************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 proci.phase.inp proci.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST proci.phase.out_freqs : haplotype frequency estimates proci.phase.out_pairs : most likely haplotype pairs for each individual proci.phase.out_recom : estimates of recombination parameters proci.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 49 Positions of loci: 107 267 295 320 346 414 415 750 1073 1328 1338 1359 1636 1650 1677 1678 1799 1963 2359 2589 3141 3341 3345 3347 3390 3409 3670 3900 4051 4194 4316 4677 5057 5081 6177 6279 6294 6448 6510 6554 6630 6742 6824 6893 7004 7027 7198 7599 7681 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file proci.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 TTGTCCGTGCCATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 2.000000 2 TTGTCCGTGCCGTCGCATGCGTCGGATGAGCGGTAAGACGAAGTGGAAG 3.000000 3 TTGTCCGTGCCGCTATGCGCGTCGGTTGAGCGATGAGACAAACTGGAAG 1.000000 4 TTGTCCGTGCCGCTATGCGTGTCGGATGGGCGAGGAGACGAAGTGGAAG 1.000000 5 TTGTCCGTGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 10.000000 6 TTGTCCGTGTGATCGCATGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 2.000000 7 TTGTCCGTGTGATCGCATGCGTCGGATGAGCGGTAAGACGAAGTGGAAG 3.000000 8 TTGTCCGTACCGCTATGCGCGTCGGTTGAGCGATGAGACAAACTGGAAG 4.000000 9 TTGTCCGCGCCGCTATGCGCGTCGGTTGAGCGATGAGACAAACTGGAAG 1.000000 10 TTGTCCGCGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 1.000000 11 TTGTCCATGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 11.000000 12 TTGTCCATGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGAGA 1.000000 13 TTGTCCACGCCGCTATGCGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 1.000000 14 TTGTCCACGCCGCTATGCGCGTCGAATGACCGATGAAACGAAGTAGAAG 3.000000 15 TTGTCTGTGCCGTCGCATGCGTCGGATGAGCGGTAAGACGAAGTGGAAG 9.000000 16 TTGTCTGTGCCGCTATGCGTGTCGGATGGGCGAGGAGACGAAGTGGAAG 2.000000 17 TTGTCTGTGCCGCTATGCACCTCGGATGAGCGATGAGTCGAAGCGGAAG 7.000000 18 TTGTCTGTGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 2.000000 19 TTCTCCATGCCGTCACACGCGTCGGATGAGGGATGAGACGAAGTGGAAG 1.000000 20 CTCGACGTGCCGCTATGCGCGTCGGATGAGCGATGAGACAAACTGGAAG 1.000000 21 CTCGATGTGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 1.000000 22 CTCGATGTACCGCTATGCGCGTCGGTTGAGCGATGAGACAAACTGGAAG 1.000000 23 CTCGATGCGCCGTCACACGCGTCGGATGAGGGATGAGACGAAGTGGAAG 1.000000 24 CTCGATGCGCCGTCGCATGCGTCGGATGAGCGGTAAGACGAAGTGGAAG 2.000000 25 CTCGATGCGTGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 1.000000 26 CTCGATGCGTGATCACACGCGTCGGATGAGCGATGAGTCGAAGCGGAAG 1.000000 27 CTCGATGCGTGATCACACGCGAGAGAAGAGCGATGAGTCGAAGCGAAAG 4.000000 28 CCCGACGTGCCGTCGCATGCGTCGGATGAGCGGTAAGACGAAGTGGAAG 3.000000 29 CCCGACGTGCCGCTATGCGCGTCGGATGAGCGATGCGTCGGGGCGGGGA 1.000000 30 CCCGACGTGCCGCTATGCGCGTCGGATGAGCGATGAGACGAAGTGGAAG 1.000000 31 CCCGACGTGCCGCTATGCGCGTCGGATGAGCGATGAGACAAACTGGAAG 1.000000 32 CCCGACGTGCCGCTATGCGCGTCGGATGAGCAATGAAATGAAGTGGAAG 3.000000 33 CCCGACGTACCGTCACACGCGAGAGAAGAGCGATGAGTCGAAGCGAAAG 1.000000 34 CCCGACGTACCGCTATGCGCGTCGGTTGAGCGATGAGACAAACTGGAAG 4.000000 35 CCCGACGTATGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGGGA 2.000000 36 CCCGACGTATGATCACACGCGTCGGATAAGCGATGCGTCGGGGCGGAGA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,6) D002: (5,17) D003: (17,34) D004: (5,16) D005: (6,9) D006: (13,17) D007: (8,11) D008: (11,17) D009: (20,32) D010: (16,19) D011: (23,29) D012: (5,17) D013: (17,34) D014: (8,18) D015: (1,14) D016: (14,32) D033: (8,32) D034: (4,11) D035: (14,17) D036: (2,5) D037: (3,30) D038: (11,15) D039: (5,26) D040: (15,31) E001: (10,28) E002: (2,34) E003: (15,21) E004: (5,35) E005: (5,25) E006: (24,36) E007: (7,28) E008: (5,15) E009: (2,27) E010: (18,27) E011: (22,35) E012: (5,11) E013: (5,15) E014: (15,15) E015: (7,11) E016: (27,34) E017: (11,27) E018: (11,24) E019: (11,33) E020: (7,11) E021: (11,28) E022: (12,15) E023: (8,15) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 T T G T C C G T G (C) (C) A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C C G T G (T) (G) A T C G C A T