************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 sem7a.phase.inp sem7a.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST sem7a.phase.out_freqs : haplotype frequency estimates sem7a.phase.out_pairs : most likely haplotype pairs for each individual sem7a.phase.out_recom : estimates of recombination parameters sem7a.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 58 Positions of loci: 300 1815 4777 4950 4955 4977 6207 6299 6363 6983 6999 7079 7098 8193 8271 8314 8900 9042 9260 9388 9570 9903 10367 10399 11508 11579 11660 12776 13064 14379 14552 14916 14969 15322 15332 16091 16500 16638 16859 17784 17964 18294 18703 19393 20276 20800 21326 21704 22409 22587 23611 23681 24340 25247 25491 25608 26857 27069 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file sem7a.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGTCGATCCGCCACT 2.000000 2 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGTCGATCTGCCACT 3.000000 3 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGTCGACCCGCCACC 1.000000 4 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGTCGACCCACCACC 12.000000 5 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGTCGACCTGCCACT 2.000000 6 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCACGGCGACCCACCACC 10.000000 7 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCCCGTCGATCCGCCACT 1.000000 8 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCCCCCCGGCGACCCACCACC 5.000000 9 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCGCCACGGCGACCCGCCACC 1.000000 10 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGCACGCGGCGCCCCGGCGACCCACCACC 3.000000 11 TGTATGGACAGCCTGTGGGGTGAGCCTCAGGTGCTTCGCCCCACATTAATTCGTTGCC 1.000000 12 TGTATGGAGACCCTGTGGGGCGAGCACCGGGCACGCCGCCCCACGTCGATCCGCCACC 2.000000 13 TGTATGGAGACCCTGTGGGGCGAGCACCGGGCACGCCGCCCCACGTCGACCCACCACC 13.000000 14 TGTATGGAGACCCTGTGGGGCGAGCACCGGGCACGCCGCCCCCCGTCGACCCACCACC 2.000000 15 TGTATGGAGACCCTGTGGGGCGAGCACCGGGCACGCCGCCCTACGTCGACCCACCACC 3.000000 16 TGTATGGCGAGTCTGTGGGGTGAGCACCAGGTGCGTCGCCCCACGTCGATCCGCCACT 1.000000 17 TGTATGGCGAGTCTGTGGGGTGAGCACCAGGTGCGTCGCCCTCCGTCGATCCGCCACT 1.000000 18 TGTATGGCGAGTCTGTGGGGTAAGTACCAGGTGCTTCGCCCCACATTAATTCGTTGCC 2.000000 19 TGTATGGCGAGTCTGTGGGGTAAGTACCAGGTGCTTCGCCCTACATTAATTCGTTACC 2.000000 20 TGTATGGCGAGTCTGTGGGGTAAGTACCAGGTGCTTCGCGCCCCGTCGATCTGCCACT 2.000000 21 TGCGTAGACAGCCTGTAGAGCGGTCCTCACGTGTGCGTTCCCACGTCGATCCGCCACT 1.000000 22 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCCACGTCGATCTGCCACT 1.000000 23 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCCATATTAATTCGTTACC 1.000000 24 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCCCCGGCGACCCACCACC 1.000000 25 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCTACATTAATTCGTTGCC 2.000000 26 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCTCCGTCGACCCACCACC 1.000000 27 TGCGTAGACAGCCTGCAGAGCGGTCCTCACGTGTGCGTTCCTCCATTAATTCGTTGCC 4.000000 28 TGCGTAGACAGCGTGTAGAGCGGTCCTCACATGTGCGTTCCCACGTCGATCCGCCACT 1.000000 29 TGCGTAGACAGCGTGTAGAGCGGTCCTCACATGTGCGTTCCTACGTCGACCCACCACC 1.000000 30 TGCGTAGACAGCGTGTAGAGCGGTCCTCACATGTGCGTTCTTCCGTCGGTCTGCCAAT 4.000000 31 TCCGCACAGCGCCCATACGACGGTCCTTACGTGTGCGTTCCCCTATTAATTCGTTACC 1.000000 32 CCCGCACAGCGCCCATACGACGGTCCTCACGTGTGCGTTCCTACATTAATTCGTTACC 2.000000 33 CCCGCACAGCGCCCATACGACGGTCCTTACGTGTGCGTTCCCATATTAATTCGTTACC 1.000000 34 CCCGCACAGCGCCCATACGACGGTCCTTACGTGTGCGTTCCCCCATTAATTCGTTACC 1.000000 35 CCCGCACAGCGCCCATACGACGGTCCTTACGTGTGCGTTCCCCTATTAATTCGTTACC 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (1,7) DY02: (8,35) DY03: (1,30) DY04: (10,30) DY05: (8,8) DY06: (3,27) DY07: (23,33) DY08: (6,25) DY09: (24,32) DY10: (17,27) DY11: (19,32) DY12: (5,35) DY13: (16,30) DY14: (6,10) DY15: (8,27) DY16: (22,35) DY17: (5,30) DY18: (19,34) DY19: (6,8) DY20: (10,29) DY21: (26,31) DY22: (25,27) DY23: (6,6) DY24: (21,28) E101: (6,13) E102: (4,13) E103: (11,15) E104: (4,13) E105: (2,6) E106: (4,14) E107: (13,15) E108: (4,13) E109: (2,4) E110: (13,13) E111: (6,9) E112: (14,18) E113: (2,4) E114: (4,6) E115: (13,20) E116: (4,13) E117: (4,4) E118: (4,13) E119: (6,13) E120: (12,15) E121: (4,13) E122: (18,20) E123: (12,13) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A T C C G C C A C T T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C [C] C C C C G T C G A T C C G C C A C T 0 DY02 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C C C G [G] C G A C C C A C C A C C C C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C C T A T T A A T T C G T T A C C 0 DY03 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A T C C G C C A C T T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C T T C C G T C G G T C T G C C A A T 0 DY04 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C