************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /home/qyi/lib/phase/PHASE2 -d1 vegft.phase.inp vegft.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST vegft.phase.out_freqs : haplotype frequency estimates vegft.phase.out_pairs : most likely haplotype pairs for each individual vegft.phase.out_recom : estimates of recombination parameters vegft.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 44 Positions of loci: 674 836 1955 2415 2523 2575 2622 3031 3057 3300 3504 4244 4618 5092 5104 5574 6166 6468 6486 7245 7368 7447 7574 7620 7959 7969 8349 8794 9109 9162 9229 9512 10549 10554 10585 11035 11073 11189 11357 11667 12534 13049 13210 13323 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file vegft.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CCT 2 ACCCDACTCAGCCTACTACAAIG 2 CCTCGGGCAGTCCCGG 1.000000 2 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CCTCGGGCAGTCCCGG 5.000000 3 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CCTCCGGCATCCCCAG 1.000000 4 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CCTTGGGCAGTCCTGG 3.000000 5 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CTTCCGGCATCCCCAG 2.000000 6 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CTCCGGGCGGCCCCGG 1.000000 7 CCT 2 ACCCIACTCCATCTATCGTAADG 2 CTCCCGGTAGCGCCAG 3.000000 8 CCT 2 ACCCIACTCCATCTATCGTAADG 4 CCTCGACCGGCCCCGG 1.000000 9 CCT 2 ACCCIACTCCATCTATCGTAGDG 2 TCTCGGGCAGCCCCGG 1.000000 10 CCT 2 ACCCIACTTCATTTATCGTAADG 2 CCTCGGGCAGCCCCAG 1.000000 11 CCT 2 ACCCIACTTCATTTATCGTAADG 2 CCTCGGGCAGCCTTGG 1.000000 12 CCT 2 ACCCIACTTCATTTATCGTAADG 2 CCTCGGGCAGTCCCGG 2.000000 13 CCT 2 ACCCIACTTCATTTATCGTAADG 2 CCTCGACCGGCCTTGG 2.000000 14 CCT 2 ACCCIACTTCATTTATCGTAADG 2 CTCCCGGTAGCGCCAG 3.000000 15 CCT 2 ACCCIACTTCATTTATCGTAADG 2 TCTCGGGCAGCCCCGG 7.000000 16 CCT 2 ACCCIACTTCATTTATCGTAADG 2 TCTCGGGCAGCCTCGG 1.000000 17 CCT 2 ACCCIACTTCATTTATCGTAADG 2 TCTCGACCGGCCTTGG 1.000000 18 CCT 2 ACCCIACTTCATTTATCGTAADG 4 CCTCGACCGGCCTTGG 1.000000 19 CCT 2 ACCCIACTTCATTTATCGTAAIG 2 CTCCCGGTAGCGCCAG 2.000000 20 CCT 2 ACCGIACTCCGCCTACTACAADG 2 CCTCGGGCAGCCCCAG 1.000000 21 CCT 2 ACCGIACTCCGCCTACTACAADG 2 CCTCGGGCAGTCCCGG 1.000000 22 CCT 2 ACCGIACTCCGCCTACTACAAIG 2 CCTCGGGCAGTCCCGG 2.000000 23 CCT 2 ACCGIACTCCGCCTACTACAAIG 2 CCTCGACCGGCCCCGG 1.000000 24 CCT 2 ACCGIACTCCGCCTACTATAAIG 2 CCTCGGGCGGCCCCGG 1.000000 25 CCT 3 GCCCIACTCCGCCGGTCGCAAIG 2 CCTCCGGTAGCGCCAG 1.000000 26 CCT 3 GCCCIACTCCGCCGGTCGCAAIG 4 CCTCGACCGGCCCCGG 1.000000 27 CCT 3 GTCCDACTCCGCCTATCGTTAIG 3 CCTCCGGCAGCCCCAA 2.000000 28 CCT 3 GTCCDATTCCGCCTATCGTTAIG 2 CCTCGGGCAGTCCCGG 1.000000 29 CCT 3 GTCCDATTCCGCCTATCGTTAIA 2 TCTCGGGCAGCCCCGG 1.000000 30 CCT 3 GTCCDATTCCGCCTATCGTTAIA 3 CCTCGGGCAGCCCCGG 1.000000 31 CCT 3 GTCCDATTCCGCCTATCGTTAIA 3 CCTCCGGCAGCCCCAA 1.000000 32 CCT 3 GTCCDATTCCGCCTATCGTTAIA 3 CTCCCGGTAGCGCCAG 2.000000 33 CCT 3 GTTCDACTCCGTTTATCGTAADG 2 CCTCGACCGGCCTTGG 1.000000 34 CCT 4 GCCCIACTCCATCTATCGTAADG 2 CCTTGGGCAGTCCTGG 1.000000 35 CCT 4 GCCCIACCCCGCCGATCGTAAIG 2 CCTCGGGCGGCCCTGG 1.000000 36 CCT 4 GCCCIACCCCGCCGATCGTAAIG 2 CCCCCGGTAGCGCCAG 2.000000 37 CCT 4 GCCCIACCCCGCCGATCGTAGDG 2 CCTCCGGTAGCGCCAG 1.000000 38 CTT 3 GTCCDACTCCGCCTACTATAAIG 2 CCTCGGGCAGTCCTGG 1.000000 39 CTT 3 GTCCDACTCCGCCTACTATAAIG 2 CTCCCGGTAGCGCCAG 2.000000 40 CTT 3 GTCCDACTCCGCCTACTATAAIG 2 TCTCGGGCAGCCCCGG 1.000000 41 TCT 3 GTTCDACTCCGCCTACTATAAIG 2 CCTCGGGCGGCCCCGG 1.000000 42 TCT 3 GTTCDACTCCGCCTACTATAAIG 2 CCTCCGGCAGCCCCAA 