************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 e2f3x.phase.inp e2f3x.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST e2f3x.phase.out_freqs : haplotype frequency estimates e2f3x.phase.out_pairs : most likely haplotype pairs for each individual e2f3x.phase.out_recom : estimates of recombination parameters e2f3x.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 28 Positions of loci: 79714 79861 80371 80887 81339 81443 81639 81806 83113 83667 83900 84542 84601 84610 84790 84834 85286 85613 85633 86189 86270 86923 86930 86933 91036 91502 92028 92050 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file e2f3x.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCAACCCACGTGATTCGCGAATCGCTCT 29.000000 2 GCAACCCACGTGATTCGCGAATCGTTCA 2.000000 3 GCAACCCACGTGATCCGCGAATCGCTCT 1.000000 4 GCAACCCACGTGGTTCGCGAGTCACTGT 1.000000 5 GCAACCCACGTGGTTCGCGAGTCATTCA 1.000000 6 GCAACCCACGCGATTCGCGAATCGCTCT 1.000000 7 GCAACCCAGGTGATTCGCGAATCGCTCT 6.000000 8 GCAACCCAGGTGGTCCTCGAGTCGCTCT 2.000000 9 GCAACCCAGGTAGTCCTAGAGCCACTCT 1.000000 10 GCAACCCAGGTAGGCCTAAAGCCACTCT 1.000000 11 GCAACCCAGGCGATTCGCGAATCGCTCT 2.000000 12 GCAACCCAGGCGGTCCGCGGGTCGCTCT 3.000000 13 GCAACCCAGGCGGTCCGCGGGTCGCCCT 3.000000 14 GCAACCCAGGCGGTCCGCGGGTCACTCT 1.000000 15 GCAACCCAGGCAGTCCGAGAGTCACTCT 2.000000 16 GCAACCCAGATAGTCCTAGAGTCATTCA 1.000000 17 GCAACCCGGGTGATTCGCGAATCGCTCT 1.000000 18 GCAACCTAGGTGATTCGCGAATCGCTCT 9.000000 19 GCAACCTAGGTGATTCGCGAATCGCTCA 1.000000 20 GCAATCCGGGTAGTCCTAGAGCCACTCT 1.000000 21 GCAATCCGGGTAGGTCTAGAGCCACTCT 1.000000 22 GCAATCCGGGTAGGCCTAGAGCCACTCT 9.000000 23 GCAATCCGGGCGGTCCTAGAGTCGCTCT 1.000000 24 GCAATCCGGGCGGGCTGCGAGTGGCTGT 1.000000 25 GCAATCCGGGCAGTCCGAGAGTCACTCT 2.000000 26 GCAGCCCAGGTGATTCGCGAATCGCTCT 1.000000 27 GCAGCCCAGGTAGTCCTAAAGCCACTCT 1.000000 28 GCAGCCCAGGTAGGCCTAAAGCCACTCT 4.000000 29 GCAGCCCAGGCGGTCCGCGGGTCGCCCT 1.000000 30 GCAGCCCAGGCGGGCTGCGAGTCGCTGT 4.000000 31 GCAGCTCAGGCGGGCTGCGAGTGGCTGT 6.000000 32 GCAGCTCAGATAGTCCTAGAGTCGCTCT 1.000000 33 GCGACCCAGGTGGGCCGCGAGTCGCTCT 3.000000 34 GCGACCCAGGCGGTCCGCGAGTGGCCCT 2.000000 35 GCGACCCAGGCGGTCCGCGGGTCGCCCT 1.000000 36 GCGACCCAGGCAGTCCGAGAGTCACTCT 1.000000 37 GCGACCCAGATAGTCCTAGAGTCATTCA 1.000000 38 GTAGCTCAGGCGGGTTGCGAGTGGCCCT 1.000000 39 GTGACCCAGGTGATTCGCGAATCGCTCT 1.000000 40 GTGACCCAGGTAGGCCTAAAGCCACTCT 3.000000 41 GTGACCCAGATAGTCCTCGAGTCATTCA 1.000000 42 GTGACCCAGATAGTCCTAGAGTCACTCT 2.000000 43 GTGACCCAGATAGTCCTAGAGTCATTCA 39.000000 44 GTGGCCCAGATAGTCCTAGAGTCATTCA 1.000000 45 CCAACCCACGTGATTCGCGAATCGCTCT 3.000000 46 CCAGCTCAGGCGGGCTGCGAGTGGCTGT 12.000000 47 CCAGCTCAGGCGGGCTGCGAGTGGCTGA 1.000000 48 CCAGCTCAGATAGTCCTAGAGTCGCTCT 4.000000 49 CCAGCTCAGATAGTCCTAGAGTCGCCCT 2.000000 50 CCGACCCAGATAGTCCTAGAGTCACTCT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,7) P002: (1,1) P003: (10,15) P004: (3,30) P005: (18,44) P006: (41,43) P007: (33,43) P008: (1,22) P009: (37,43) P010: (18,43) P011: (1,25) P012: (17,43) P013: (1,43) P014: (1,16) P015: (1,18) P016: (1,22) P017: (29,30) P018: (18,49) P019: (1,48) P020: (15,18) P021: (8,36) P022: (43,46) P023: (4,43) P024: (31,46) P025: (1,7) P026: (9,45) P027: (11,32) P028: (43,46) P029: (43,43) P030: (1,43) P031: (18,48) P032: (13,50) P033: (18,46) P034: (7,22) P035: (43,43) P036: (1,22) P037: (7,43) P038: (30,42) P039: (22,43) P040: (31,46) P041: (40,40) P042: (1,49) P043: (45,46) P044: (43,43) P045: (2,20) P046: (1,11) P047: (1,1) P048: (1,39) P049: (1,22) P050: (8,46) P051: (1,43) P052: (22,22) P053: (43,43) P054: (43,46) P055: (38,43) P056: (25,48) P057: (13,40) P058: (5,46) P059: (34,34) P060: (43,47) P061: (12,28) P062: (43,43) P063: (43,43) P064: (24,35) P065: (30,46) P066: (31,43) P067: (33,43) P068: (7,42) P069: (1,43) P070: (21,31) P071: (2,31) P072: (18,48) P073: (7,43) P074: (1,18) P075: (1,1) P076: (31,43) P077: (27,46) P078: (1,43) P079: (1,43) P080: (12,23) P081: (19,43) P082: (22,28) P083: (1,46) P084: (26,43) P085: (28,33) P086: (28,45) P087: (12,13) P088: (6,43) P089: (1,14) P090: (1,43) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A G G T G A T T C G C G A A T C G C T C T 0 P002 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A C G T G A T T C G C G A A T C G C T C T 0 P003 G C A A C C C A G G T A G G C C T A A A G C C A C T C T G C A A C C C A G G C A G T C C G A G A G T C A C T C T 0 P004 G C A A C C C A C G T G A T C C G C G A A T C G C T C T G C A G C C C A G G C G G G C T G C G A G T C G C T G T 0 P005 G C A (A) C C T A G G T G A T T C G C G A A T C G C T C T G T G (G) C C C A G A T A G T C C T A G A G T C A T T C A 0 P006 G T G A C C C A G A T A G T C C T C G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P007 G C G A C C C A G G T G G G C C G C G A G T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P008 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P009 G C G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P010 G C A A C C T A G G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P011 G C A A C C C A [C] G T G A T T C G C G A A T C G C T C T G C A A T C C G G G C A G T C C G A G A G T C A C T C T 0 P012 G C A A C C [C] (G) G G T G A T T C G C G A A T C G C T C T G T G A C C C (A) G A T A G T C C T A G A G T C A T T C A 0 P013 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P014 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A G A T A G T C C T A G A G T C A T T C A 0 P015 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C T A G G T G A T T C G C G A A T C G C T C T 0 P016 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P017 G C A G C C C A G G C G G T C C G C G G G T C G C C C T G C A G C C C A G G C G G G C T G C G A G T C G C T G T 0 P018 G C A A C C T A G G T G A T T C G C G A A T C G C T C T C C A G C T C A G A T A G T C C T A G A G T C G C C C T 0 P019 G C A A C C C A C G T G A T T C G C G A A T C G C T C T C C A G C T C A G A T A G T C C T A G A G T C G C T C T 0 P020 G C A A C C C A G G C A G T C C G A G A G T C A C T C T G C A A C C T A G G T G A T T C G C G A A T C G C T C T 0 P021 G C (A) A C C C A G G T G G T C C T C G A G T C G C T C T G C (G) A C C C A G G C A G T C C G A G A G T C A C T C T 0 P022 G T G A C C C A G A T A G T C C T A G A G T C A T T C A [C] C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P023 G C A A C C C A C G T G G T T C G C G A G T C A (C) T (G) (T) G T G A C C C A G A T A G T C C T A G A G T C A (T) T (C) (A) 0 P024 G C A G C T C A G G C G G G C T G C G A G T G G C T G T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P025 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A G G T G A T T C G C G A A T C G C T C T 0 P026 (G) C A A C C C A G G T A G T C C T A G A G C C A C T C T (C) C A A C C C A C G T G A T T C G C G A A T C G C T C T 0 P027 G C A A C C C A G G C G A T T