************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 ckmxx.phase.inp ckmxx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST ckmxx.phase.out_freqs : haplotype frequency estimates ckmxx.phase.out_pairs : most likely haplotype pairs for each individual ckmxx.phase.out_recom : estimates of recombination parameters ckmxx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 43 Positions of loci: 275 363 944 990 2512 2658 2724 3920 3934 4475 4964 7212 7599 7901 7917 7975 7995 8013 8043 9304 9511 9612 9613 11592 11610 11669 12564 12891 13106 13192 13231 13275 13279 14216 15785 16632 18104 18389 18931 19346 19997 20194 20208 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file ckmxx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCCCACTCCCTCAGGGGTATTTTGTCGGCGACAGGICTGACCG 2.000000 2 CCCCACTCCCTCAGGGGTATTTTGTCGGCGACAGGICTGACCA 1.000000 3 CCCCACTCCTTCAGGGGTATTTTACCGGAAACCAGICTAGCCA 2.000000 4 CCCCACTCTCTCAGGGGTACCCCGTCGGCGACAGGICTGACCG 1.000000 5 CCCCACTTTCTCAGGGGTACCCCGTCGGCGACAGGICTGACCG 1.000000 6 CCCCACTTTCTCAGGGGTATTCCGTCGACGGCCGGITTAAACA 1.000000 7 CCCCACTTTCTCAGGGGTATTCCATGGGCGACAGGICTGACCG 3.000000 8 CCCCACTTTCTCAGGGGTATTTCGTCGGCGACAGGICTGACCG 1.000000 9 CCCCACTTTCTCAGGGGTATTTTGTCGGCGACAGGICTGACCG 7.000000 10 CCCCACTTTCTCAGGGGTATTTTGTCGGCGACAGGICTGACCA 1.000000 11 CCCCACTTTCTCAGGGGTATTTTGTCGGCGATAGGITTAAACA 2.000000 12 CCCCACTTTCTCAGGGGTATTTTGCCGGCGACAGGICTGGCCA 1.000000 13 CCCCACTTTCTCAGGGGTATTTTATCGGCGACCGGITTAAACA 2.000000 14 CCCCACTTTCTCAGGGGTATTTTACCGGAAACCGGICTAGCCA 1.000000 15 CCCCACTTTCTCAGGGGTATTTTACCGGAAACCAGICTAGCCA 2.000000 16 CCCCACTTTCTCAGGGGTGTTCCATCGGCGACCGGICCAACCA 1.000000 17 CCCCACTTTCTCAGGGGCATCTCGTCGGCGACAGGICTGACCG 1.000000 18 CCCCACTTTCTCAGGGGCATCTCATGGGCGACAGGICTGACCG 1.000000 19 CCCCACTTTCTTTCCAGCACCCCGTCGGCGACAGGICTGACCG 2.000000 20 CCCCAGTTTCTCAGGGGTATTTTATCGACGGCCGGICTGACCG 2.000000 21 CCCCAGTTTCTCAGGGGCGCCCCGTCGACAACCGGITTAAACA 1.000000 22 CCCCAGTTTCTCTGGGGTACTTTATCGGCGACCGGICTAACCA 1.000000 23 CCCCAGTTTCTCTGGGGTACTTTATCGGCGACCGGICCAACCA 1.000000 24 CCCCAGTTTCTCTGGGGTATCTCGTCGGCGACAGGICTGACCG 1.000000 25 CCCCTGTCCTCCAGGGGTGTTCCGTCGACGGCCGGITTAACCA 1.000000 26 CCCCTGTCCTCCAGGGGTGTTCCGTCGACGGCCGGITTAAACA 13.000000 27 CCCCTGTCCTCCAGGGGTGTTCCGTCGACGGCCGGITCAAACA 1.000000 28 CCCCTGTCCTCCAGGGGTGTTCCGTCGACGGCCGADCTAACTA 1.000000 29 CCCCTGTCCTCCAGGGGTGTTCCGTCGGCGACCGGICCAACCA 1.000000 30 CCCCTGTCCTCCAGGGGTGTTTTGTCGACGGCCGGITTAAACA 1.000000 31 CCCCTGTCCTCCAGGGATGTTCCGTCGACGGCCGGITCAAACA 1.000000 32 CCCCTGTCCTCCAGGGATGTTCCGTCGACGGCCGADCTAACTA 1.000000 33 CCCCTGTCCTCCAGGGATGTTCCGTCGGCGACAGGICTGACCG 2.000000 34 CCCCTGTCCTCTTGCGGCACCCCGTCGACGGCCGADCTAACTA 1.000000 35 CCCCTGTTTCTCTGGGGCATCTCGTCGGCGACAGGICTGACCG 1.000000 36 CCCCTGACCTTTTGCGGTGCCCCGTCGACGGCCGGITTAAACA 3.000000 37 CCCCTGACCTTTTGCGGTGCCCCGTCGACGGCCGADCTAACTA 2.000000 38 CCCCTGACCTTTTGCGGTGCCCCATCGACGGCCGGITTAAACA 1.000000 39 CCCCTGACCTTTTGCGGCACCCCGTCGACGGCCGADCTAACTA 7.000000 40 CCCCTGACCTTTTGCGGCGCCCCGTCGACGGCCGADCTAACTA 2.000000 41 CATAACTCCCTCTCCGATGCTTCATCAGCGACCGGICTAACCA 1.000000 42 CATAACTTCCTTTCCGGCACCCCGTCGACGGCCGADCCAACTA 1.000000 43 CATAACACCCTCTCCGATGCTTCATCAGCGACCGGICTAACCA 