G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 D002 T T G T C C G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D003 T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G C C C G A C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G 0 D004 T T G T C (C) G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C (T) G T G C C G C T A T G C G T G T C G G A T G G G C G A G G A G A C G A A G T G G A A G 0 D005 T T G T C C G (T) G [T] [G] A T C G C A T G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C C G (C) G [C] [C] [G] C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G 0 D006 T T G T C C A C G C C G C T A T G C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D007 T T G T C C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 D008 T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D009 C (T) C G A C G T G C C G C T A T G C G C G T C G G A T G A G C G A T G A G A C A A A C T G G A A G C (C) C G A C G T G C C G C T A T G C G C G T C G G A T G A G C A A T G A A A T G A A G T G G A A G 0 D010 T T (G) T C T G T G C C G C T A T G C G T G T C G G A T G G G C G A G G A G A C G A A G T G G A A G T T (C) T C C A T G C C G T C A C A C G C G T C G G A T G A G G G A T G A G A C G A A G T G G A A G 0 D011 C (T) C G A (T) G (C) G C C G T C A C A C G C G T C G G A T G A G G G A T G A G A C G A A G T G G A A G C (C) C G A (C) G (T) G C C G C T A T G C G C G T C G G A T G A G C G A T G C G T C G G G G C G G G G A 0 D012 T T G T C C G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D013 T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G C C C G A C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G 0 D014 T T G T C (C) G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G T T G T C (T) G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 D015 T T G T C C G T G C C A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C C A C G C C G C T A T G C G C G T C G A A T G A C C G A T G A A A C G A A G T A G A A G 0 D016 T T G T C C A C G C C G C T A T G C G C G T C G A A T G A C C G A T G A A A C G A A G T A G A A G C C C G A C G T G C C G C T A T G C G C G T C G G A T G A G C A A T G A A A T G A A G T G G A A G 0 D033 T T G T C C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G C C C G A C G T G C C G C T A T G C G C G T C G G A T G A G C A A T G A A A T G A A G T G G A A G 0 D034 T T G T C C (G) T G C C G C T A T G C G T G T C G G A T G G G C G A G G A G A C G A A G T G G A A G T T G T C C (A) T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 D035 T T G T C C A C G C C G C T A T G C G C G T C G A A T G A C C G A T G A A A C G A A G T A G A A G T T G T C T G T G C C G C T A T G C A C C T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D036 T T G T C C G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G T T G T C C G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 D037 T T G T C C G T G [C] [C] [G] C T A T G C G C G T C G G T T G A G C G A T G A G A C (A) A A [C] T G G A A G C C C G A C G T G C C G C T A T G C G C G T C G G A T G A G C G A T G A G A C (G) A A [G] T G G A A G 0 D038 T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 D039 (T) T (G) (T) (C) (C) G (T) G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A (C) T (C) (G) (A) (T) G (C) G T G A T C A C A C G C G T C G G A T G A G C G A T G A G T C G A A G C G G A A G 0 D040 T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G C C C G A C G T G C C G C T A T G C G C G T C G G A T G A G C G A T G A G A C A A A C T G G A A G 0 E001 (T) (T) (G) (T) (C) C G (C) G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A (C) (C) (C) (G) (A) C G (T) G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E002 (T) (T) (G) (T) (C) C G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G (C) (C) (C) (G) (A) C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G 0 E003 (T) T (G) (T) (C) T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G (C) T (C) (G) (A) T G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E004 T T G T C C G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A