C G C G A A T C G C T C T G C A G C T C A G A T A G T C C T A G A G T C G C T C T 0 P028 G T G A C C C A G A T A G T C C T A G A G T C A T T C A C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P029 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P030 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P031 G C A A C C T A G G T G A T T C G C G A A T C G C T C T C C A G C T C A G A T A G T C C T A G A G T C G C T C T 0 P032 G C (A) A C C C A G G C G G T C C G C G G G T C G C C C T C C (G) A C C C A G A T A G T C C T A G A G T C A C T C T 0 P033 G C A A C C T A G G T G A T T C G C G A A T C G C T C T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P034 G C A A C C C A G G T G A T T C G C G A A T C G C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P035 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P036 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P037 G C A A C C C A G G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P038 G C A G C C C A G G C G G G C T G C G A G T C G C T G T G T G A C C C A G A T A G T C C T A G A G T C A C T C T 0 P039 G C A A T C C G G G T A G G C C T A G A G C C A C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P040 [G] C A G C T C A G G C G G G C T G C G A G T G G C T G T [C] C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P041 G T G A C C C A G G T A G G C C T A A A G C C A C T C T G T G A C C C A G G T A G G C C T A A A G C C A C T C T 0 P042 G C A A C C C A C G T G A T T C G C G A A T C G C T C T C C A G C T C A G A T A G T C C T A G A G T C G C C C T 0 P043 C C A A C C C A C G T G A T T C G C G A A T C G C T C T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P044 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P045 G C A A C C C A C G T G A T T C G C G A A T C G (T) T C (A) G C A A T C C G G G T A G T C C T A G A G C C A (C) T C (T) 0 P046 G C A A C C C A (C) G T G A T T C G C G A A T C G C T C T G C A A C C C A (G) G C G A T T C G C G A A T C G C T C T 0 P047 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A C G T G A T T C G C G A A T C G C T C T 0 P048 G C A A C C C A (C) G T G A T T C G C G A A T C G C T C T G T G A C C C A (G) G T G A T T C G C G A A T C G C T C T 0 P049 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P050 G C A A C C C A G G T G G T C C T C G A G T C G C T C T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P051 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P052 G C A A T C C G G G T A G G C C T A G A G C C A C T C T G C A A T C C G G G T A G G C C T A G A G C C A C T C T 0 P053 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P054 G T G A C C C A G A T A G T C C T A G A G T C A T T C A C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P055 G T A G C T C A G G C G G G (T) T G C G A G T G G C C C T G T G A C C C A G A T A G T (C) C T A G A G T C A T T C A 0 P056 G C A A T C C G G G C A G T C C G A G A G T C A C T C T C C A G C T C A G A T A G T C C T A G A G T C G C T C T 0 P057 G C A A C C C A G G C G G T C C G C G G G T C G C C C T G T G A C C C A G G T A G G C C T A A A G C C A C T C T 0 P058 G C A A C C C A C G T G G T T C G C G A G T C A (T) T (C) (A) C C A G C T C A G G C G G G C T G C G A G T G G (C) T (G) (T) 0 P059 G C G A C C C A G G C G G T C C G C G A G T G G C C C T G C G A C C C A G G C G G T C C G C G A G T G G C C C T 0 P060 G T G A C C C A G A T A G T C C