1.000000 43 TCT 3 GTTCDACTCCGCCTACTATAAIG 2 CTCCCGGTAGCGCCAG 3.000000 44 TCT 3 GTTCDACTCCGCCTACTATAAIG 3 CCTCCGGCAGCCCCAA 1.000000 45 TCT 3 GTTCDACTCCGCCTACTATAAIG 4 CCTCGACCGGCCTTGG 1.000000 46 TCT 3 GTTCDACTCAGCCTACTACAAIG 2 CTCCCGGTAGCGCCAG 2.000000 47 TCT 3 GTTCDACTCAGCCTACTACAAIG 2 TCTCGGGCAGCCCCGG 6.000000 48 TCT 3 GTTCDACTCAGCCTACCACAADG 2 CCTCGACCGGCCTTGG 1.000000 49 TCT 3 GTTCDACTCAGCCTACCACAGDG 2 CCTCGGGCAGTCCCGG 2.000000 50 TCT 3 GTTCDACTCAGCCTACCACAGDG 2 CTCCCGGTAGCGCCAG 5.000000 51 TCT 3 GTTCDACTCAGCCTACCACAGDG 2 TCTCGGGCAGCCCCGG 1.000000 52 TCT 3 GTTCDACTCAGCCTACCACAGDG 4 CCTCGGGCAGTCCCGG 1.000000 53 TCT 3 GTTCDACTCAGCCTACCATAGDG 4 CCTCGGGCGGCCCCGG 1.000000 54 TCT 3 GTTCDGCTCAGCCTACCACAADG 2 CCTCGGGCAGTCCCGG 1.000000 55 TCC 3 GTTCDGCTCAGCCTACCACAADG 2 CCTCGGGCAGCCCCGG 1.000000 56 TCC 3 GTTCDGCTCAGCCTACCACAADG 2 CCTCGGGCAGCCCCAG 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (21,38) D002: (5,54) D003: (4,4) D004: (5,6) D005: (45,56) D006: (1,25) D007: (24,26) D008: (8,50) D009: (7,7) D010: (37,51) D011: (2,35) D012: (16,23) D013: (9,41) D014: (46,55) D015: (10,34) D016: (4,22) D033: (33,7) D034: (20,47) D035: (36,50) D036: (2,3) D037: (2,22) D038: (13,30) D039: (36,52) D040: (2,49) E001: (32,44) E002: (14,53) E003: (19,27) E004: (47,50) E005: (18,47) E006: (2,15) E007: (15,27) E008: (17,47) E009: (39,43) E010: (40,48) E011: (47,47) E012: (12,46) E013: (29,49) E014: (15,42) E015: (11,14) E016: (14,28) E017: (15,39) E018: (15,43) E019: (15,50) E020: (15,31) E021: (13,50) E022: (19,43) E023: (12,32) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 C C T 2 A C C G I A C T C C G C C T A C T A C A A (D) G 2 C C T C G G G C A G [T] C C (C) G G C T T 3 G T C C D A C T C C G C C T A C T A T A A (I) G 2 C C T C G G G C A G [T] C C (T) G G 0 D002 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C (T) T C (C) G G C A (T) (C) C C C (A) G [T] C T 3 G T T C D G C T C A G C C T A C C A C A A D G 2 C (C) T C (G) G G C A (G) (T) C C C (G) G 0 D003 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T T G G G C A G T C C T G G C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T T G G G C A G T C C T G G 0 D004 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C T T C C G G C A T C C C C A G C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C T C C G G G C G G C C C C G G 0 D005 T C (T) 3 G T T C D (A) C T C (C) G C C T A C (T) A (T) A A (I) G 4 C C T C G A C C G G C C T T G G T C (C) 3 G T T C D (G) C T C (A) G C C T A C (C) A (C) A A (D) G 2 C C T C G G G C A G C C C C A G 0 D006 C C T 2 A C C C D A C T C A G C C T A C T A C A A I G 2 C C T C (G) G G (C) A G (T) (C) C C (G) G C C T 3 G C C C I A C T C C G C C G G T C G C A A I G 2 C C T C (C) G G (T) A G (C) (G) C C (A) G 0 D007 C C T 2 A C C G I A C T C C G C C T A C T A T A A I G 2 C C T C G G G C G G C C C C G G C C T 3 G C C C I A C T C C G C C G G T C G C A A I G 4 C C T C G A C C G G C C C C G G 0 D008 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G (4) C (C) (T) C (G) (A) (C) (C) (G) G C (C) C C (G) G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G (2) C (T) (C) C (C) (G) (G) (T) (A) G C (G) C C (A) G 0 D009 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C T C C C G G T A G C G C C A G C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C T C C C G G T A G C G C C A G 0 D010 C C T 4 G C C C I A C C C C G C C G A T C G T A G [D] G 2 (C) C T C (C) G G (T) A G C (G) C C [A] G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 (T) C T C (G) G G (C) A G C (C) C C [G] G 0 D011 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T C G G G C (A) G (T) C C (C) G G C C T 4 G C C C I A C C C C G C C G A T C G T A A I G 2 C C T C G G G C (G) G (C) C C (T) G G 0 D012 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 (T) C T C G (G) (G) C (A) G C C (T) C G G C C T 2 A C C G I A C T C C G C C T A C T A C A A I G 2 (C) C T C G (A) (C) C (G) G C C (C) C G G 0 D013 C C T 2 A C C C I A C T C C A T C T A T C G T A (G) D G 2 (T) C T C G G G C (A) G C C C C G G T C T 3 G T T C D A C T C C G C C T A C T A T A (A) I G 2 (C) C T C G G G C (G) G C C C C G G 0 D014 T C (T) 3 G T T C D (A) C T C A G C C T A C (T) A C A A (I) G 2 C T C C C G G T A G C G C C (A) G T C (C) 3 G T T C D (G) C T C A G C C T A C (C) A C A A (D) G 2 C C T C G G G C A G C C C C (G) G 0 D015 C C T (2) (A) C C C I A C T (T) C A T (T) T A T C G T A A D G 2 C C T C G G G C A G C C C C A G C C T (4) (G) C C C I A C T (C) C A T (C) T A T C G T A A D G 2 C C T T G G G C A G T C C T G G 0 D016 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T (T) G G G C A G T C C (T) G G C C T 2 A C C G I A C T C C G C C T A C T A C A A I G 2 C C T (C) G G G C A G T C C (C) G G 0 D033 C C T (3) (G) (T) (T) C (D) A C T [C] C (G) T (T) T A T C G T A A D G 2 C C T C G A C C G G C C T T G G C C T (2) (A) (C) (C) C (I) A C T C C (A) T (C) T A T C G T A A D G 2 C T C C C G G T A G C G C C A G 0 D034 C C T 2 A C C G I A C T C C G C C T A C T A C A A (D) G 2 (C) C T C G G G C A G C C C C (A) G T C T 3 G T T C D A C T C A G C C T A C T A C A A (I) G 2 (T) C T C G G G C A G C C C C (G) G 0 D035 C C T 4 G C C C I A C C C C G C C G A T C G T A A I G 2 C C C C C G G T A G C G C C A G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 C T C C C G G T A G C G C C A G 0 D036 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T C G G G C A G T C C C G G C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T C [C] G G C A T C C C C A G 0 D037 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T C G G G C A G T C C C G G C C T 2 A C C G I A C T C C G C C T A C T A C A A I G 2 C C T C G G G C A G T C C C G G 0 D038 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C C T C G (A) (C) C (G) G C C (T) (T) G G C C T 3 G T C C D A T T C C G C C T A T C G T T A I A 3 C C T C G (G) (G) C (A) G C C (C) (C) G G 0 D039 C C T 4 G C C C I A C C C C G C C G A T C G T A A I G 2 C C C C C G G T A G C G C C A G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 4 C C T C G G G C A G T C C C G G 0 D040 C C T 2 A C C C I A C T C C A T C T A T C G T A A D G 2 C C T C G G G C A G T C C C G G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 C C T C G G G C A G T C C C G G 0 E001 C C T 3 G T C C D A T T C C G C C T A T C G T T A I A 3 C T C C C G G T A G C G C C A G T C T 3 G T T C D A C T C C G C C T A C T A T A A I G 3 C C T C C G G C A G C C C C A A 0 E002 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G (2) C (T) (C) C (C) G G (T) (A) G C (G) C C (A) G T C T 3 G T T C D A C T C A G C C T A C C A T A G D G (4) C (C) (T) C (G) G G (C) (G) G C (C) C C (G) G 0 E003 C C T 2 A C C C I A C T T C A T T T A T C G T A A I G 2 C T C C C G G T A G C G C C A G C C T 3 G T C C D A C T C C G C C T A T C G T T A I G 3 C C T C C G G C A G C C C C A A 0 E004 T C T 3 G T T C D A C T C A G C C T A C (T) A C A (A) (I) G 2 T C T C G G G C A G C C C