1.000000 44 GCCCACTTCCTTTGCGGTACCCCGTCGGCGACAGGICTGACCG 2.000000 45 GCCCACTTCCTTTGCGGTACCTTGTCGGCGACAGGICTGACCG 2.000000 46 GCCCACTTCCTTTCCGGCACCCCGTCGACGGCCGADCTAACTA 1.000000 47 GCCCACTTCCTTTCCGGCACCCCGTCGGCGACAGGICTGACCG 5.000000 48 GCCCACTTCCTTTCCGACACCCCGTCGGCGACAGGICTGACCG 1.000000 49 GCCCACTTCCTTTCCAGCACCCCGTCGGCGACAGGICTGACCG 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (9,44) D002: (9,27) D003: (21,33) D004: (9,9) D005: (7,9) D006: (3,5) D007: (15,26) D008: (11,35) D009: (7,9) D010: (10,13) D011: (36,47) D012: (4,20) D013: (16,26) D014: (6,24) D015: (18,23) D016: (11,47) D033: (13,15) D034: (2,29) D035: (1,26) D036: (7,39) D037: (3,22) D038: (8,26) D039: (25,33) D040: (17,20) E001: (9,44) E002: (1,31) E003: (26,37) E004: (14,34) E005: (26,40) E006: (26,26) E007: (12,49) E008: (26,28) E009: (41,46) E010: (43,45) E011: (26,37) E012: (19,39) E013: (26,30) E014: (39,47) E015: (26,40) E016: (39,48) E017: (38,39) E018: (39,42) E019: (36,47) E020: (19,45) E021: (36,47) E022: (39,49) E023: (26,32) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C C C A C T [T] [T] C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G G C C C A C T T C C T T T G C G G T A C C C C G T C G G C G A C A G G I C T G A C C G 0 D002 C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C (T) G A C C G C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T (C) A A A C A 0 D003 C C C C A G T T T C T C A G G G G C G (C) (C) C C G T C G (A) C (A) A C (C) G G I (T) T (A) A (A) C (A) C C C C T G T C C T C C A G G G A T G (T) (T) C C G T C G (G) C (G) A C (A) G G I (C) T (G) A (C) C (G) 0 D004 C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G 0 D005 C C C C A C T T T C T C A G G G G T A T T C C A T G G G C G A C A G G I C T G A C C G C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G 0 D006 C C C C A C T (C) (C) (T) T C A G G G G T A T T T T A C C G G A A A C C A G I C T A G C C A C C C C A C T (T) (T) (C) T C A G G G G T A C C C C G T C G G C G A C A G G I C T G A C C G 0 D007 C C C C A C T T T C T C A G G G G T A T T T T A C C G G A A A C C A G I C T A G C C A C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A 0 D008 C C C C (A) [C] T T T C T C (A) G G G G (T) A T (T) T (T) G T C G G C G A T A G G I T T A A A C A C C C C (T) [G] T T T C T C (T) G G G G (C) A T (C) T (C) G T C G G C G A C A G G I C T G A C C G 0 D009 C C C C A C T T T C T C A G G G G T A T T C C A T G G G C G A C A G G I C T G A C C G C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G 0 D010 C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T [G] A C C A C C C C A C T T T C T C A G G G G T A T T T T A T C G G C G A C C G G I T T A A A C A 0 D011 C C C C T G A C C T T T T G C G G [T] [G] C C C C G T C G A C G G C C G G I T T A A A C A G C C C A C T T C C T T T [C] C G G [C] A C C C C G T C G G C G A C A G G I C T G A C C G 0 D012 C C C C A C T C T C T C A G G G G T A C C C C G T C G G C G A C A G G I C T G A C C G C C C C A G T T T C T C A G G G G T A T T T T A T C G A C G G C C G G I C T G A C C G 0 D013 C C C C (A) (C) T (T) (T) (C) (T) C A G G G G T G T T C C (A) T C G (G) C G A C [C] G G I (C) (C) A A (C) C A C C C C (T) (G) T (C) (C) (T) (C) C A G G G G T G T T C C (G) T C G (A) C G [G] C C G G I (T) (T) A A (A) C A 0 D014 C C C C A (C) T T T C T C (A) G G G G T A T (T) C C G T C G A C G G C C G G I T T A A A C A C C C C A (G) T T T C T C (T) G G G G T A T (C) T C G T C G G C G A C A G G I C T G A C C G 0 D015 C C C C A (C) T T T C T C (A) G G G G C A T C T C A T G G G C G A C A G G I C (T) G A C C G C C C C A (G) T T T C T C (T) G G G G T A C T T T A T C G G C G A C C G G I C (C) A A C C A 0 D016 C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A (T) A G G I (T) T (A) A (A) C (A) G C C C A C T T C C T T T C C G G C A C C C C G T C G G C G A (C) A G G I (C) T (G) A (C) C (G) 0 D033 C C C C A C T T T C T C A G G G G T A T T T T A T C G G C G A C C G G I T T A A A C A C C C C A C T T T C T C A G G G G T A T T T T A C C G G A A A C C A G I C T A G C C A 0 D034 C C C C A C T C C C T C A G G G G T A T T T T G T C G G C G A C A G G I C T [G] A C C A C C C C T G T C C T C C A G G G G T G T T C C G T C G G C G A C [C] G G I C C A A C C A 0 D035 C C C C A C T C C C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A 0 D036 C C C C A C T T T C T C A G G G G T A T T C C A T G G G C G A C A G G I C T G A C C G C C C C T G A C C T T T T G C G G C A C C C C G T C G A C G G C C G A D C T A A C T A 0 D037 C C C C A C T C C T T C A G G G G T A T T T T A C C G G A A A C C A G I C T A G C C A C C C C A G T T T C T C T G G G G T A C T T T A T C G G C G A C C G G I C T A A C C A 0 D038 C C C C A C T T T C T C A G G G G T A T T T C G T C G G C G A C A G G I C T G A C C G C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A 0 D039 C C C C T G T C C T C C A G G G (G) T G T T C C G T C G A C G G C C G G I T T A A C C A C C C C T G T C C T C C A G G G (A) T G [T] [T] C C G T C G G C G A C A G G I C T G A C C G 0 D040 C C C C A C T T T C T C A G G G G (C) A [T] [C] [T] [C] G T C G G C G A C A G G I C T G A C C G C C C C A G T T T C T C A G G G G (T) A T T T T A T C G A C G G C C G G I C T G A C C G 0 E001 C C C C A C T T T C T C A G G G G T A T T T T G T C G G C G A C A G G I C T G A C C G G C C C A C T T C C T T T G C G G T A C C C C G T C G G C G A C A G G I C T G A C C G 0 E002 C C C C A C T C C C T C A G G G (G) T A T T T T G T C G G C G A C A G G I C (T) G A C C G C C C C T G T C C T C C A G G G (A) T G T T C C G T C G A C G G C C G G I T (C) A A A C A 0 E003 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G [G] (I) (T) T A A (A) (C) A C C C C T G A C C T T T T G C G G T G C C C C G T C G A C G G C C G [A] (D) (C) T A A (C) (T) A 0 E004 C C C C A C T T T C T C A G G G G T A T T T T A C C G G A A A C C G G I C T A G C C A C C C C T G T C C T C T T G C G G C A C C C C G T C G A C G G C C G A D C T A A C T A 0 E005 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G (G) [I] (T) T A A (A) (C) A C C C C T G A C C T T T T G C G G C G C C C C G T C G A C G G C C G (A) [D] (C) T A A (C) (T) A 0 E006 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A 0 E007 C C C C A C T T T C T C A G G G G T A T T T T G (C) C G G C G A C A G G I C T [G] (G) C C (A) G C C C A C T T C C T T T C C A G C A C C C C