T A G A G T C A T T C A C C A G C T C A G G C G G G C T G C G A G T G G C T G A 0 P061 G C A A C C C A G G C G G T C C G C G G G T C G C T C T G C A G C C C A G G T A G G C C T A A A G C C A C T C T 0 P062 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P063 G T G A C C C A G A T A G T C C T A G A G T C A T T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P064 G C (A) A (T) C C (G) G G C G G G C T G C G A G T G G C T G T G C (G) A (C) C C (A) G G C G G T C C G C G G G T C G C C C T 0 P065 G C A G C C C A G G C G G G C T G C G A G T C G C T G T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P066 G C A G C T C A G G C G G G C T G C G A G T G G C T G T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P067 G C G A C C C A G G T G G G C C G C G A G T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P068 G C A A C C C A G G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A C T C T 0 P069 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P070 G C A A T C C G G G T A G G (T) C T A G A G C C A C T C T G C A G C T C A G G C G G G (C) T G C G A G T G G C T G T 0 P071 G C A A C C C A C G T G A T T C G C G A A T C G T T C A G C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P072 G C A A C C T A G G T G A T T C G C G A A T C G C T C T C C A G C T C A G A T A G T C C T A G A G T C G C T C T 0 P073 G C A A C C C A G G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P074 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C T A G G T G A T T C G C G A A T C G C T C T 0 P075 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G C A A C C C A C G T G A T T C G C G A A T C G C T C T 0 P076 G C A G C T C A G G C G G G C T G C G A G T G G C T G T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P077 G C A G C C C A G G T A G (T) C C T A A A G C C A C T C T C C A G C T C A G G C G G (G) C T G C G A G T G G C T G T 0 P078 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P079 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P080 G C A A (C) C C (A) G G C G G T C C G C G G G T C G C T C T G C A A (T) C C (G) G G C G G T C C T A G A G T C G C T C T 0 P081 G C A A C C T A G G T G A T T C G C G A A T C G C T C A G T G A C C C A G A T A G T C C T A G A G T C A T T C A 0 P082 G C A A T C C G G G T A G G C C T A G A G C C A C T C T G C A G C C C A G G T A G G C C T A A A G C C A C T C T 0 P083 G C A A C C C A C G T G A T T C G C G A A T C G C T C T C C A G C T C A G G C G G G C T G C G A G T G G C T G T 0 P084 G C A (G) C C C A G G T G A T T C G C G A A T C G C T C T G T G (A) C C C A G A T A G T C C T A G A G T C A T T C A 0 P085 G C A G C C C A G G T A G G C C T A A A G C C A C T C T G C G A C C C A G G T G G G C C G C G A G T C G C T C T 0 P086 (G) C A G C C C A G G T A G G C C T A A A G C C A C T C T (C) C A A C C C A C G T G A T T C G C G A A T C G C T C T 0 P087 G C A A C C C A G G C G G T C C G C G G G T C G C T C T G C A A C C C A G G C G G T C C G C G G G T C G C C C T 0 P088 G C A A C C C A C G (C) G A T T C G C G A A T C G C T C T G T G A C C C A G A (T) A G T C C T A G A G T C A T T C A 0 P089 G C A A C C C A C G T G A T T C G C G A A T C (G) C T C T G C A A C C C A G G C G G T C C G C G G G T C (A) C T C T 0 P090 G C A A C C C A C G T G A T T C G C G A A T C G C T C T G T G A C C C A G A T A G T C C T A G A G T C A T T C 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 