C G G T C T 3 G T T C D A C T C A G C C T A C (C) A C A (G) (D) G 2 C T C C C G G T A G C G C C A G 0 E005 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G (4) (C) C T C G (A) (C) C (G) G C C (T) (T) G G T C T 3 G T T C D A C T C A G C C T A C T A C A A I G (2) (T) C T C G (G) (G) C (A) G C C (C) (C) G G 0 E006 C C T 2 A C C C I A C T (C) C A T (C) T A T C G T A A D G 2 C C T C G G G C A G T C C C G G C C T 2 A C C C I A C T (T) C A T (T) T A T C G T A A D G 2 T C T C G G G C A G C C C C G G 0 E007 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 T C T C G G G C A G C C C C G G C C T 3 G T C C D A C T C C G C C T A T C G T T A I G 3 C C T C C G G C A G C C C C A A 0 E008 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 T C T C G (A) (C) C (G) G C C (T) (T) G G T C T 3 G T T C D A C T C A G C C T A C T A C A A I G 2 T C T C G (G) (G) C (A) G C C (C) (C) G G 0 E009 C T T 3 G T C C D A C T C C G C C T A C T A T A A I G 2 C T C C C G G T A G C G C C A G T C T 3 G T T C D A C T C C G C C T A C T A T A A I G 2 C T C C C G G T A G C G C C A G 0 E010 C T T 3 G T C C D A C T C C G C C T A C T A T A A I G 2 (T) C T C G (G) (G) C (A) G C C (C) (C) G G T C T 3 G T T C D A C T C A G C C T A C C A C A A D G 2 (C) C T C G (A) (C) C (G) G C C (T) (T) G G 0 E011 T C T 3 G T T C D A C T C A G C C T A C T A C A A I G 2 T C T C G G G C A G C C C C G G T C T 3 G T T C D A C T C A G C C T A C T A C A A I G 2 T C T C G G G C A G C C C C G G 0 E012 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C (C) (T) C (G) G G (C) A G (T) (C) C C (G) G T C T 3 G T T C D A C T C A G C C T A C T A C A A I G 2 C (T) (C) C (C) G G (T) A G (C) (G) C C (A) G 0 E013 C C T 3 G T C C D A T T C C G C C T A T C G T T A I A 2 (T) C T C G G G C A G (C) C C C G G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 (C) C T C G G G C A G (T) C C C G G 0 E014 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 (T) C T C (G) G G C A G C C C C (G) (G) T C T 3 G T T C D A C T C C G C C T A C T A T A A I G 2 (C) C T C (C) G G C A G C C C C (A) (A) 0 E015 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C C T C G G G C A G C C (T) (T) (G) G C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C T C C C G G T A G C G (C) (C) (A) G 0 E016 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C (T) (C) C (C) G G (T) A G (C) (G) C C (A) G C C T 3 G T C C D A T T C C G C C T A T C G T T A I G 2 C (C) (T) C (G) G G (C) A G (T) (C) C C (G) G 0 E017 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 (T) (C) (T) C (G) G G (C) A G C (C) C C (G) G C T T 3 G T C C D A C T C C G C C T A C T A T A A I G 2 (C) (T) (C) C (C) G G (T) A G C (G) C C (A) G 0 E018 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 (T) (C) (T) C (G) G G (C) A G C (C) C C [G] G T C T 3 G T T C D A C T C C G C C T A C T A T A A I G 2 (C) (T) (C) C (C) G G (T) A G C (G) C C [A] G 0 E019 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 (T) (C) (T) C [G] G G (C) A G C (C) C C (G) G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 (C) (T) (C) C [C] G G (T) A G C (G) C C (A) G 0 E020 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G (2) (T) C T C (G) G G C A G C C C C (G) (G) C C T 3 G T C C D A T T C C G C C T A T C G T T A I A (3) (C) C T C (C) G G C A G C C C C (A) (A) 0 E021 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C (C) (T) C (G) (A) (C) (C) (G) G C (C) (T) (T) G G T C T 3 G T T C D A C T C A G C C T A C C A C A G D G 2 C (T) (C) C (C) (G) (G) (T) (A) G C (G) (C) (C) [A] G 0 E022 C C T 2 A C C C I A C T T C A T T T A T C G T A A I G 2 C T C C C G G T A G C G C C A G T C T 3 G T T C D A C T C C G C C T A C T A T A A I G 2 C T C C C G G T A G C G C C A G 0 E023 C C T 2 A C C C I A C T T C A T T T A T C G T A A D G 2 C (C) (T) C (G) G G (C) A G (T) (C) C C (G) G C C T 3 G T C C D A T T C C G C C T A T C G T T A I A 3 C (T) (C) C (C) G G (T) A G (C) (G) C C (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 ? 