CTGCCTCTTGCGDDACCGTGCAG 1.000000 41 CTGCCTCTTGCGDDACCGTGCGG 12.000000 42 CTGCCTCTTGCGDDACCGTGTGG 53.000000 43 CTGCCTCTTGCGDDACTGTGTGG 1.000000 44 CTGCCTCTTGCGIDCACGCCCAG 1.000000 45 CTGCCTCTTGGAIICACCTGCAG 1.000000 46 CTGCCTTCCTGAIICATCTGCAA 1.000000 47 CTGCCTTTTGCGDDCACGCCCGG 1.000000 48 CTGCCTTTTGCGDDCACGTGCAG 2.000000 49 CTGCCTTTTGCGDDCATCTCCAG 1.000000 50 CTGCCTTTTGCGDDCATCTGCGG 1.000000 51 CTGCCTTTTGCGIDCACGCCCAG 2.000000 52 CTGCCTTTTGCGIDCACGCCCAA 1.000000 53 CTGCCTTTTGCGIDCACGCCCGG 4.000000 54 CTGCCTTTTGCGIDCACGCGCAG 1.000000 55 CTGCCTTTTGCGIDCACGTGCGG 1.000000 56 CTGCCTTTTGCGIDCACGTGTGG 1.000000 57 CTGCTCCCCTGAIDCACGCGTGG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,32) D002: (14,51) D003: (52,56) D004: (11,39) D005: (51,53) D006: (18,23) D007: (41,54) D008: (50,53) D009: (3,22) D010: (26,49) D011: (31,57) D012: (7,25) D013: (15,42) D014: (6,53) D015: (26,32) D016: (53,55) D033: (4,42) D034: (8,38) D035: (48,44) D036: (17,48) D037: (41,47) D038: (5,41) D039: (9,10) D040: (2,13) E001: (42,42) E002: (33,42) E003: (42,42) E004: (35,37) E005: (21,43) E006: (42,42) E007: (34,42) E008: (42,42) E009: (42,42) E010: (21,41) E011: (42,42) E012: (34,42) E013: (35,42) E014: (42,42) E015: (34,42) E016: (41,42) E017: (26,42) E018: (42,42) E019: (34,42) E020: (42,42) E021: (36,42) E022: (26,42) E023: (40,42) E024: (26,42) H101: (36,42) H102: (21,42) H103: (21,42) H104: (26,42) H105: (26,46) H106: (21,21) H107: (21,42) H108: (10,17) H109: (21,42) H110: (26,42) H111: (21,42) H112: (17,21) H113: (21,37) H114: (20,21) H115: (17,21) H116: (16,45) H117: (42,42) H118: (41,42) H119: (24,39) H120: (16,42) H121: (12,42) H122: (26,42) X125: (26,26) X126: (26,41) X127: (27,42) X128: (42,42) X129: (26,27) X130: (26,26) X131: (26,27) X132: (26,41) X133: (26,41) X134: (19,26) X135: (26,28) X136: (26,28) X137: (26,26) X138: (16,29) X139: (26,41) X140: (27,42) X141: (39,42) X142: (27,42) X143: (19,41) X144: (26,26) X145: (26,26) X146: (27,39) X147: (26,30) X148: (41,42) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 (A) C T C C T (T) C C T G G D (I) C A C (C) (T) (G) C A G (C) T G C C T (C) T T G C G D (D) C A C (G) (C) (C) C A G 0 D002 C C T C T C C C C T G A I D C A (T) (C) (T) (G) C A G C T G C C T T T T G C G I D C A (C) (G) (C) (C) C A G 0 D003 C T G C C T T T T G C G I D C A C G C C C (A) (A) C T G C C T T T T G C G I D C A C G T G T (G) (G) 0 D004 C C T C T C C C C T G A I D C A C G C G (C) (A) G C T G C C T C T T G C G D D A C C C T G (T) (G) G 0 D005 C T G C C T T T T G C G I D C A C G C C C A G C T G C C T T T T G C G I D C A C G C C C G G 0 D006 C (C) (T) C (T) (C) C T C T G A I (D) C A C G C G (T) (G) G C (T) (G) C (C) (T) C T C G C G D (I) C A C G T G (C) (A) G 0 D007 C T G C C T C T T G C G D D A C C G T G C (G) G C T G C C T T T T G C G I D C A C G C G C (A) G 0 D008 C T G C C T T T T G C G (D) D C A T C T (G) C G G C T G C C T T T T G C G (I) D C A C G C (C) C G G 0 D009 (A) C T (C) (T) (C) (C) (C) C T G A I [D] C A C G T G C A G (C) C T (T) (C) (T) (T) (T) T G C G I D C A C G C C C A G 0 D010 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T T T T G C G D D C A T C T C C A G 0 D011 C T G C C T C T T G C G D (I) A C C G T G (C) G G C T G C T C C C C T G A I (D) C A C G C G (T) G G 0 D012 (A) T G C C T T C C T C G D (D) (A) A C (G) C G C (A) G (C) T G C C T C T T G C G D (I) (C) A C (C) C G C (G) G 0 D013 C C T C T C C T C T G A I I C A C (C) T G C (A) G C T G C C T C T T G C G D D A C C (G) T G T (G) G 0 D014 (A) T G C C T (C) T T G C G I I C A C G T G C G G (C) T G C C T (T) T T G C G I D C A C G C C C G G 0 D015 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D C A C G C C C A G 0 D016 C T G C C T T T T G C G I D C A C G C C C G G C T G C C T T T T G C G I D C A C G T G C G G 0 D033 (A) (C) (T) C (T) (C) C (C) T G C G D (I) (C) (A) C G T G (C) (A) G (C) (T) (G) C (C) (T) C (T) T G C G D (D) (A) (C) C G T G (T) (G) G 0 D034 (A) T G C C T (T) T T G C G D D (C) A C G C C C A G (C) T G C C T (C) T T G C G D D (A) C C C T G T A G 0 D035 C T G C C T (T) T T G C G (D) D C A C G T G C A G C T G C C T (C) T T G C G (I) D C A C G C C C A G 0 D036 C C T C T C C T C T G A I I C C C C T C C G G C T G C C T T T T G C G D D C A C G T G C A G 0 D037 C T G C C T C T T G C G D D A C C G T G C G G C T G C C T T T T G C G D D C A C G C C C G G 0 D038 (A) T G C C T C T T G C G D D (C) C C (C) T G (T) (A) G (C) T G C C T C T T G C G D D (A) C C (G) T G (C) (G) G 0 D039 (A) T G C C T T T T G C G I D C A C C T G C G G (C) C T C C T C C C T G A D D C A T C C G C G G 0 D040 (A) C T C C T T C C T G A I D C A C G (C) (C) C [A] G (C) C T C T C C C C T G A I D C A C G (T) (G) C A G 0 E001 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E002 C T G C C T C T T G C G D D A A C (C) T G C A G C T G C C T C T T G C G D D A C C (G) T G T G G 0 E003 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E004 C T G C C T C T T G C G D D A A C G T G C A A C T G C C T C T T G C G D D A C C C T C C G G 0 E005 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C T G T G T G G 0 E006 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E007 C T G C C T C T T G C G D D A A C G T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 E008 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E009 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E010 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G C G G 0 E011 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E012 C T G C C T C T T G C G D D A A C G T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 E013 C T G C C T C T T G C G D D A A C G T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 E014 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E015 C T G C C T C T T G C G D D A A C G T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 E016 C T G C C T C T T G C G D D A C C G T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 E017 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 E018 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E019 C T G C C T C T T G C G D D A A C G T G C A G C T G C C T C T T G C G D D A C C G T G [T] G G 0 E020 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 E021 C T G C C T C T T G C G D D A A C G T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 E022 C [T] G C C T C [T] [T] G C G D [I] [C] [A] C [C] T G C [A] G C T G C C T C T T G C G D [D] [A] [C] C [G] T G [T] [G] G 0 E023 C T G C C T C T T G C G D D A C C G T G (C) A G C T G C C T C T T G C G D D A C C G T G (T) G G 0 E024 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 H101 C T G C C T C T T G C G D D A A C G T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 H102 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 H103 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 H104 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 H105 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T T C C T G A I I C A T C T G C A A 0 H106 C C T T C T T C C T G A I I C A T C T G C A A C C T T C T T C C T G A I I C A T C T G C A A 0 H107 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 H108 C C T C C T C C C T G A D D C A T C C G C G G C C T C T C C T C T G A I I C C C C T C C G G 0 H109 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 H110 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 H111 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C G T G T G G 0 H112 C C T C T C C T C T G A I I C C C C T C C G G C C T T C T T C C T G A I I C A T C T G C A A 0 H113 C C T T C T T C C T G A I I C A T C T G C A A C T G C C T C T T G C G D D A C C C T C C G G 0 H114 C C T T C T T C C T G A D I C A C C C C C A G C C T T C T T C C T G A I I C A T C T G C A A 0 H115 C C T C T C C T C T G A I I C C C C T C C G G C C T T C T T C C T G A I I C A T C T G C A A 0 H116 C C T C T C C T C T G A I I C A C C T G C (G) G C T G