G C C C C G G C G A C C C A C C A C C T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C T T C C G T C G G T C T G C C A A T 0 DY05 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C C C G G C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C C C G G C G A C C C A C C A C C 0 DY06 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C G C C A C C T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T C C A T T A A T T C G T T G C C 0 DY07 T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C C A T A T T A A T T C G T T A C C C C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C A T A T T A A T T C G T T A C C 0 DY08 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T A C A T T A A T T C G T T G C C 0 DY09 T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C C C C G G C G A C C C A C C A C C C C C G C A C A G C G C C C A T A C G A C G G T C C T C A C G T G T G C G T T C C T A C A T T A A T T C G T T A C C 0 DY10 T G T A T G G C G A G T C T G T G G G G T G A G C A C C A G G T G C G T C G C C C T C C G T C G A T C C G C C A C [T] T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T C C A T T A A T T C G T T G C C 0 DY11 T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C C C T A C A T T A A T T C G T T A C C C C C G C A C A G C G C C C A T A C G A C G G T C C T C A C G T G T G C G T T C C T A C A T T A A T T C G T T A C C 0 DY12 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C T G C C A C T C C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C C T A T T A A T T C G T T A C C 0 DY13 T G T A T G G C G A G T C T G T G G G G T G A G C A C C A G G T G C G T C G C C (C) (C) (A) C G T C G (A) T C (C) G C C A (C) T T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C (T) (T) (C) C G T C G (G) T C (T) G C C A (A) T 0 DY14 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C (C) C C A C G G C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C (G) C C C C G G C G A C C C A C C A C C 0 DY15 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C C C G G C G A C C C A C C A C C T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T C C A T T A A T T C G T T G C C 0 DY16 T G C G T A G A C A G C C T G [C] A G A G C G G T C C T C A C G T G T G C G T T C C C A (C) (G) T (C) (G) A T (C) (T) G (C) (C) A C (T) C C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C C (T) (A) T (T) (A) A T (T) (C) G (T) (T) A C (C) 0 DY17 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C T G C C A C T T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C T T C C G T C G G T C T G C C A A T 0 DY18 T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C C C T A C A T T A A T T C G T T A C C C C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C C C A T T A A T T C G T T A C C 0 DY19 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C C C G G C G A C C C A C C A C C 0 DY20 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C G C C (C) C G G C G A C C C A C C A C C T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C C T (A) C G T C G A C C C A C C A C C 0 DY21 T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T C C G [T] C G A C C C A C C A C C T C C G C A C A G C G C C C A T A C G A C G G T C C T T A C G T G T G C G T T C C C C T A T T A A T T C G T T A C C 0 DY22 T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T A C A T T A A T T C G T T G C C T G C G T A G A C A G C C T G C A G A G C G G T C C T C A C G T G T G C G T T C C T C C A T T A A T T C G T T G C C 0 DY23 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C 0 DY24 T G C G T A G A C A G C C T G T A G A G C G G T C C T C A C G T G T G C G T T C C C A C G T C G A T C C G C C A C T T G C G T A G A C A G C G T G T A G A G C G G T C C T C A C A T G T G C G T T C C C A C G T C G A T C C G C C A C T 0 E101 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E102 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G [T] C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E103 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G T G C T T C G C C C (C) A C A T T A A T T C G T T G C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C (T) A C G T C G A C C C A C C A C C 0 E104 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E105 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A T C T G C C A C T T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C 0 E106 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C (A) C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C (C) C G T C G A C C C A C C A C C 0 E107 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C T A C G T C G A C C C A C C A C C 0 E108 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E109 