2 A C = G I = = = = = = = = = = = = = C = = (D) = = = = = = = = = ? ? ? ? = = (C) = = ? T ? 3 G T = C D = = = = = = = = = = = = = T = = (I) = = = = = = = = = ? ? ? ? = = (T) = = 0 D002 ? = = 2 A C C = I A = = = C A T = = = T = G T = = = = = = (T) = = (C) = = = = (T) (C) = = = (A) = ? = = 3 G T T = D G = = = A G C = = = C = A C = = = = = = (C) = = (G) = = = = (G) (T) = = = (G) = 0 D003 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 D004 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C = = = A T = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = G = = = G G = = = = G = 0 D005 = = (T) = = = = = = (A) = = = (C) = = = = = = (T) = (T) = = (I) = 4 = = = = = A C = G = = = T T G = = = (C) = = = = = = (G) = = = (A) = = = = = = (C) = (C) = = (D) = 2 = = = = = G G = A = = = C C A = 0 D006 = = = 2 A = = = D = = = = A = ? = T A C T A = = = = = = = = = = (G) = = (C) = = (T) (C) = = (G) = = = = 3 G = = = I = = = = C = ? = G G T C G = = = = = = = = = = (C) = = (T) = = (C) (G) = = (A) = 0 D007 = = = 2 A = = G = = = = = = = = = T A C T A T = = = ? 2 = = = = = G G = = = = = = = = = = = = 3 G = = C = = = = = = = = = G G T C G C = = = ? 4 = = = = = A C = = = = = = = = = 0 D008 C = = 2 A C C = I = = = = C A T = = = T = G T = A = = (4) = (C) (T) = (G) (A) (C) (C) (G) = = (C) = = (G) = T = = 3 G T T = D = = = = A G C = = = C = A C = G = = (2) = (T) (C) = (C) (G) (G) (T) (A) = = (G) = = (A) = 0 D009 = = = = = = ? = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 D010 C = = 4 = C C = I = ? C = C = = = G = T = G T = = ? = = (C) = = = (C) = = (T) = = = (G) = ? ? = T = = 3 = T T = D = ? T = A = = = T = C = A C = = ? = = (T) = = = (G) = = (C) = = = (C) = ? ? = 0 D011 = = = 2 A = = = = = ? T = = A T = T = = = = = = = D = = = = = = = = = = (A) = (T) = = (C) = = = = = 4 G = = = = = ? C = = G C = G = = = = = = = I = = = = = = = = = = (G) = (C) = = (T) = = 0 D012 = = = = = = = C = = = ? T = A T T = = T C G T = = D = = (T) = = = = (G) (G) = (A) = = = (T) = = = = = = = = = = G = = = ? C = G C C = = C T A C = = I = = (C) = = = = (A) (C) = (G) = = = (C) = = = 0 D013 C = = 2 A C C = I = = = = = A T = = = T C G = = (G) D = = (T) = = = = = = = (A) = = = = = = = T = = 3 G T T = D = = = = = G C = = = C T A = = (A) I = = (C) = = = = = = = (G) = = = = = = = 0 D014 = = (T) = = = = = = (A) = = = = = = ? = = = (T) = = = = (I) = = = T C = C = = T = = = G = = (A) ? = = (C) = = = = = = (G) = = = = = = ? = = = (C) = = = = (D) = = = C T = G = = C = = = C = = (G) ? 0 D015 = = = (2) (A) = = = = = = = (T) = = = (T) = = = = = = = = = = = = = = C = = = = = = C = = C A = = = = (4) (G) = = = = = = = (C) = = = (C) = = = = = = = = = = = = = = T = = = = = = T = = T G = 0 D016 = = = = = = = C = = = = ? = A T = = = T C G T = = D = = = = = (T) = = = = = = = = = (T) = ? = = = = = = = G = = = = ? = G C = = = C T A C = = I = = = = = (C) = = = = = = = = = (C) = ? 