P001 = = = ? ? = = = C = = = = = = = = = = ? = = = = = = = = = = = ? ? = = = G = = = = = = = = = = ? = = = = = = = = 0 P002 = = = = = = = = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = ? ? = = = = ? = = = = = = = = = = = = 0 P003 = = = = = = = = = ? ? = = G = = T = A ? = C = = = = = = = = = = = = = = = ? ? = = T = = G = G ? = T = = = = = = 0 P004 = = = A = = = = ? ? ? = A T = C = = = = A = = = = = C = = = = G = = = = ? ? ? = G G = T = = = = G = = = = = G = 0 P005 = C A (A) = = T = = G = G A = T = G ? ? ? ? = = G C = = T = T G (G) = = C = = A = A G = C = T ? ? ? ? = = A T = = A 0 P006 = = = = = = = = = = = = = = = = = C ? = = = = = = = = = = = = = = = = = = = = = = = = = = A ? = = = = = = = = = 0 P007 = ? = = = = = = = G = ? ? ? ? ? G C = = = = = G C = = T = ? = = = = = = = A = ? ? ? ? ? T A = = = = = A T = = A 0 P008 = = = = C = = A C = = G A T T = G C = = A T = G = = ? ? = = = = T = = G G = = A G G C = T A = = G C = A = = ? ? 0 P009 = C = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = T = ? ? ? = = = = = = = = = = = = = = = = = = = = = = 0 P010 = C A = = = T = = G = G A = T = ? C = = A = = G C = = T = T G = = = C = = A = A G = C = ? A = = G = = A T = = A 0 P011 ? ? ? = C = ? ? ? ? ? ? ? ? ? ? ? C = = A = = G ? = = = ? ? ? = T = ? ? ? ? ? ? ? ? ? ? ? A = = G = = A ? = = = 0 P012 = C A = = = ? (G) = G = G A = T = G C = = A = = G C = = T = T G = = = ? (A) = A = A G = C = T A = = G = = A T = = A 0 P013 = ? A = = = = = C ? ? G A = T = G C = = A = = G C = = T = ? G = = = = = G ? ? A G = C = T A = = G = = A T = = A 0 P014 = = = = = = = = C G = G A = T = G C = = A = = G C = ? ? = = = = = = = = G A = A G = C = T A = = G = = A T = ? ? 0 P015 = = = ? = = C = C = = = = = = = = = = = = = = = = = = = = = = ? = = T = G = = = = = = = = = = = = = = = = = = = 0 P016 = = = = C = = A C = = G A T T = G C = = A T = G = = = = = = = = T = = G G = = A G G C = T A = = G C = A = = = = 0 P017 = = = = = = = = = = = = = T = C = = = G = = = = = C C = = = = = = = = = = = = = = G = T = = = A = = = = = T G = 0 P018 G = = A = C T = = G = ? ? ? ? ? ? C = = A = = = = T = = C = = G = T C = = A = ? ? ? ? ? ? A = = G = = = = C = = 0 P019 G = = A = C = = C G = G A = T = G C = = A = = = = = = ? C = = G = T = = G A = A G = C = T A = = G = = = = = = ? 0 P020 = = = = = = C = = = C A G = C = = A = = G = = A = = = = = = = = = = T = = = T G A = T = = C = = A = = G = = = = 0 P021 = = (A) = = = = = = = T G = = = = T C = = = = = G = = ? ? = = (G) = = = = = = = C A = = = = G A = = = = = A = = ? ? 0 P022 ? ? G A = C = = = A T A = T = C T A = = = = C A T = C A ? ? A G = T = = = G C G = G = T G C = = = = G G C = G T 0 P023 = C A = = = = = C G = G = = T = G C = = = = = = (C) = (G) (T) = T G = = = = = G A = A = = C = T A = = = = = = (T) = (C) (A) 0 P024 G = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P025 = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = = = 0 P026 (G) = = = = = = = G = = A G = C = T A = = G C = A = = = = (C) = = = = = = = C = = G A = T = G C = = A T = G = = = = 0 P027 = = = A = C = = = G C G A = T = G C = = A = = = = = = ? = = = G = T = = = A T A G = C = T A = = G = = = = = = ? 0 P028 G T G A = C = = = A T A = T = C T A = = = = C A T = C A C C A G = T = = = G C G = G = T G C = = = = G G C = G T 0 P029 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P030 = C A = = = = = C G = G A = T = G C = = A = = G C = = T = T G = = = = = G A = A G = C = T A = = G = = A T = = A 0 P031 G = = A = C T = = G = G A = T = G C = = A = = = = = = ? C = = G = T C = = A = A G = C = T A = = G = = = = = = ? 