C C T C T T G G A I I C A C C T G C (A) G 0 H117 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 H118 C T G C C T C T T G C G D D A C C G T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 H119 C T G C C T C T C T G A I [I] C A C (G) T G (C) (A) G C T G C C T C T T G C G D [D] [A] [C] C (C) T G (T) (G) G 0 H120 C C T C T C C T C T G A I I C A C C T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 H121 C C T C T C C C C T G A I D C A C G C G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 H122 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G T G G 0 X125 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C A G 0 X126 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G C G G 0 X127 C T G C C T C T T G C G D I C A C C T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 X128 C T G C C T C T T G C G D D A C C G T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 X129 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C G G 0 X130 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C A G 0 X131 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C G G 0 X132 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G C G G 0 X133 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G C G G 0 X134 C C T T C T T C C T C G D (D) (A) (C) C (G) T G (T) (G) G C T G C C T C T T G C G D (I) (C) (A) C (C) T G (C) (A) G 0 X135 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C G T G C A G 0 X136 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C G T G C A G 0 X137 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C A G 0 X138 C C T C T C C T C T G A I I C A C (C) T G C G G C T G C C T C T T G C G D I C A C (G) T G C G G 0 X139 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D D A C C G T G C G G 0 X140 C T G C C T C T T G C G D I C A C C T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 X141 C T G C C T C T T G C G D D A C C C T G T G G C T G C C T C T T G C G D D A C C G T G T G G 0 X142 C T G C C T C T T G C G D I C A C C T G C G G C T G C C T C T T G C G D D A C C G T G T G G 0 X143 C C T T C T T C C T C G D D A C C G T G (T) G G C T G C C T C T T G C G D D A [C] C G T G (C) G G 0 X144 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C A G 0 X145 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C A C C T G C A G 0 X146 C T G C C T C T T G C G D I C A C C T G C G G C T G C C T C T T G C G D D A C C C T G T G G 0 X147 C T G C C T C T T G C G D I C A C C T G C A G C T G C C T C T T G C G D I C C C G T G C G G 0 X148 C T G C C T C T T G C G D D A C C G T G C G G C T G C C T C T T G C G D D A C C G T G T G G 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) C T = = = (T) C C T G = = (I) = = = (C) (T) (G) = = = (C) T G = = = (C) T T G C = = (D) = = = (G) (C) (C) = = = 0 D002 = C T = T C C C C T ? A = = = = (T) (C) (T) (G) = = = = T G = C T T T T G ? G = = = = (C) (G) (C) (C) = = = 0 D003 = = = = = = = = = = = = = = = = = = C C C (A) (A) = = = = = = = = = = = = = = = = = = T G T (G) (G) 0 D004 = C T = T C = C C T G A I = C A = G C = (C) (A) = = T G = C T = T T G C G D = A C = C T = (T) (G) = 0 D005 = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = G = 0 D006 = (C) (T) = (T) (C) = = = T G A I (D) = = = = C = (T) (G) = = (T) (G) = (C) (T) = = = G C G D (I) = = = = T = (C) (A) = 0 D007 = = = = = = C = = = = = D = A C = = T = = (G) = = = = = = = T = = = = = I = C A = = C = = (A) = 0 D008 = = = = = = = = = = = = (D) = = = T C T (G) = = = = = = = = = = = = = = = (I) = = = C G C (C) = = = 0 D009 (A) = = (C) (T) (C) (C) (C) C T G A = ? ? ? = = T G = = = (C) = = (T) (C) (T) (T) (T) T G C G = ? ? ? = = C C = = = 0 D010 = = = = = = C = = = = = = I = = C = = G = = = = = = = = = T = = = = = = D = = T = = C = = = 0 D011 = ? = = C T = T T G C G D (I) A C = = T = (C) = = = ? = = T C = C C T G A I (D) C A = = C = (T) = = 0 D012 (A) = = = = = T C C T = = = (D) (A) = = (G) = = = (A) = (C) = = = = = C T T G = = = (I) (C) = = (C) = = = (G) = 0 D013 = C T = T C = = C T G A I I C A = (C) = = C (A) = = T G = C T = = T G C G D D A C = (G) = = T (G) = 0 D014 (A) = = = = = (C) = = = = = = I = = = = T G = = = (C) = = = = = (T) = = = = = = D = = = = C C = = = 0 D015 = = = = = = = = = = = = = I = = = C T G = = = = = = = = = = = = = = = = D = = = G C C = = = 0 D016 = = = = = = = = = ? = = = = = = = = C C = = = = = = = = = = = = ? = = = = = = = = T G = = = 0 D033 (A) (C) (T) = (T) (C) = (C) = = = = = (I) (C) (A) = = = = (C) (A) = (C) (T) (G) = (C) (T) = (T) = = = = = (D) (A) (C) = = = = (T) (G) = 0 D034 (A) = = = = = (T) = = = = = = = (C) A = G C C C = = (C) = = = = = (C) = = = = = = = (A) C = C T G T = = 0 D035 = = = = = = (T) = = = = = (D) = = = = = T G = = = = = = = = = (C) = = = = = (I) = = = = = C C = = = 0 D036 = C T = T C C = C T G A I I = C = C = C = G = = T G = C T T = T G C G D D = A = G = G = A = 0 D037 = = = = = = C = = = = = = = A C = = T G = = = = = = = = = T = = = = = = = C A = = C C = = = 0 D038 (A) = = = = = = = = = = = = = (C) = = (C) = = (T) (A) = (C) = = = = = = = = = = = = = (A) = = (G) = = (C) (G) = 0 D039 (A) T G = = = T T T G C G I = = = C = T = = = = (C) C T = = = C C C T G A D = = = T = C = = = = 0 D040 (A) = = = C T T ? ? = = = = = = = = = (C) (C) = ? ? (C) = = = T C C ? ? = = = = = = = = = (T) (G) = ? ? 0 E001 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E002 = = = = = = = = = = = = = = = A = (C) = = C A = = = = = = = = = = = = = = = = C = (G) = = T G = 0 E003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E004 = = = = = = = = = = = = = = = A = G = G = A A = = = = = = = = = = = = = = = C = C = C = G G 0 E005 ? C T T = = T C C T G A I I C A = C = = C A A ? T G C = = C T T G C G D D A C = G = = T G G 0 E006 ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 0 E007 = = = = = = = = = = = = = = = A = = = = C A = = = = = = = = = = = = = = = = C = = = = T G = 0 E008 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E009 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E010 = C T T = = T C C T G A I I C A T C = = = A A = T G C = = C T T G C G D D A C C G = = = G G 0 E011 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = 0 E012 = = = = = = = = = = = = = = = A = = = = C A = = = = = = = = = = = = = = = = C = = = = T G = 0 E013 = = = = = = = = = = = = = = = A = = = = C A A = = = = = = = = = = = = = = = C = = = = T G G 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = = = = = ? = = = = = A = = = = C A = = = = = = = = = = ? = = = = = C = = = = T G = 0 E016 = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = T = = 0 E017 = = = = = = = = = = = = = I C A = C = = C A = = = = = = = = = = = = = = D A C = G = = T G = 0 E018 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E019 = = = = = = = = = = = = = = = A = = ? ? ? A = = = = = = = = = = = = = = = = C = = ? ? ? G = 0 E020 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E021 = = = = = = = = = = = = = = = A = = = = C = = = = = = = = = = = = = = = = = C = = = = T = = 0 E022 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0 E023 = = = = = = = = = = = = = = = = = = = = (C) A = = = = = = = = = = = = = = = = = = = = = (T) G = 0 E024 = ? ? = = = = = = = = = = I C A = C = = C A = = ? ? = = = = = = = = = = D A C = G = = T G = 0 H101 = = = = = = = ? ? = = = = = = A = = = = C = = = = = = = = = ? ? = = = = = = C = = = = T = = 0 H102 = C T T = = T C C T G A I I C A T C = = C A A = T G C = = C T T G C G D D A C C G = = T G G 0 H103 = C T T = = T C C T G A I I C A T C = = C A A = T G C = = C T T G C G D D A C C G = = T G G 0 H104 = = = = = = = = = = = = = I C A = C = = C A = = = = = = = = = = = = = = D A C = G = = T G = 0 H105 = = = = = = C T T G C G D = = = C = = = = = G = = = = = = T C C T G A I = = = T = = = = = A 0 H106 = = = = = = = ? ? = = = = ? ? ? = = = = = = = = = = = = = = ? ? = = = = ? ? ? = = = = = = = 0 H107 = C T T = = T C C T G A I I C A T C = = C