0 D033 = = ? (3) (G) (T) (T) = (D) = = = ? = (G) = (T) = = = = = ? ? = = = = = C T = G A C C G ? ? C T T G = = = ? (2) (A) (C) (C) = (I) = = = ? = (A) = (C) = = = = = ? ? = = = = = T C = C G G T A ? ? G C C A = 0 D034 C = = 2 A C C G I = = = = C = = ? ? ? = = = = ? = (D) = = (C) = = = = = = = ? = = = = = (A) = T = = 3 G T T C D = = = = A = = ? ? ? = = = = ? = (I) = = (T) = = = = = = = ? = = = = = (G) = 0 D035 ? = = 4 = C C = I = ? C = C = = ? ? = T = G ? = A I = = = C = = = = = = = ? ? = = = = = ? = = 3 = T T = D = ? T = A = = ? ? = C = A ? = G D = = = T = = = = = = = ? ? = = = = = 0 D036 ? = ? = = = = = = = = = = = = = ? ? ? = = = ? ? = = = = = = = = ? = = = = G T = = = G = ? = ? = = = = = = = = = = = = = ? ? ? = = = ? ? = = = = = = = = ? = = = = T C = = = A = 0 D037 = = ? = = = = C = = = = = = A T ? ? ? T C G ? = = D = = = = = = = = = = = = = = = = = = = = ? = = = = G = = = = = = G C ? ? ? C T A ? = = I = = = = = = = = = = = = = = = = = = 0 D038 = = ? 2 A C = = I = C = T = A T T = = = = = = A = D G 2 = = = = = (A) (C) = (G) = = = (T) (T) = = = = ? 3 G T = = D = T = C = G C C = = = = = = T = I A 3 = = = = = (G) (G) = (A) = = = (C) (C) = = 0 D039 C = = 4 = C C ? I = = C = C = = = G ? T = G T = A I = 2 = = C = C = = T ? = C G = = A = T = = 3 = T T ? D = = T = A = = = T ? C = A C = G D = 4 = = T = G = = C ? = T C = = G = 0 D040 C = ? 2 A C C = I = = = = C A T = = = T = G T = A = = = = = = = = = = = = = = = = = = = T = ? 3 G T T = D = = = = A G C = = = C = A C = G = = = = = = = = = = = = = = = = = = = 0 E001 C = ? = = = C = = = T = = = = = ? = = T C G ? ? = = A = = T C = = = = T = = = G ? = = G T = ? = = = T = = = C = = = = = ? = = C T A ? ? = = G = = C T = = = = C = = = C ? = = A 0 E002 ? ? ? 2 A C C = I = = = T C A ? ? = = T = ? = = A = = (2) = (T) (C) = (C) = = (T) (A) = = (G) = = (A) = ? ? ? 3 G T T = D = = = C A G ? ? = = C = ? = = G = = (4) = (C) (T) = (G) = = (C) (G) = = (C) = = (G) = 0 E003 = ? = 2 A C = = I = = = T = A T T = = = = = = A = = = 2 = T C = = = = T = = = G = = = G = ? = 3 G T = = D = = = C = G C C = = = = = = T = = = 3 = C T = = = = C = = = C = = = A 0 E004 = = = = = = = = = = = = = = = = = = = = (T) = = = (A) (I) = = T C T = G = = C = = = C = = G = = = = = = = = = = = = = = = = = = = = = (C) = = = (G) (D) = = C T C = C = = T = = = G = = A = 0 E005 C = = 2 A C C = I = = = T C A T T = = T C G T = = D = (4) (C) = = = = (A) (C) = (G) = = = (T) (T) = = T = = 3 G T T = D = = = C A G C C = = C T A C = = I = (2) (T) = = = = (G) (G) = (A) = = = (C) (C) = = 0 E006 = = = = = = = = = = = = (C) = = = (C) = = = = = = = = = = = C = = = = = = = = = T = = = = = = = = = = = = = = = = = (T) = = = (T) = = = = = = = = = = = T = = = = = = = = = C = = = = = 0 E007 = = = 2 A C = = I = = = T = A T ? = = = = = = A = D = 2 T = = = G = = = = = = = = ? ? ? = = = 3 G T = = D = = = C = G C ? = = = = = = T = I = 3 C = = = C = = = = = = = = ? ? ? 0 E008 C = = 2 A C C = I = = = T C A T T = = T C G T = = D = = = = = = = (A) (C) = (G) = = = (T) (T) ? = T = = 3 G T T = D = = = C A G C C = = C T A C = = I = = = = = = = (G) (G) = (A) = = = (C) (C) ? = 0 E009 C T ? = = = C = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = T C ? = = = T = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0 E010 C T = = = = C = = = = = = C = = ? = = = T = T = = I = = (T) = = = = (G) (G) = (A) = = = (C) (C) = = T C = = = = T = = = = = = A = = ? = = = C = C = = D = = (C) = = = = (A) (C) = (G) = = = (T) (T) = = 0 E011 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? 