C C C G A C G T A T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E005 T T G T C C G (T) G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A C T C G A T G (C) G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E006 C (T) C G A (T) G (C) (G) C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G C (C) C G A (C) G (T) (A) T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G A G A 0 E007 T T G T C C G T G T G A T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G C C C G A C G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E008 T T G T C (C) G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C (T) G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E009 T T G T C C G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G C T C G A T G C G T G A T C A C A C G C G A G A G A A G A G C G A T G A G T C G A A G C G A A A G 0 E010 T T G T C T G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A C T C G A T G C G T G A T C A C A C G C G A G A G A A G A G C G A T G A G T C G A A G C G A A A G 0 E011 C (T) C G A (T) G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G C (C) C G A (C) G T A T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E012 T T G T C C G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E013 T T G T C (C) G T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A T T G T C (T) G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E014 T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E015 T T G T C C (G) T G T G A T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G T T G T C C (A) T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E016 C T C G A T G C G T G A T C A C A C G C G A G A G A A G A G C G A T G A G T C G A A G C G A A A G C C C G A C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G 0 E017 T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A C T C G A T G C G T G A T C A C A C G C G A G A G A A G A G C G A T G A G T C G A A G C G A A A G 0 E018 (T) T (G) (T) (C) (C) (A) (T) G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A (C) T (C) (G) (A) (T) (G) (C) G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E019 (T) (T) (G) (T) (C) C (A) T (G) T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A (C) (C) (C) (G) (A) C (G) T (A) C C G T C A C A C G C G A G A G A A G A G C G A T G A G T C G A A G C G A A A G 0 E020 T T G T C C (G) T G T G A T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G T T G T C C (A) T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A 0 E021 T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G G G A C C C G A C G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E022 T T G T C C A T G T G A T C A C A C G C G T C G G A T A A G C G A T G C G T C G G G G C G G A [G] [A] T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A G 0 E023 T T G T C C G T A C C G C T A T G C G C G T C G G T T G A G C G A T G A G A C A A A C T G G A A G T T G T C T G T G C C G T C G C A T G C G T C G G A T G A G C G G T A A G A C G A A G T G G A A 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 = = = = = = = = = (C) (C) = = = A = = C = = ? = = = = ? = = = = ? = = ? = = = = = = = = = = = = = = = = = = = = = = = = (T) (G) = = = G = = T = = ? = = = = ? = = = = ? = = ? = = = = = = = = = = = = = = = 0 D002 = = = = = C = = = T G A T C = C A = G = G = = = = = = A = = ? = = = = C = = = = G G ? ? ? ? ? G A = = = = = T = = = C C G C T = T G = A = C = = = = = = G = = ? = = = = A = = = = A A ? ? ? ? ? A G 0 D003 T T G T C T = = G = = = = = = = = = A = C = = = = A = = = = ? = = = = = = T = G = = G C = = = = = C C C G A C = = A = = = = = = = = = G = G = = = = T = = = = ? = = = = = = A = A = = C T = = = = = 0 D004 = = = = = (C) = = = T G A T C = C ? ? = C = = = = = = = ? A ? ? = = T = ? ? T = = G G = C = = G G A = = = = = (T) = = = C C G C T = T ? ? = T = = = = = = = ? G ? ? = = G = ? ? A = = A A = T = = A A G 0 D005 = = = = = = = (T) = ? ? ? T C G C ? T = = = = = = = A = A = = ? = = ? = C = T = G G G ? ? ? ? ? G A = = = = = = = (C) = ? ? ? C T A T ? C = = = = = = = T = G = = ? = = ? = A = A = A A A ? ? ? ? ? A G 0 D006 = = = = = C A C = = = = = = = = ? = G = G = = = = = = A = = = = = = = C = = = = G G = = = = G G A = = = = = T G T = = = = = = = = ? = A = C = = = = = = G = = = = = = = A = = = = A A = = = = A A G 0 D007 = = = = = = G = A C C G C T = T G = = = = = = = = T = G = = ? = ? ? = A = A = A A A C T = = A A G = = = = = = A = G T G A T C = C A = = = = = = = = A = A = = ? = ? ? = C = T = G G G G C = = G G A 0 D008 = = = = = C A = = T G A T C = C A = G = G = = = = = = A = = = = = = = C = = = = G G = = = = G G A = = = = = T G = = C C G C T = T G = A = C = = = = = = G = = = = = = = A = = = = A A = = = = A A G 0 D009 = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = ? = C A = = C = = = = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = ? = T G = = G = = = = = = 0 D010 = = (G) = = T G = = = = = C T = T G = = T = = = = = = = = G = C = = G = = = = = = = = ? ? ? ? ? = = = = (C) = = C A = = = = = T C = C A = = C = = = = = = = = A = G = = T = = = = = = = = ? ? ? ? ? = = 0 D011 = (T) = = = (T) = (C) = = = = T C = C A = = = = = = = = = = = = = G = = = = A = A = = A A = T = = A A G = (C) = = = (C) = (T) = = = = C T = T G = = = = = = = = = = = = = C = = = = C = T = = G G = C = = G G A 0 D012 = = = = = C = = = T G A T C = C A = G = G = = = = = = A = = = = = = = C = = = = G G = = = = G G A = = = = = T = = = C C G C T = T G = A = C = = = = = = G = = = = = = = A = = = = A A = = = = A A G 0 D013 T T G T C T = = G ? ? ? = = = = = ? A = C = = = = A = = = = = = = = = = = T = G = = G C = = = = = C C C G A C = = A ? ? ? = = = = = ? G = G = = = = T = = = = = = = = = = = A = A = = C T = = = = = 0 D014 = = = = = (C) = = A C C G C T = T G = = = = = = = = T = G = = ? = = = = A = A = A A ? ? ? ? ? ? A G = = = = = (T) = = G T G A T C = C A = = = = = = = = A = A = = ? = = = = C = T = G G ? ? ? ? ? ? G A 0 D015 = = = = = = G T = = = A T C = C A = = = = = = = G = = A = G = = ? ? = C G T = = G G = C G = G G A = = = = = = A C = = = G C T = T G = = = = = = = A = = G = C = = ? ? = A A A = = A A = T A = A A G 0 D016 T T G T C = A C = = = = = = = = ? = = = = = = = A = = = = C = G ? ? = = = = C = = = = = A = = = = C C C G A = G T = = = = = = = = ? = = = = = = = G = = = = G = A ? ? = = = = T = = = = = G = = = = 0 D033 T T G T C = = = A = = = = = = = = = = = = = = = = T = = = = = G = = = = G = C A = = C = = = = = = C C C G A = = = G = = = = = = = = = = = = = = = = A = = = = = A = = = = A = T G = = G = = = = = = 0 D034 = = = = = = (G) = = C C G C T = T G = = T = = = = = = = G G = = = = G = A = A = = A A ? ? ? ? ? A G = = = = = = (A) = = T G A T C = C A = = C = = = = = = = A A = = = = T = C = T = = G G ? ? ? ? ? G A 0 D035 = = = = = C A C = = = = = ? ? ? ? = G = G = = = A = = = = C = = = = = = A A = = = = = T A = = = = = = = = = T G T = = = = = ? ? ? ? = A = C = = = G = = = = G = = = = = = G T = = = = = C G = = = = 0 D036 = = = = = = = = = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G = = = = = = = = = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A 0 D037 T T G T C = = = = ? ? ? = = = = = = = = = = = = = T = = = = = = = = = = = = = (A) = = ? ? ? ? ? = = C C C G A = = = = ? ? ? = = = = = = = = = = = = = A = = = = = = = = = = = = = (G) = = ? ? ? ? ? = = 0 D038 = = = = = C A = = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A = = = = = T G = = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G 0 D039 (T) = (G) (T) (C) (C) = (T) ? = = = = = = = = = = = = = = = = = = A = = = = = = = C = = = = G G = = = = G G A (C) = (C) (G) (A) (T) = (C) ? = = = = = = = = = = = = = = = = = = G = = = = = = = A = = = = A A = = = = A A G 0 D040 T T G T C T = = = = = = T C G C A T = = = = = = = = = = = = = = ? ? A = = = = G = = G = = = = = = C C C G A C = = = = = = C T A T G C = = = = = = = = = = = = = = ? ? G = = = = A = = C = = = = = = 0 E001 (T) (T) (G) (T) (C) = = (C) = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G ? ? (C) (C) (C) (G) (A) = = (T) = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A ? ? 