0 P032 G = (A) = = = = = = G C G = = = = G C = G = = = G = C = = C = (G) = = = = = = A T A = = = = T A = A = = = A = T = = 0 P033 G = = A = C T = = = T = A T T C = = = = A = C = = = C = C = = G = T C = = = C = G G C T = = = = G = G = = = G = 0 P034 = = = = C = = A = = = G A T T = G C = = A T = G = = = = = = = = T = = G = = = A G G C = T A = = G C = A = = = = 0 P035 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P036 = = = = C = = A C = = G A T T = G C = = A T = G = = = = = = = = T = = G G = = A G G C = T A = = G C = A = = = = 0 P037 = C A = = = = = = G = G A = T = G C = = A = = G C = = T = T G = = = = = = A = A G = C = T A = = G = = A T = = A 0 P038 = C A G = = = = = G C G = G = T G C = = = = = G = = G = = T G A = = = = = A T A = T = C T A = = = = = A = = C = 0 P039 = C A = T = = G = G = ? ? ? ? ? ? = = = = C = = C = = T = T G = C = = A = A = ? ? ? ? ? ? = = = = T = = T = = A 0 P040 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P041 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 P042 G = = A = C ? ? C G = G A = T = G C = = A = = = = T = = C = = G = T ? ? G A = A G = C = T A = = G = = = = C = = 0 P043 = = = A = C = = C = ? = A T T C = = = = A = C = = = C = = = = G = T = = G = ? = G G C T = = = = G = G = = = G = 0 P044 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P045 = = = = C = = A C = = G A = T = G C = = A T = G (T) = = (A) = = = = T = = G G = = A G = C = T A = = G C = A (C) = = (T) 0 P046 = = = = = = = = (C) = T = = = = = = = = = = = = = = = = = = = = = = = = = (G) = C = = = = = = = = = = = = = = = = = 0 P047 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = 0 P048 = C A = = = = = (C) = = = = = = = = = = = = = = = = = = = = T G = = = = = (G) = = = = = = = = = = = = = = = = = = = 0 P049 = = = ? C = = A C = = G A T T = G C = = A T = G = = = = = = = ? T = = G G = = A G G C = T A = = G C = A = = = = 0 P050 G = = A = C = = = = T = = T = C T = = = = = C = = = C ? C = = G = T = = = = C = = G = T G = = = = = G = = = G ? 0 P051 = C A = = = = = C G = G A = T = G C = = A = = G C = = T = T G = = = = = G A = A G = C = T A = = G = = A T = = A 0 P052 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 P053 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 0 P054 G T G A = C = = = A T A = T = C ? A = = = = C A T = C A C C A G = T = = = G C G = G = T ? C = = = = G G C = G T 0 P055 = = A G = T = = = G C ? = G (T) T ? C = = = = G G C C = T = = G A = C = = = A T ? = T (C) C ? A = = = = C A T T = A 0 P056 G = = A T C = G = G C = = = = = G = = = = = = A = = = ? C = = G C T = A = A T = = = = = T = = = = = = G = = = ? 0 P057 = C A = = = = = = = C G = T = = G C G G = T = G = C = = = T G = = = = = = = T A = G = = T A A A = C = A = T = = 0 P058 G = = A = C = = C = T = = T T C = = = = = = C A (T) = (C) (A) C = = G = T = = G = C = = G C T = = = = = = G G (C) = (G) (T) 0 P059 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P060 G T G A = C = = = A T A = T = C ? A = = = = C A T = C = C C A G = T = = = G C G = G = T ? C = = = = G G C = G = 0 P061 = = = A = = = = = = C G = T = = G C G G = T = G = = = = = = = G = = = = = = T A = G = = T A A A = C = A = = = = 0 P062 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P063 