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A T C T G C C A C T T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C 0 E110 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E111 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C (C) C C A C G G C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C (G) C C A C G G C G A C C C G C C A C C 0 E112 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C (C) C G T C G A C C C A C C A C C T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C C C C (A) C A T T A A T T C G T T G C C 0 E113 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A T C T G C C A C T T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C 0 E114 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C 0 E115 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C (A) C G T C G A C C C A C C A C C T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C G C C (C) C G T C G A T C T G C C A C T 0 E116 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E117 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C 0 E118 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G [T] C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E119 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G G C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E120 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C (C) A C G T C G A T C C G C C A C [C] T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C (T) A C G T C G A C C C A C C A C C 0 E121 T G T A T G G A C A G C C T G T G G G G T G A G C C T C A G G C A C G C G G C C C C A C G T C G A C C C A C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 0 E122 T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C C C C (A) C A T T A A T T C G T T G C C T G T A T G G C G A G T C T G T G G G G T A A G T A C C A G G T G C T T C G C G C C (C) C G T C G A T C T G C C A C T 0 E123 T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C [C] A C G T C G A T C C G C C A C C T G T A T G G A G A C C C T G T G G G G C G A G C A C C G G G C A C G C C G C C C C A C G T C G A C C C A C C A C C 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 DY01 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = C = = = = = = = = = = = = = = = 0 DY02 T G T A T G G = C A = = = T G = G G = G T = A G = = = ? ? G = C A C = = = G C = = = = C G ? C G ? ? C = A C C = ? ? C C C G C A C = G C = = = C A = A C = A C = G T = = = ? ? C = T G T = = = T T = = = = T A ? T A ? ? T = G T T = ? ? 0 DY03 = = T A = G = = = = = = C = = = G = G = T = A G = = = = = G G C A C = = = G C = C C A = = = = = A = = C = = = = C = = = C G = A = = = = = = G = = = A = A = C = G T = = = = = C A T G T = = = T T = T T C = = = = = G = = T = = = = A = 0 DY04 = = T A = G = = = = = = C = = = G = G = T = A G = = = = = G G C A C = = = G C G C C = = = G = = A C = C A = = = C C = = C G = A = = = = = = G = = = A = A = C = G T = = = = = C A T G T = = = T T C T T = = = T = = G T = T G = = = A T 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 DY06 = = T A = G = = = = = = = = = T G = G = T = A G = = = = = G = C A C = = = G C = = C A = G = C G = C C = = C C A = = = = C G = A = = = = = = = = = C A = A = C = G T = = = = = C = T G T = = = T T = = T C = A = T A = T T = = T T G = = 0 DY07 T G = = T = G = C A = = = T G C = G A G = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C = = C = C = G C = = = C A T = C G A = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY08 = = T A = G = = = = = = = = = T G = G = T = A G = = = = = G = C ? C = = = G C = ? C = = G G C G ? C C = A C C A = = = = C G = A = = = = = = = = = C A = A = C = G T = = = = = C = T ? T = = = T T = ? T = = A T T A ? T T = G T T G = = 0 DY09 T G = = T = G = C A = = = T G C = G A G ? ? = = = = = = = = = = = = = = = = = = ? C C = G G C G = C C = A C C = = = C C = = C = C = G C = = = C A T = C G A ? ? = = = = = = = = = = = = = = = = = = ? T A = A T T A = T T = G T T = = = 0 DY10 = = T A = G = C G = = T = = = T G = G = T = A G = A C ? ? G = = = C = T C G C = = = = = G ? C G ? ? C = = C C A ? ? = = C G = A = A C = = C = = = C A = A = C = G T = C T ? ? C = = = T = C G T T = = = = = A ? T A ? ? T = = T T G ? ? 