G (T) C G G C G A C A G G I C T [G] (A) C C (G) 0 E008 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G A D C T A A C T A 0 E009 C A T A A C [T] C C C T C T C C [G] A T G C T T C A T C A G C G A C C G G I C T A A C C A G C C C A C T T C C T T T [C] C G G [C] A C C C C G T C G A C G G C C G A D C T A A C T A 0 E010 C A T A A C [A] C C C T C T C C [G] A T G C T T C A T C A G C G A C C G G I C T A A C C A G C C C A C T T C C T T T [G] C G G [T] A C C T T G T C G G C G A C A G G I C T G A C C G 0 E011 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G [G] (I) (T) T A A (A) (C) A C C C C T G A C C T T T T G C G G T G C C C C G T C G A C G G C C G [A] (D) (C) T A A (C) (T) A 0 E012 C C C C A C T T T C T T T C C A G C A C C C C G T C G G C G A C A G G I C T G A C C G C C C C T G A C C T T T T G C G G C A C C C C G T C G A C G G C C G A D C T A A C T A 0 E013 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G G I T T A A A C A C C C C T G T C C T C C A G G G G T G T T T T G T C G A C G G C C G G I T T A A A C A 0 E014 C C C C T G A C C T T T T G C G G C A C C C C G T C G A C G G C C G A D C T A A C T A G C C C A C T T C C T T T C C G G C A C C C C G T C G G C G A C A G G I C T G A C C G 0 E015 C C C C T G T C C T C C A G G G G T G T T C C G T C G A C G G C C G (G) (I) (T) T A A [A] (C) A C C C C T G A C C T T T T G C G G C G C C C C G T C G A C G G C C G (A) (D) (C) T A A [C] (T) A 0 E016 C C C C T G A C C T T T T G C G (G) C A C C C C G T C G A C G G C C G A D C T A A C T A G C C C A C T T C C T T T C C G (A) C A C C C C G T C G G C G A C A G G I C T G A C C G 0 E017 C C C C T G A C C T T T T G C G G [T] [G] C C C C (A) T C G A C G G C C G G I T T A A A C A C C C C T G A C C T T T T G C G G [C] [A] C C C C (G) T C G A C G G C C G A D C T A A C T A 0 E018 C C C C T G A C C T T T T G C G G [C] A C C C C G T C G A C G G C C G A D C (T) A A C T A C A T A A C T T C C T T T [C] C G G [C] A C C C C G T C G A C G G C C G A D C (C) A A C T A 0 E019 C C C C T G A C C T T T T G C G G [T] [G] C C C C G T C G A C G G C C G G I T T A A A C A G C C C A C T T C C T T T [C] C G G [C] A C C C C G T C G G C G A C A G G I C T G A C C G 0 E020 (C) C C C A C T T (T) C T T T C C [A] G C A C C C C G T C G G C G A C A G G I C T G A C C G (G) C C C A C T T (C) C T T T [G] C G G [T] A C C T T G T C G G C G A C A G G I C T G A C C G 0 E021 C C C C T G A C C T T T T G C G G [T] [G] C C C C G T C G A C G G C C G G I T T A A A C A G C C C A C T T C C T T T [C] C G G [C] A C C C C G T C G G C G A C A G G I C T G A C C G 0 E022 C C C C T G A C C T T T T G C G G C A C C C C G T C G A C G G C C G A D C T A A C T A G C C C A C T T C C T T T C C A G C A C C C C G T C G G C G A C A G G I C T G A C C G 0 E023 C C C C T G T C C T C C A G G G (G) T G T T C C G T C G A C G G C C G G I T T A A A C A C C C C T G T C C T C C A G G G (A) T G T T C C G T C G A C G G C C G A D C T A A C T 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 C = = = = = = ? ? = = C A = G = = = = T T T T = = = = ? = = = = = = = = = = = = = = = G = = = = = = ? ? = = T T = C = = = = C C C C = = = = ? = = = = = = = = = = = = = = = 0 D002 = = = = A