0 E002 (T) (T) (G) (T) (C) = = = G = = = T C G C A T = = = = = = = A = = = = = = G = A = = = = G = = G = = = = = = (C) (C) (C) (G) (A) = = = A = = = C T A T G C = = = = = = = T = = = = = = A = G = = = = A = = C = = = = = = 0 E003 (T) = (G) (T) (C) = = = = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G (C) = (C) (G) (A) = = = = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A 0 E004 T T G T C = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C C G A = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E005 T = G T C C = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = C G A T = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E006 = (T) = = = (T) = (C) (G) C C G = = G = ? T = = = = = = = = = G = = = = G = A A = A = = A A = T = = = A G = (C) = = = (C) = (T) (A) T G A = = A = ? C = = = = = = = = = A = = = = A = G C = T = = G G = C = = = G A 0 E007 T T G T C = = = = T G A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C C C G A = = = = C C G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E008 = = = = = (C) = = = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A = = = = = (T) = = = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G 0 E009 T = G T C C = T = C C G = = G = = T = = = T C G = = T = = = = = G = A = = A = = = = = T = G = = = C = C G A T = C = T G A = = A = = C = = = A G A = = A = = = = = A = G = = T = = = = = C = A = = = 0 E010 T = G T C = = T ? = = = = = = = = = = = = T C G = = T A = = = = = = = C = = = = G G = = = G G G A C = C G A = = C ? = = = = = = = = = = = = A G A = = A G = = = = = = = A = = = = A A = = = A A A G 0 E011 = (T) = = = (T) = = = C C G C T = T G = = = = = = = = T = G = = = = = = = A = A = A A A C T = = A A G = (C) = = = (C) = = = T G A T C = C A = = = = = = = = A = A = = = = = = = C = T = G G G G C = = G G A 0 E012 = = = = = = G = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = 0 E013 = = = = = (C) = = = T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A = = = = = (T) = = = C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G 0 E014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E015 = = = = = = (G) = = = = = = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A A G = = = = = = (A) = = = = = = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G G A 0 E016 = T = = = T = C G T G A T C = C A = = = = A G A = A A = = = = = = = = = = T = G = = G C = A = = = = C = = = C = T A C C G C T = T G = = = = T C G = T T = = = = = = = = = = A = A = = C T = G = = = 0 E017 T = G T C C A T = = = = = = = = = = = = = T C G = = T A = = = = ? ? = C = = = = G G = = = G G G A C = C G A T G C = = = = = = = = = = = = = A G A = = A G = = = = ? ? = A = = = = A A = = = A A A G 0 E018 (T) = (G) (T) (C) (C) (A) (T) = T G A = = A = = C = = = = = = = = = A = ? ? = A = G C = T = = G G = C = = G G A (C) = (C) (G) (A) (T) (G) (C) = C C G = = G = = T = = = = = = = = = G = ? ? = G = A A = A = = A A = T = = A A G 0 E019 (T) (T) (G) (T) (C) = (A) = (G) T G A = = = = = = = = = T C G = = T A = ? ? = = = ? ? ? = = = G G = = = G G G A (C) (C) (C) (G) (A) = (G) = (A) C C G = = = = = = = = = A G A = = A G = ? ? = = = ? ? ? = = = A A = = = A A A G 0 E020 = = = = = = (G) = = = = = = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A ? G = = = = = = (A) = = = = = = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G ? A 0 E021 T T G T C = A = ? T G A = = A = = C = = = = = = = = = A = = = = A = G C = T = = G G = C = = G ? ? C C C G A = G = ? C C G = = G = = T = = = = = = = = = G = = = = G = A A = A = = A A = T = = A ? ? 0 E022 = = = = = C A = ? T G A = = A = = C = = = = = = = = = A = = = = A = G C ? T = = G G = C = = = ? ? = = = = = T G = ? C C G = = G = = T = = = = = = = = = G = = = = G = A A ? A = = A A = T = = = ? ? 0 E023 = = = = = C = = A = = = C T A T G C = = = ? ? ? ? ? = = = = = = A = ? ? ? = = A = = C = = = = = = = = = = = T = = G = = = T C G C A T = = = ? ? ? ? ? = = = = = = G = ? ? ? = = G = = G = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = 0.64 0.64 = = = 1.00 = = 1.00 = = ? = = = = ? = = = = ? = = ? = = = = = = = = = = = = = = = = = = = = 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 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 = = = = = = = = = = 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 = = 1.00 1.00 1.00 = = = = = = = 0.70 = ? ? ? 