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P064 = = (A) = (T) = = (G) = = = = = G = T = = = A = = G = = T G = = = (G) = (C) = = (A) = = = = = T = C = = = G = = C = = C C = 0 P065 G = = = = C = = = = = = = = = = = = = = = = C = = = = = C = = = = T = = = = = = = = = = = = = = = = G = = = = = 0 P066 = C A ? = T = = = G C G = G = T G C = = = = G G C = G T = T G ? = C = = = A T A = T = C T A = = = = C A T = C A 0 P067 = C = = = = = = = G = G = G = = G C = = = = = G C = = T = T = = = = = = = A = A = T = = T A = = = = = A T = = A 0 P068 = C A = = = = = = G = G A = T = ? C = = A = = G ? = = = = T G = = = = = = A = A G = C = ? A = = G = = A ? = = = 0 P069 = C A = = = = = ? G = G A = T = G C = = A = = G ? = = T = T G = = = = = ? A = A G = C = T A = = G = = A ? = = A 0 P070 = = = A T C = G = = T ? = = (T) C T A = = = C C A = = C = = = = G C T = A = = C ? = = (C) T G C = = = T G G = = G = 0 P071 = = = ? = C = = C = T = A T T C = = = = A = C = T = C A = = = ? = T = = G = C = G G C T = = = = G = G = C = G T 0 P072 G = = A = C T = = G = G A = T = G C = = A = = = = = = ? C = = G = T C = = A = A G = C = T A = = G = = = = = = ? 0 P073 = C A = = = = = = G = G A ? T = G C = = A = = G C = = T = T G = = = = = = A = A G ? C = T A = = G = = A T = = A 0 P074 = = = = = = C = C ? ? = = = = = = = = = = = = = = = = = = = = = = = T = G ? ? = = = = = = = = = = = = = = = = = 0 P075 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P076 = C A G = T = = = G C G = G = T G C = = = = G G C = G T = T G A = C = = = A T A = T = C T A = = = = C A T = C A 0 P077 G = = = = C = = = = ? A = (T) = ? T A A = = C C A = = C = C = = = = T = = = = ? G = (G) = ? G C G = = T G G = = G = 0 P078 = C A = = = = = C G = G A = T = G C = = A = = G C = = T = T G = = = = = G A = A G = C = T A = = G = = A T = = A 0 P079 = C A = = = = = C G = G A = T = G C = = A = = G C = = T = T G = = = = = G A = A G = C = T A = = G = = A T = = A 0 P080 = = = = (C) = = (A) = = = = = = = = G C = G = = = = = = = = = = = = (T) = = (G) = = = = = = = = T A = A = = = = = = = = 0 P081 = C A = = = T = = G = G A = T = G C = = A = = G C = = = = T G = = = C = = A = A G = C = T A = = G = = A T = = = 0 P082 = = = A T = ? ? = = = = = = = = = = G = = = = = = = = = = = = G C = ? ? = = = = = = = = = = A = = = = = = = = = 0 P083 G = = A = C = = C = ? = A T T C = = = = A = C = = = C = C = = G = T = = G = ? = G G C T = = = = G = G = = = G = 0 P084 = C A (G) = = = = = G = G A = T = G C = = A = = G C = = T = T G (A) = = = = = A = A G = C = T A = = G = = A T = = A 0 P085 = = A G = = = = = = = A = = = = T A A = = C = A = = = = = = G A = = = = = = = G = = = = G C G = = T = G = = = = 0 P086 (G) = = G = = = = G = = A G G C = T A A = G C = A = = = = (C) = = A = = = = C = = G A T T = G C G = A T = G = = = = 0 P087 = = = = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = 0 P088 = C A = = = = = C G (C) G A = T = G C = = A = = G C = = T = T G = = = = = G A (T) A G = C = T A = = G = = A T = = A 0 P089 = = = = = = = = C = T = A = T = = = = A A = = (G) = = = = = = = = = = = = G = C = G = C = = = = G G = = (A) = = = = 0 P090 = C A = = = = = ? ? ? G A = T = G C = = A = = G C = ? ? = T G = = = = = ? ? ? A G = C = T A = = G = = A T = ? ? 