C = T T C ? = = = = = = = A = = T T = = = = G = = ? = A = ? = C (T) G = C = G = = = = T G = C C T ? = = = = = = = G = = C C = = = = A = = ? = C = ? = T (C) A = A = A 0 D003 = = = = A = = T T C T = = = = = G C = (C) (C) = = = = = = (A) = (A) = = (C) = = = (T) = (A) = (A) = (A) = = = = T = = C C T C = = = = = A T = (T) (T) = = = = = = (G) = (G) = = (A) = = = (C) = (G) = (C) = (G) 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 D005 = = = = = = = = = = ? = = = = = = = = = = C C A = G = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = T T G = C = = = = = = = = ? = = = = = = = = 0 D006 ? ? ? ? = = = (C) (C) (T) = = = = = = = = = T T T T ? ? ? ? ? A A = = C A = = = = A G ? ? ? ? ? ? ? = = = (T) (T) (C) = = = = = = = = = C C C C ? ? ? ? ? C G = = A G = = = = G A ? ? ? 0 D007 = = = = A C = T T C T = = = = = = = A = = T T A C = = G A A A = = A = = C = = G C = = = = = = T G = C C T C = = = = = = = G = = C C G T = = A C G G = = G = = T = = A A = = 0 D008 = = = = (A) ? ? = = = = = (A) = = = = (T) = = (T) = (T) = = = = = = = = T = = = = T = A = ? = A = = = = (T) ? ? = = = = = (T) = = = = (C) = = (C) = (C) = = = = = = = = C = = = = C = G = ? = G 0 D009 = = = = = = = = = = = = = = = = = = = = = C C A = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T T G = C = = = = = = = = = = = = = = = = = 0 D010 = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = A = = = C = ? = C = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = C = = = T = ? = A = = 0 D011 C = = = T G A C = T = = ? ? ? ? ? ? ? = = = = = = = = A ? ? ? ? ? ? = = T = A = A = A G = = = A C T T = C = = ? ? ? ? ? ? ? = = = = = = = = G ? ? ? ? ? ? = = C = G = C = G 0 D012 = = = = = C = C = = = = = = = = = = = C C C C G = = = G ? ? ? ? ? ? = = = = = = = = = = = = = = G = T = = = = = = = = = = = T T T T A = = = A ? ? ? ? ? ? = = = = = = = = = 0 D013 = = = = (A) (C) = (T) (T) (C) (T) = = = = = = = = = = = = (A) = = = (G) ? ? ? ? ? = = = (C) (C) ? = (C) = = = = = = (T) (G) = (C) (C) (T) (C) = = = = = = = = = = = = (G) = = = (A) ? ? ? ? ? = = = (T) (T) ? = (A) = = 0 D014 = = = = = (C) = ? ? = = = (A) = = = = = = = (T) C = = = = = A = = G = C = = = T = A = A = A = = = = = (G) = ? ? = = = (T) = = = = = = = (C) T = = = = = G = = A = A = = = C = G = C = G 0 D015 = = = = = (C) = = = = = = (A) = = = = C = T C = C = = G = = = = = = A = = = = (T) G = = = G = = = = = (G) = = = = = = (T) = = = = T = C T = T = = C = = = = = = C = = = = (C) A = = = A 0 D016 C = = = = = = = T = = C A G G = = T = T T T T = = = = = = = = (T) = = = = (T) = (A) = (A) = (A) G = = = = = = = C = = T T C C = = C = C C C C = = = = = = = = (C) = = = = (C) = (G) = (C) = (G) 0 D033 = = = = = = = = = = = = = = = = = = = = = = = = T = = = ? ? ? ? ? G = = T = = A A = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = ? ? ? ? ? A = = C = = G C = = 0 D034 = = = = A C = = = C T = = = = = = = A ? ? ? ? = = = = = ? ? ? ? ? ? = = = T ? = = = = = = = = T G = = = T C = = = = = = = G ? ? ? ? = = = = = ? ? ? ? ? ? = = = C ? = = = = 0 D035 = = = = A C = = = C ? = = = = = = = A = = T T = = = = G = = A = A = = = C = G = ? = G = = = = T G = = = T ? = = = = = = = G = = C C = = = = A = = G = C = = = T = A = ? = A 0 D036 = = = = A C T T T C = C A = G = = T = T T = = A = G = G = = A = A = G I = = G = = C G = = = = T G A C C T = T T = C = = C = C C = = G = C = A = = G = C = A D = = A = = T A 0 D037 = = = = = C = C C T = = A = = = = = = T = = = = C = = = A A = = = A = = = = = G = = = = = = = = G = T T C = = T = = = = = = C = = = = T = = = C G = = = G = = = = = A = = = 0 D038 = = = = A C = T T C T = = = = = = = A = = T = = = = = G = = A = A = = = C ? G = C = G = = = = T G = C C T C = = = = = = = G = = C = = = = = A = = G = C = = = T ? A = A = A 0 D039 = = = = = = = = = = = = = = = = (G) = = ? ? ? ? = = = = ? = = G = C = = = T = A = = = A = = = = = = = = = = = = = = = = (A) = = ? ? ? ? = = = = ? = = A = A = = = C = G = = = G 0 D040 = = = = = C = ? ? = ? = = = = = = (C) = ? ? ? ? G = = = G = = A = A = ? = = = = = ? = = = = = = = G = ? ? = ? = = = = = = (T) = ? ? ? ? A = = = A = = G = C = ? = = = = = ? = = 0 E001 ? ? = = = = = ? T = = C A = G = = = = T T T T = = = = = = = = = = = = = = = = = = = = ? ? = = = = = ? C = = T T = C = = = = C C C C = = = = = = = = = = = = = = = = = = = = 0 E002 ? ? = = A C = = = C T = = = = = (G) = A = = T T = = = = G = = A = A = = = C (T) G = C = G ? ? = = T G = = = T C = = = = = (A) = G = = C C = = = = A = = G = C = = = T (C) A = A = A 0 E003 = = = = = = T = = = C C A = G = = = = T T = = = = = = = = = = = = = ? (I) (T) = = = (A) (C) = = = = = = = A = = = T T T = C = = = = C C = = = = = = = = = = = = = ? (D) (C) = = = (C) (T) = 0 E004 = = = = A C = T T C T C A = G = = T = T T T T A C = = G A A A = = = G I = = = G = C = = = = = T G = C C T C T T = C = = C = C C C C G T = = A C G G = = = A D = = = A = T = 0 E005 = = = = = = T = = = C C A = G = = T = T T = = = = = = = = = = = = = (G) ? (T) = = = (A) (C) = = = = = = = A = = = T T T = C = = C = C C = = = = = = = = = = = = = (A) ? (C) = = = (C) (T) = 0 E006 = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? ? = = = = 0 E007 C = = = = = = = T = = C A G G G = T = T T T T = (C) = = = ? = ? ? ? = ? = = = ? (G) = = (A) G = = = = = = = C = = T T C C A = C = C C C C = (T) = = = ? = ? ? ? = ? = = = ? (A) = = (G) 0 E008 = = = = = ? = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = G ? T = = = ? ? ? = = = = = ? = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = A ? C = = = ? ? ? 0 E009 C A T A = ? ? C = = = C ? ? ? ? ? ? ? = T T = A = = A G = = A = = ? G I = = = = = C = G C C C = ? ? T = = = T ? ? ? ? ? ? ? = C C = G = = G A = = G = = ? A D = = = = = T = 0 E010 C A T A ? ? ? C = = = C ? ? ? ? ? ? ? = T = C A = = A = = = = = C = ? = = = A = = = A G C C C ? ? ? T = = = T ? ? ? ? ? ? ? = C = T G = = G = = = = = A = ? = = = G = = = G 0 E011 = = = = = = T = = = ? C A = G = = = = T T = = ? ? ? ? ? = = = ? ? = ? (I) (T) ? ? = (A) (C) = = = = = = = A = = = ? T T = C = = = = C C = = ? ? ? ? ? = = = ? ? = ? (D) (C) ? ? = (C) (T) = 0 E012 = = = = A C T T T C = = = C = A = = = = = = = = = = = G ? ? ? ? ? ? G I = = G = = C G = = = = T G A C C T = = = G = G = = = = = = = = = = = A ? ? ? ? ? ? A D = = A = = T A 0 E013 = = = = = = = = = = = = = = = = = = = = = C C ? ? ? ? = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = T T ? ? ? ? = = = = = = = = ? = = = = = = = 0 E014 C = = = T G A C = T = = = G = = = = = = = = = = = = = ? = = G = C = A D = ? A = = T A G = = = A C T T = C = = = C = = = = = = = = = = = = = ? = = A = A = G I = ? G = = C G 0 E015 = = = = = = T = = = C C A = G = = T = T T = = = = = = = = = = = = = (G) (I) (T) = = = ? (C) = = = = = = = A = = = T T T = C = = C = C C = = = = = = = = = = = = = (A) (D) (C) = = = ? (T) = 0 E016 C = = = T G A C = T = = = G = = (G) = = = = = = = = = = A = = G = C = A D = = ? = = T A G = = = A C T T = C = = = C = = (A) = = = = = = = = = = G = = A = A = G I = = ? = = C G 0 E017 = = = = = ? ? = = = = = ? ? ? ? ? ? ? = = = = (A) = = = = = = = = = ? G I T = = = A C = = = = = = ? ? = = = = = ? ? ? ? ? ? ? = = = = (G) = = = = = = = = = ? A D C = = = C T = 0 E018 = C C C T G A C = T = = ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = (T) ? = = = = = A T A A C T T = C = = ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = (C) ? = = = = 0 E019 C = = = T G A C = T = = ? ? ? ? ? ? ? = = = = = = = = ? ? ? ? ? ? ? = = T = A = ? = A G = = = A C T T = C = = ? ? ? ? ? ? ? = = = = = = = = ? ? ? ? ? ? ? = = C = G = ? = G 0 E020 (C) = = = = = = = (T) = = = ? ? ? ? ? ? ? = = C C = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = (C) = = = ? ? ? ? ? ? ? = = T T = = = = = = = = = = = = = = = = = = = = 0 E021 C = = = T G A C = T = = ? ? ? ? ? ? ? = = = = = = = = A = = G = C = ? = T = A = A = A G = = = A C T T = C = = ? ? ? ? ? ? ? = = = = = = = = G = = A = A = ? = C = G = C = G 0 E022 C = = = T G A C = T = = = G = G = = = = = = = = = = ? ? = = G = C = A D = = A = ? ? ? G = = = A C T T = C = = = C = A = = = = = = = = = = ? ? = = A = A = G I = = G = ? ? ? 0 E023 = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = G I T = = = A C = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = A D C = = = C T = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 0.99 = = = = = = ? ? = = 1.00 1.00 = 1.00 = = = = 1.00 1.00 0.95 0.95 = = = = ? = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 ? = = = = = = = 1.00 = = 1.00 1.00 = = = = 0.98 = = ? = 0.98 = ? = 0.98 0.60 0.98 = 0.98 = 0.98 = = = = 0.94 = = 0.94 0.94 0.94 0.94 = = = = = 0.95 0.94 = 0.82 0.82 = = = = = = 0.68 = 0.67 = = 0.68 = = = 0.68 = 0.68 = 0.68 = 0.68 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = ? = = = = = = = = ? ? ? ? = = = 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 = = = = = = 0.54 ? ? = = = = = 0.65 = = = = 0.58 = = 0.80 = 0.80 = = = = = = = = 1.00 = = = = 1.00 = 1.00 = ? = 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = 1.00 = = = 1.00 = ? = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = = ? ? ? ? ? ? ? = = = = = = = = 1.00 ? ? ? ? ? ? = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 ? ? ? ? ? ? = = = = = = = = = = = = = 0.68 0.68 = 0.68 0.68 0.68 0.68 = = = = = = = = = = = = 0.83 = = = 0.83 ? ? ? ? ? = = = 0.83 0.83 ? = 0.83 = = = = = = = 0.57 = ? ? = = = 0.61 = = = = = = = 0.80 0.91 = = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 = 1.00 = = = = = 0.84 = = = = = = 0.81 = = = = 0.90 = 0.97 0.98 = 0.98 = = 0.95 = = = = = = 0.95 = = = = 0.59 0.95 = = = 0.95 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 0.75 = = = = 0.75 = 0.75 = 0.75 = 0.75 = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = 0.95 ? = = = = = = = 0.95 = = 0.95 0.95 = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 = 1.00 = ? = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = 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 = = 0.98 = = = = = = 0.99 = = = = 1.00 = = = 1.00 1.00 = = = 1.00 = = = = = 1.00 = = = = = = = 0.98 0.98 = 0.98 0.98 0.98 0.98 = = = = = = = 0.98 = = 0.97 = = = = = 0.94 = = 0.94 = 0.94 = = = 0.94 ? 0.94 = 0.94 = 0.94 = = = = = = = = = = = = = = = = 0.83 = = ? ? ? ? = = = = ? = = 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 0.94 0.94 = = = = = = = = = = = = = = = = = = = = ? ? = = 0.91 0.91 = = = 0.91 0.91 = = = = = 0.79 = 0.91 = = 0.91 0.91 = = = = 0.96 = = 0.96 = 0.96 = = = 0.96 0.68 0.96 = 0.96 = 0.96 = = = = = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = = = = 1.00 1.00 = = = = = = = = = = = = = ? 0.57 0.57 = = = 0.57 0.57 = = = = = 0.95 0.95 = 0.95 0.95 0.95 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 = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = 0.66 ? 0.66 = = = 0.66 0.66 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? ? = = = = 1.00 = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 0.52 = = = ? = ? ? ? = ? = = = ? 0.56 = = 0.56 = = = = = ? = = = = = = = = = = = = = = = = = ? ? ? ? ? = = = = = = 1.00 ? 1.00 = = = ? ? ? 1.00 1.00 1.00 1.00 = ? ? 1.00 = = = 1.00 ? ? ? ? ? ? ? = 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 = = ? 1.00 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 ? ? ? 1.00 = = = 1.00 ? ? ? ? ? ? ? = 1.00 = 1.00 1.00 = = 1.00 = = = = = 1.00 = ? = = = 1.00 = = = 1.00 = = = = = = 1.00 = = = ? 1.00 1.00 = 1.00 = = = = 1.00 1.00 = = ? ? ? ? ? = = = ? ? = ? 0.54 0.54 ? ? = 0.54 0.54 = = = = = 0.98 0.98 0.98 0.98 0.97 0.98 = = = 0.98 = 0.98 = = = = = = = = = = = 1.00 ? ? ? ? ? ? 1.00 1.00 = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 ? ? ? ? = = = = = = = = ? = = = = = = = 0.97 = = = 0.97 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 = = = = = = = = = = = = = 0.70 0.70 0.70 = = = ? 0.70 = 0.94 = = = 0.94 0.94 0.94 0.94 = 0.94 = = = 0.94 = = 0.60 = = = = = = = = = = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = = ? = = 1.00 1.00 = = = = = ? ? = = = = = ? ? ? ? ? ? ? = = = = 0.60 = = = = = = = = = ? 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = = ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = 0.58 ? = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = = ? ? ? ? ? ? ? = = = = = = = = ? ? ? ? ? ? ? = = 0.99 = 0.99 = ? = 0.99 0.90 = = = = = = = 0.90 = = = ? ? ? ? ? ? ? = = 0.93 0.93 = = = = = = = = = = = = = = = = = = = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = = ? ? ? ? ? ? ? = = = = = = = = 1.00 = = 1.00 = 1.00 = ? = 1.00 = 1.00 = 1.00 = 1.00 0.97 = = = 0.97 0.97 0.97 0.97 = 0.97 = = = 0.97 = 0.94 = = = = = = = = = = ? ? = = 1.00 = 1.00 = 1.00 1.00 = = 1.00 = ? ? ? = = = = = = = = = = = = = = = = 0.54 = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = = 1.00 1.00 = END PHASEPROBS