1.00 1.00 1.00 1.00 ? 1.00 = = = = = = = 1.00 = 1.00 = = ? = = ? = 1.00 = 1.00 = 1.00 1.00 1.00 ? ? ? ? ? 1.00 1.00 = = = = = 0.99 0.99 0.99 = = = = = = = = ? = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = = = = = = 0.93 = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = ? = ? ? = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = = = = 0.99 0.99 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 = 0.51 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = ? = 1.00 1.00 = = 1.00 = = = = = = = = 0.51 = = 0.99 0.98 = = = = = 1.00 1.00 = 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = 1.00 = = 1.00 = = = = = = = = ? ? ? ? ? = = = 0.89 = = = 0.89 = 0.89 = = = = 0.93 0.93 = 0.93 0.93 = = = = = = = = = = = = = 0.93 = = = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = 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 0.99 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 = = = = = = = = = = 0.73 = = 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 = = = = 0.90 0.90 0.90 0.90 0.90 = = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = = 1.00 = = = = = = = = = = = = 0.76 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 = = = = = = = 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = = 1.00 1.00 ? ? ? ? ? 1.00 1.00 = = = = = 1.00 1.00 1.00 = = = = = ? ? ? ? = 1.00 = 1.00 = = = 1.00 = = = = 1.00 = = = = = = 1.00 1.00 = = = = = 1.00 1.00 = = = = = = = = = = = = = 0.99 0.99 0.99 = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 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 = = = = = = = = = = = = = 0.58 = = ? ? ? ? ? = = = = = = = 0.97 0.97 = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 0.66 = 0.66 0.66 0.66 0.66 = 0.66 ? = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = = = = 1.00 1.00 = = = = 1.00 1.00 1.00 0.90 0.90 0.90 0.90 0.90 0.90 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = ? ? 1.00 = = = = 1.00 = = 1.00 = = = = = = 0.84 0.84 0.84 0.84 0.84 = = 0.51 = 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 ? ? 0.52 0.52 0.52 0.52 0.52 = = = 0.99 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = 1.00 = = = = = = 1.00 = 1.00 = = = = 1.00 = = 1.00 = = = = = = 0.82 = 0.82 0.82 0.82 = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = 0.86 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.68 = = = 0.68 = 0.79 0.84 1.00 1.00 1.00 = = 1.00 = ? 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 0.92 0.92 0.92 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 = = = 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 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 = = = 0.96 = 0.96 0.96 0.96 = = 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 = 0.55 = = = 0.55 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = = = = = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0.87 = = = 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.85 = = = = = = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 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 = = = 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 0.81 = 0.81 0.81 0.81 0.81 0.81 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 0.87 0.87 0.87 0.87 0.87 = 0.87 = 0.86 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 = = = = = = 0.85 = = = = = = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 ? 1.00 0.93 0.93 0.93 0.93 0.93 = 0.93 = ? 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = 1.00 = = = = 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 ? ? = = = = = 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 = = = ? ? = = = = = 0.91 = = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = ? ? ? ? ? = = = = = = 1.00 = ? ? ? = = 1.00 = = 1.00 = = = = = = END PHASEPROBS