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 = = 0.99 0.99 0.56 = = 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 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = ? ? = 1.00 = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = 1.00 1.00 = 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 = 1.00 1.00 = = 1.00 = = 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 = = = = = = = = 0.96 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 0.99 = ? ? = = = ? = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = 1.00 = ? ? ? ? ? ? 1.00 = = 1.00 = = = = 1.00 = = 0.97 = = 1.00 = 1.00 = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = = = = ? = = = = = = 0.99 = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = = 1.00 = = 1.00 = = = = = = 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 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 1.00 = = = = = = 0.63 = 0.63 0.63 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = 0.64 = = = = = = = 0.90 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = 0.93 = 0.95 = = = 1.00 0.96 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = = = = ? 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 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 = = = = = = ? 0.93 = 0.80 = = = = = = 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 = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = = = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 = = = = = 1.00 = = 0.99 = = 1.00 1.00 = 1.00 = = 1.00 = 1.00 = ? ? ? ? ? ? = = = = 1.00 = = 1.00 = = 1.00 ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 1.00 = = 1.00 = 1.00 ? ? 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = = = 0.99 = = = = = 1.00 = 1.00 = = 1.00 = ? = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.94 = = 0.94 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 0.96 = 1.00 0.76 = = 0.76 = = = = = = = = 0.78 = 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 = = = = 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 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 = = = 1.00 1.00 ? = 1.00 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 = = = ? = 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 1.00 1.00 = = = = = = 1.00 1.00 0.72 = 0.72 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 = = = = 0.99 = = = = = = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.62 = 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 1.00 = 0.99 = = = = = = = 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 1.00 1.00 = 1.00 = = 1.00 ? = = 0.51 1.00 1.00 1.00 = = = 1.00 1.00 1.00 = = 1.00 = = = = ? = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = 1.00 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 = 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 1.00 0.98 = = = = 1.00 = = = = ? 1.00 = 0.50 = ? 1.00 1.00 1.00 = = 1.00 1.00 1.00 = = 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 0.99 = = 0.99 = = = = 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 = = = = = = = = = 0.95 = = 1.00 = 1.00 = = 1.00 = ? = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = = = 1.00 = = 0.97 0.97 0.59 = = = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = 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 = = 0.99 = = = = 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 = = = = = 0.98 1.00 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 = = 0.55 = = = = = 1.00 1.00 = = = = = ? ? ? 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 1.00 = ? ? END PHASEPROBS