0 DY11 T G T A T G ? C = A = T = T G = G G = G T A A G T A C = = G = = = C T T C G C = = = = ? = = = = = = = = = = = = = = C C C G C A ? A = C = C = C A = A C = A C G G T C C T = = C = = = T G C G T T = = = = ? = = = = = = = = = = = = = = 0 DY12 T G T A T G G = C A = = = T G = G G = G T = A G = = = C = G = C A C = = = G C = = = A C G = C G = C C T = C C = = T C C C G C A C = G C = = = C A = A C = A C = G T = = = T = C = T G T = = = T T = = = C T A = T A = T T C = T T = = C 0 DY13 = = T A = G = C G = = T C = = = G = G = T = A G = A C = = G G = = C = T C G C = (C) (C) (A) = = = = = (A) = = (C) = = = = (C) = = = C G = A = A C = = C G = = = A = A = C = G T = C T = = C A = = T = C G T T = (T) (T) (C) = = = = = (G) = = (T) = = = = (A) = 0 DY14 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) = = A ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = C ? = = = = = = = = = = = = = = 0 DY15 = = T A = G ? = = = = = = = = T G = G = T = A G = = = = = G = C A C = = = G C = = C = = G G C G = C C = A C C A = = = = C G = A ? = = = = = = = = C A = A = C = G T = = = = = C = T G T = = = T T = = T = = A T T A = T T = G T T G = = 0 DY16 T G = = T = G = C A = = = ? ? ? = G A G = = = = = = = C = = = = = = = = = = = = = = A (C) (G) = (C) (G) = = (C) (T) = (C) (C) = = (T) C C = = C = C = G C = = = ? ? ? = C G A = = = = = = = T = = = = = = = = = = = = = = C (T) (A) = (T) (A) = = (T) (C) = (T) (T) = = (C) 0 DY17 = = T A = G = = = = = = C = = = G = G = T = A G = = = = = G G C A C = = = G C = C C A = = = = = A C = = = = = = C = = = C G = A = = = = = = G = = = A = A = C = G T = = = = = C A T G T = = = T T = T T C = = = = = G T = = = = = = A = 0 DY18 T G T A T G G C = A = T = T G = G G = G T A A G T A C ? ? G = = = C T T C G C = = T A = = ? = = ? ? = = = = = = ? ? C C C G C A C A = C = C = C A = A C = A C G G T C C T ? ? C = = = T G C G T T = = C C = = ? = = ? ? = = = = = = ? ? 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = C = = = = = = = = = = = = = = = 0 DY20 = = T A = G ? = = = = = C = = = G = G = T = A G = = = = = G G C A C = = = G C G = C (C) = = G = = = = = = = = = = = = = = C G = A ? = = = = = G = = = A = A = C = G T = = = = = C A T G T = = = T T C = T (A) = = T = = = = = = = = = = = = 0 DY21 = G = = T = G = C A = = = T G C = G A G = = = = = = = C = = = = = = = = = = = = = T = C G ? C G = C C = A C C = = = = C = = C = C = G C = = = C A T = C G A = = = = = = = T = = = = = = = = = = = = = C = T A ? T A = T T = G T T = = = 0 DY22 = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = ? = A = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? = = = ? = C = = = = = = = = = = = = = = = 0 DY23 = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY24 = = = = = = ? = = = = = C ? = = = = = = = = ? ? = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = G ? = = = = = = = = ? ? = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E101 = = ? ? ? ? = = C = G = = = = = = = = = T = = = = C T = A = = = = = = = G = = = = = = = = G = = = = = = = = = = = = = = ? ? ? ? = = G = C = = = = = = = = = C = = = = A C = G = = = = = = = C = = = = = = = = T = = = = = = = = = = = = 0 E102 = = = = = = = = C = G = = = = = = = = = T = = = = C T ? ? = = = ? = = = G = = = = = = = = ? = = ? ? = = = = = = ? ? = = = = = = = = G = C = = = = = = = = = C = = = = A C ? ? = = = ? = = = C = = = = = = = = ? = = ? ? = = = = = = ? ? 0 E103 = = ? ? ? ? = = C = G = = = = = = = = = T = = = = C T = A = = T G = T T = = = = = (C) = = A = T A = T T = G T T G ? ? = = ? ? ? ? = = G = C = = = = = = = = = C = = = = A C = G = = C A = G C = = = = = (T) = = G = C G = C C = A C C A ? ? 0 E104 = = = = = = = = C = G = = = = = = = = = T = = = = C T = A = = = = = = = G = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = G = C = = = = = = = = = C = = = = A C = G = = = = = = = C = = ? ? = = = = = = = = = = = = = = = = = 0 E105 ? = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? = = = = = T = = = T = T G = = = = T ? = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? = = = = = G = = = C = C A = = = = C 0 E106 = = ? ? ? ? = = C = G = = = = = = = = = T = = = = C T = A = = = = = = = G = = = = = (A) = = = = = = = = = = = = = = = = = ? ? ? ? = = G = C = = = = = = = = = C = = = = A C = G = = = = = = = C = = = = = (C) = = = = = = = = = = = = = = = 0 E107 = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = C = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = T = = = = = = = = = = = = = = = = 0 E108 = = = = = = = = ? = G = = ? ? ? = = = = T = = = = C T ? ? = = = ? = = = G = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = C = = ? ? ? = = = = C = = = = A C ? ? = = = ? = = = C = = = ? = = = = = = = = = = = = = = = = = 0 E109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = = = T = T G = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = = = C = C A = = = = C 0 E110 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = ? ? 