0 E012 C = = 2 A C C = I ? = = T C A T T = = T C G T = = D = = = (C) (T) = (G) = = (C) = = (T) (C) = = (G) = T = = 3 G T T = D ? = = C A G C C = = C T A C = = I = = = (T) (C) = (C) = = (T) = = (C) (G) = = (A) = 0 E013 C = = = = = C = = = T = = C = = = = = T = G T T A I A = (T) = = = = = = = = = (C) = = = = = T = = = = = T = = = C = = A = = = = = C = A C A G D G = (C) = = = = = = = = = (T) = = = = = 0 E014 C = = 2 A C C = I = = = T = A T T = = T C G = = = D = = (T) = = = (G) = = = = = = = = = (G) (G) T = = 3 G T T = D = = = C = G C C = = C T A = = = I = = (C) = = = (C) = = = = = = = = = (A) (A) 0 E015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C T = G = = C = = = C (T) (T) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T C = C = = T = = = G (C) (C) (A) = 0 E016 = = = 2 A C = = I = C = ? = A T T = = = = = = A = D = = = (T) (C) = (C) = = (T) = = (C) (G) = = (A) = = = = 3 G T = = D = T = ? = G C C = = = = = = T = I = = = (C) (T) = (G) = = (C) = = (T) (C) = = (G) = 0 E017 = C ? 2 ? ? ? = I = = = T = A T T = = ? C ? = ? = D = = (T) (C) (T) = (G) = = (C) = = = (C) = = (G) = = T ? 3 ? ? ? = D = = = C = G C C = = ? T ? = ? = I = = (C) (T) (C) = (C) = = (T) = = = (G) = = (A) = 0 E018 C = = 2 A C C = I = = = T = A T ? = = T C G = = = D = = (T) (C) (T) = (G) = = (C) = = = (C) = = ? = T = = 3 G T T = D = = = C = G C ? = = C T A = = = I = = (C) (T) (C) = (C) = = (T) = = = (G) = = ? = 0 E019 C = = 2 A C C = I = = = T C A T T = = T = G T = A = = = (T) (C) (T) = ? ? ? (C) = = = (C) = = (G) = T = = 3 G T T = D = = = C A G C C = = C = A C = G = = = (C) (T) (C) = ? ? ? (T) = = = (G) = = (A) = 0 E020 = = = 2 A C = = I = C = T = A T T = = = = = ? ? = ? G (2) (T) = = = (G) = = = = = = = = = (G) (G) = = = 3 G T = = D = T = C = G C C = = = = = ? ? = ? A (3) (C) = = = (C) = = = = = = = = = (A) (A) 0 E021 C = = 2 A C C = I = = = T C A T T = = T = G T = A = = = = (C) (T) = (G) (A) (C) (C) (G) = = (C) (T) (T) ? = T = = 3 G T T = D = = = C A G C C = = C = A C = G = = = = (T) (C) = (C) (G) (G) (T) (A) = = (G) (C) (C) ? = 0 E022 C = = 2 A C C = I = = = T = A T ? = = T C G = = = = = = = = = = = = = = = = = = = = = = T = = 3 G T T = D = = = C = G C ? = = C T A = = = = = = = = = = = = = = = = = = = = = = 0 E023 = ? = 2 A C = = I = ? ? T = A T T = = = = = = A = D G 2 = (C) (T) = (G) = = (C) = = (T) (C) = = (G) = = ? = 3 G T = = D = ? ? C = G C C = = = = = = T = I A 3 = (T) (C) = (C) = = (T) = = (C) (G) = = (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 = = 0.82 = = = = = = = = = ? ? ? ? = = 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 = = = = = = 0.73 = = 0.73 = = = = 0.73 0.73 = = = 0.73 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 1.00 = = = = 1.00 = = = 0.69 = = = = = = 0.69 = = = 0.69 = = = = = = 0.69 = 0.69 = = 0.69 = 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 = = = = = = = = = = 0.56 = = 0.56 = = 0.56 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 = = 0.57 = 0.59 0.59 = 0.59 0.59 0.59 0.59 0.59 = = 0.59 = = 0.59 = = = = = = = ? = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 1.00 = 1.00 = ? 1.00 = 1.00 = = = 1.00 = 1.00 = 1.00 1.00 = = ? = = 0.58 = = = 0.58 = = 0.58 = = = 0.58 = ? ? = = = = 1.00 1.00 = = = = = ? 1.00 = = 1.00 1.00 = 1.00 = = = = = = = 1.00 = = = = = = = = = = 0.60 = 0.60 = = 0.51 = = = = = = = = = 1.00 = = = ? 