A A = T G C = = C T T G C G D D A C C G = = T G G 0 H108 = = = = C T = ? ? = = = D D = A T = C G = = = = = = = T C = ? ? = = = I I = C C = T C = = = 0 H109 = C T T = = T C C T G A I I C A T C = = C A A = T G C = = C T T G C G D D A C C G = = T G G 0 H110 = = = = = = = = = = = = = I C A = C = = C A = = = = = = = = = = = = = = D A C = G = = T G = 0 H111 = C T T = = T C C T G A I I C A T C = = C A A = T G C = = C T T G C G D D A C C G = = T G G 0 H112 = = = C T C C T = = = = = = = C C = = C = G G = = = T C T T C = = = = = = = A T = = G = A A 0 H113 = C T T = = T C C T G A I I C A T = = G = A A = T G C = = C T T G C G D D A C C = = C = G G 0 H114 = = = = = = = = = = = = D = = = C = C C = = G = = = = = = = = = = = = I = = = T = T G = = A 0 H115 = = = C T C C T = = = = = = = C C = = C = G G = = = T C T T C = = = = = = = A T = = G = A A 0 H116 = C T = T C = = C T = = = = = = = = = = = (G) = = T G = C T = = T G = = = = = = = = = = = (A) = 0 H117 ? = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = 0 H118 ? = = = ? ? = = = = = = = = = = = = = = C = = ? = = = ? ? = = = = = = = = = = = = = = T = = 0 H119 ? = = = = = = = C T G A ? ? ? ? = (G) = = (C) (A) = ? = = = = = = = T G C G ? ? ? ? = (C) = = (T) (G) = 0 H120 = C T = T C = = C T G A I I C A = C = = C = = = T G = C T = = T G C G D D A C = G = = T = = 0 H121 = C T = T C = C C T G A I ? ? ? = = C = = = = = T G = C T = T T G C G D ? ? ? = = T = = = = 0 H122 = = = = = = = = = = = = = I C A = C = = C A = = = = = = = = = = = = = = D A C = G = = T G = 0 X125 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X126 = = = = = = = = = = = = = I C A = C = = = A = = = = = = = = = = = = = = D A C = G = = = G = 0 X127 = = = = = = = = = = = = = I C A = C = = C = = = = = = = = = = = = = = = D A C = G = = T = = 0 X128 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X129 = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = G = 0 X130 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X131 = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = G = 0 X132 = = = = = = = = = = = = = I C A = C = = = A = = = = = = = = = = = = = = D A C = G = = = G = 0 X133 = = = = = = = = = = = = = I C A = C = = = A = = = = = = = = = = = = = = D A C = G = = = G = 0 X134 = C T T = = T C C T = = = (D) (A) (C) = (G) = = (T) (G) = = T G C = = C T T G = = = (I) (C) (A) = (C) = = (C) (A) = 0 X135 = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = G = = = = = 0 X136 ? = = = = = = = = = = = = = = = = C = = = = = ? = = = = = = = = = = = = = = = = G = = = = = 0 X137 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X138 = C T = T C = = C T G A I = = = = (C) = = = = = = T G = C T = = T G C G D = = = = (G) = = = = = 0 X139 = = = = = = = = = = = = = I C A = C = = = A = = = = = = = = = = = = = = D A C = G = = = G = 0 X140 = = = = = = = = = = = = = I C A = C = = C = = = = = = = = = = = = = = = D A C = G = = T = = 0 X141 = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = G = = = = = 0 X142 = = = = = = = = = = = = = I C A = C = = C = = = = = = = = = = = = = = = D A C = G = = T = = 0 X143 = C T T = = T C C T = = = ? ? ? = = = = (T) = = = T G C = = C T T G = = = ? ? ? = = = = (C) = = 0 X144 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X145 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X146 = = = = = = = = = = = = = I C A = = = = C = = = = = = = = = = = = = = = D A C = = = = T = = 0 X147 = = = = = = = = = = = = = = = A = C = = = A = = = = = = = = = = = = = = = = C = G = = = G = 0 X148 = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = T = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.67 1.00 1.00 = = = 0.68 1.00 1.00 1.00 1.00 = = 0.60 = = = 0.60 0.60 0.60 = = = = 1.00 1.00 = 1.00 1.00 1.00 0.99 0.99 0.99 ? 