0 E111 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = (C) ? = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = (G) ? = = = = = = = = = = = G = = = = = 0 E112 = = = = = = = A = = C C = = = = = = = = C G = = C = = = G = = C A = G C = = = = = = (C) = G = C G = C C = A C C A = = = = = = = = = C = = G T = = = = = = = = T A = = T = = = A = = T G = T T = = = = = = (A) = A = T A = T T = G T T G = = 0 E113 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = T = T G = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = C = C A = = = = C 0 E114 = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = G = = = = = = = = = = = = 0 E115 = = = = = = = A = = C C = = = = = = = = C G = = C = = = G = = C A = G C = = = C = = (A) = = = = = = C = C A = = = = C = = = = = = = C = = G T = = = = = = = = T A = = T = = = A = = T G = T T = = = G = = (C) = = = = = = T = T G = = = = T 0 E116 = = ? ? ? ? = = C = G = = ? ? ? = = = = T = = = = C T = A = = = = ? ? = G = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = G = C = = ? ? ? = = = = C = = = = A C = G = = = = ? ? = C = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = C = G = = = = = = = = = T = = = = C T ? ? = = = = = = = G = = = = = = = = ? = = ? ? = = = = = = ? ? = = = = = = = = G = C = = = = = = = = = C = = = = A C ? ? = = = = = = = C = = = = = = = = ? = = ? ? = = = = = = ? ? 0 E119 = = = = = = = = C = G = = ? ? ? = = = = T = = = = C T = A = = = ? ? = = G = = = = = = = = G = = = = = = = = = = = = = = = = = = = = G = C = = ? ? ? = = = = C = = = = A C = G = = = ? ? = = C = = = = = = = = T = = = = = = = = = = = = 0 E120 = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = (C) = = = = = = = T = = G = = = ? ? = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = (T) = = = = = = = C = = A = = = ? ? 0 E121 = = = = = = = = C = G = = = = = = = = = T = = = = C T = A = = = = = = = G = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = G = C = = = = = = = = = C = = = = A C = G = = = = = = = C = = = = ? ? = = = = = = = = = = = = = = = 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = (A) = A = T A = = T C = T T G = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = (C) = G = C G = = C T = C C A = T 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = T = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = C = = A = = = = = 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 1.00 = = = 1.00 1.00 = = = = 1.00 1.00 ? 1.00 1.00 ? ? 1.00 = 1.00 1.00 1.00 = ? ? = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 0.94 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 0.96 0.98 0.98 = = = 0.98 = = 0.98 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 = = = = = 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 = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 ? ? = = = = = = = = = = = = = = = = = = ? 0.97 1.00 = 0.99 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 = 1.00 1.00 1.00 1.00 = = = = = 1.00 ? 1.00 1.00 ? ? 1.00 = = 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = ? = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = 0.80 0.80 0.80 = = = = = 0.80 = = 0.80 = = = = 0.80 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.83 = = 1.00 ? = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 ? = = = = = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 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 0.89 0.89 = 0.89 0.89 = = 0.89 0.89 = 0.89 0.89 = = 0.89 = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 = 1.00 1.00 1.00 = = = = = 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = ? = = ? ? = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 ? = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 1.00 0.93 = 0.93 0.81 = = 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 1.00 = 1.00 1.00 = 1.00 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 = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 ? ? = = = ? = = = 1.00 = = = = = = = = ? = = ? ? = = = = = = ? ? = = ? ? ? ? = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = = = = = 0.71 = = 1.00 = 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 ? ? = = = = = = = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = ? ? = = = = = = = = = = = = = = = = = ? = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? = = = = = 1.00 = = = 1.00 = 1.00 1.00 = = = = 1.00 = = ? ? ? ? = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = = = = 0.65 = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = 1.00 = = ? ? ? = = = = 1.00 = = = = 1.00 1.00 ? ? = = = ? = = = 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 = 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 = = 0.88 = = = = = = 1.00 = 1.00 1.00 = = = = 1.00 = = ? ? ? ? = = 1.00 = 1.00 = = ? ? ? = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = ? ? = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = 0.60 = = = = = = = 1.00 = = 1.00 = = = ? ? = = = = = = = = 1.00 = 1.00 = = = = = = = = = 1.00 = = = = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 0.84 = 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = 1.00 = = 1.00 = = = = = END PHASEPROBS