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = 0.56 = = = = 0.53 0.53 = 0.53 = = = 0.50 = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = = = 1.00 1.00 = = = 1.00 1.00 1.00 = = 0.87 1.00 = = 0.55 = = = = = = = 0.55 = = = = = = = = = 0.76 = = = = = = 0.76 = = = = = = ? = = = 0.76 = = = = 0.76 = = = 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 = = 0.82 ? = = = 0.50 0.50 = = = = = = = 0.88 = = = 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 = = = = = 0.88 = = = = = = = = = 0.88 = ? = = ? 0.58 0.58 0.58 0.59 = 0.58 = = = ? = 0.61 = 0.79 = = = = = ? ? = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? ? 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 = = 0.80 = = = = = = = ? = = = = = 0.74 = ? = = 1.00 = 1.00 1.00 = 1.00 = ? 1.00 = 1.00 = = ? ? = 1.00 = 1.00 ? = 1.00 1.00 = = = 1.00 = = = = = = = ? ? = = = = = ? = ? = = = = = = = = = = = = = ? ? ? = = = ? ? = = = = = = = = ? = = = = 1.00 1.00 = = = 1.00 = = = ? = = = = 1.00 = = = = = = 1.00 1.00 ? ? ? 1.00 1.00 1.00 ? = = 1.00 = = = = = = = = = = = = = = = = = = = = ? 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 = = = = = 0.53 0.53 = 0.53 = = = 0.78 0.78 = = 1.00 = = 1.00 = 1.00 1.00 ? 1.00 = = 1.00 = 1.00 = = = 1.00 ? 1.00 = 1.00 1.00 = 1.00 1.00 = 0.93 = = 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 1.00 = 1.00 = = = 1.00 1.00 1.00 ? ? = = 1.00 = ? = = 1.00 = = 0.74 = 0.54 0.54 = 0.51 = = 0.51 0.51 = = 0.51 = = 0.51 = = ? = 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 = = = = = = = = = = = = = = = = = = = = 0.76 = = = 0.76 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 = 0.58 0.60 = = = = 0.60 0.60 = 0.60 = = = 0.60 0.60 = = = = = = = = = = = = = = 0.81 = = = 0.81 = = = = = = = = = = = 1.00 = = = = = = = = = 1.00 = = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 1.00 ? = = = = = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = = = = = = = ? ? ? 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = 0.54 0.54 = 0.54 = = = 0.54 0.54 ? = 1.00 1.00 ? = = = 1.00 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = 0.95 0.95 = = = = 0.95 = = = = = = 0.97 = = ? = = = 0.99 = 0.97 = = 0.99 = = 0.65 = = = = 0.65 0.65 = 0.65 = = = 0.65 0.65 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 ? = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = = = 0.56 0.56 = 0.56 = = 0.56 = = 0.56 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 = 0.61 = = = = = = = = = 0.61 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = = 1.00 = = 0.57 = = = 0.57 = = = = = = = = = 0.57 0.57 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = 1.00 = = = 1.00 0.90 0.90 0.90 = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = ? = 1.00 1.00 1.00 = = = = = = 1.00 = 0.93 = = = 0.58 0.58 = 0.58 = = 0.58 = = 0.58 0.58 = = 0.58 = = 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 = = 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 = = = 1.00 = = 0.67 0.67 0.67 = 0.67 = = 0.67 = = = 0.67 = = ? = 1.00 = = 1.00 1.00 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 = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = ? ? = ? 1.00 0.72 0.64 = = = 0.64 = = = = = = = = = 0.64 0.64 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 = = = = 0.74 0.74 = 0.74 0.74 0.74 0.74 0.74 = = 0.74 0.74 0.74 ? = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 ? = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = ? = 1.00 1.00 1.00 = = 1.00 = ? ? 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 = 0.84 0.84 = 0.84 = = 0.84 = = 0.84 0.84 = = 0.84 = END PHASEPROBS