0.99 = = = = 0.52 0.54 0.57 0.69 = = = = = = = = = = = = = = = = = = = = = 0.91 0.91 1.00 0.68 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 = 0.90 0.98 = 0.61 0.58 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 0.83 0.83 = 0.83 0.83 = = = 0.97 0.97 0.97 0.97 0.84 = = = = 0.97 = 0.89 0.89 = = = = = = = 1.00 = = = = = 1.00 = 1.00 1.00 = = 0.94 = = 0.74 = = = = = = = = = = = = = 0.81 = = = 0.97 1.00 1.00 0.82 = = = 0.64 = = 0.87 0.85 0.85 0.85 0.89 0.98 0.98 0.98 0.98 = ? ? ? = = 0.94 0.94 = = = = = = = = = 0.97 = = = = = = 1.00 = = 1.00 = = 0.96 = = = = ? = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 0.57 0.98 0.98 = = 0.98 = 0.80 = = 0.69 = = = = = 0.93 0.93 0.93 0.93 = = = 0.79 0.79 = = 0.77 = = = 0.64 = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 0.92 0.92 0.91 = 0.90 = = 0.90 0.73 = 0.60 = = = = = 0.90 = = = = = = 0.95 = = = = 0.96 0.96 = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 = = = = = = = = = = = = ? = = = = = = = = 0.97 1.00 = = = 0.83 0.84 0.84 = 0.84 0.84 = 0.84 = = = = = 0.67 0.67 0.67 = = = = 0.67 0.67 = 0.55 = = = = = 0.89 = = = = = = = 0.89 1.00 = 0.91 1.00 1.00 0.98 = = = = = = = = 0.58 = = = = = 0.61 = = = = = 1.00 1.00 = = = = 1.00 1.00 = 1.00 1.00 0.98 = 1.00 1.00 1.00 1.00 0.98 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = 0.96 = = = = = = = 1.00 1.00 = = 1.00 1.00 = = = 0.74 = = = = = = = = = = = = = 0.69 = = 0.86 = = 0.59 0.78 = 0.58 1.00 1.00 = = = 0.96 1.00 1.00 1.00 1.00 1.00 0.95 = = = 0.96 = 0.97 = = = = 0.74 = = = 1.00 1.00 1.00 ? ? = = = = = = = = = 0.80 0.80 = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = 0.65 = = 0.95 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = 1.00 = 0.98 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 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = = 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 = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 = = = = 1.00 0.97 = = = = = = = = = = = = = = = = 0.98 = = = = 0.98 1.00 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = 0.99 = = = = 1.00 0.97 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 0.99 = = 1.00 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.97 = = ? ? ? 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = = = = 1.00 = = ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = 0.83 1.00 = = ? ? = = = = = = = = = = 1.00 1.00 1.00 = 0.99 = = 1.00 0.99 = = = = = = = = ? ? = = = = = = 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 = 0.99 = = 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 1.00 = = 1.00 1.00 1.00 1.00 1.00 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 = 0.99 = = 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 1.00 = = 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 = 0.93 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 = = = = = = = = = = = 0.56 = ? = = = = = = = = = = = = = = = = = = = = = = ? = = = ? ? = = = = = = = = = = = = = = 1.00 = = ? = = = = = = = 1.00 1.00 1.00 1.00 ? ? ? ? = 0.63 = = 0.63 0.60 = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 0.98 0.98 0.98 = 0.93 = = 0.96 = = = 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 = 0.99 = = 1.00 0.99 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = 0.93 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 0.99 = = 0.98 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = 0.93 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = 0.93 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = 0.88 0.88 0.88 = 0.88 = = 0.88 0.88 = = = = = = = = = = = = = = = = = = 1.00 = = = = = ? = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 1.00 0.99 = = = = 0.71 = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = 0.93 = = = = = = = = = = = = = = 1.00 1.00 1.00 = 0.99 = = 0.98 = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 0.99 = = 0.98 = = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = = ? ? ? = = = = 0.83 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = = 0.99 = = = = = = = = = = = = = = = = = 0.98 = 0.98 = = = 0.92 = = = = = = = = = = = = = = = = = = = = = 1.00 = = END PHASEPROBS