************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cd25c.phase.inp cd25c.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cd25c.phase.out_freqs : haplotype frequency estimates cd25c.phase.out_pairs : most likely haplotype pairs for each individual cd25c.phase.out_recom : estimates of recombination parameters cd25c.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 26 Positions of loci: 493 572 1993 2160 2305 3517 4182 4560 4825 5264 6412 8071 8523 15287 15658 21001 21088 21558 42032 42688 44992 45197 45823 47118 49774 49915 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cd25c.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DCGTGCCCCTTGAATAAADTGCGGCT 50.000000 2 DCGTGCCCCTTGAATAAAITGCGGCT 15.000000 3 DCGTGCCCCTCGAATAAAITGCAGCT 6.000000 4 ICGTGCCCCTTGAATAAADTGCGGCT 1.000000 5 ICGTGCCCCTTGAATAAAITGCGGCT 1.000000 6 ICATGCCCTTCAGGCAGGITGCAGCT 8.000000 7 ICATGCCCTTCAGGCAGGITGCACCT 19.000000 8 ICATGCCCTTCAGGCGGGITGCAGTC 1.000000 9 ICATGTTCCTCAGGCAGGITGCAGCT 1.000000 10 ICATGTTCCTCAGGCGGGITGCAGCT 5.000000 11 ICATGTTCCTCAGGCGGGITGCAGTC 55.000000 12 ICATTCCCCCCGAACAAGIGAGAGCT 1.000000 13 ICATTCCCCCCAGACAAGIGACAGCC 1.000000 14 IAAGTCCTCCTGAATAAADTGCGGCT 1.000000 15 IAAGTCCTCCTGAACAAGIGAGAGCT 7.000000 16 IAAGTCCTCCCGAACAAGIGAGAGCC 1.000000 17 IAAGTCCTCCCAGACAGGIGAGAGCT 1.000000 18 IAAGTCCTCCCAGACAAGIGAGAGCT 6.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (1,1) P002: (11,11) P003: (7,13) P004: (6,11) P005: (1,11) P006: (7,11) P007: (1,11) P008: (1,11) P009: (1,2) P010: (1,2) P011: (11,11) P012: (7,7) P013: (1,1) P014: (11,11) P015: (1,15) P016: (1,6) P017: (1,11) P018: (3,6) P019: (11,18) P020: (1,11) P021: (10,11) P022: (7,11) P023: (1,11) P024: (1,11) P025: (2,15) P026: (11,11) P027: (7,7) P028: (7,11) P029: (3,11) P030: (2,2) P031: (2,10) P032: (2,11) P033: (1,7) P034: (1,11) P035: (1,1) P036: (1,11) P037: (11,11) P038: (9,11) P039: (1,11) P040: (3,7) P041: (1,11) P042: (3,6) P043: (11,18) P044: (2,7) P045: (1,11) P046: (2,7) P047: (1,11) P048: (1,11) P049: (4,5) P050: (3,11) P051: (2,15) P052: (1,11) P053: (1,1) P054: (11,18) P055: (1,1) P056: (7,11) P057: (12,16) P058: (1,2) P059: (6,11) P060: (1,1) P061: (6,11) P062: (1,7) P063: (1,11) P064: (10,18) P065: (11,11) P066: (11,18) P067: (1,1) P068: (1,15) P069: (10,18) P070: (1,1) P071: (1,11) P072: (1,14) P073: (1,2) P074: (1,15) P075: (1,15) P076: (1,11) P077: (2,11) P078: (2,15) P079: (7,11) P080: (1,10) P081: (8,11) P082: (7,7) P083: (2,7) P084: (1,7) P085: (11,17) P086: (3,11) P087: (6,11) P088: (11,11) P089: (6,11) P090: (1,1) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P002 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P003 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T T C C C C C C A G A C A A G I G A C A G C C 0 P004 I C A T G C C C T T C A G G C A G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P005 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P006 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P007 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P008 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P009 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A I T G C G G C T 0 P010 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A I T G C G G C T 0 P011 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P012 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P013 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P014 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P015 D C G T G C C C C T T G A A T A A A D T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P016 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A G C T 0 P017 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P018 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G C C C T T C A G G C A G G I T G C A G C T 0 P019 I C A T G T T C C T C A G G C G G G I T G C A G T C I A A G T C C T C C C A G A C A A G I G A G A G C T 0 P020 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P021 I C A T G T T C C T C A G G C G G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P022 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P023 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P024 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P025 D C G T G C C C C T T G A A T A A A I T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P026 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P027 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P028 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P029 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P030 D C G T G C C C C T T G A A T A A A I T G C G G C T D C G T G C C C C T T G A A T A A A I T G C G G C T 0 P031 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G C T 0 P032 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P033 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P034 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P035 D C G T G C C C C T T G A A T A A A [D] T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P036 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P037 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P038 I C A T G T T C C T C A G G C (A) G G I T G C A G C T I C A T G T T C C T C A G G C (G) G G I T G C A G T C 0 P039 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P040 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P041 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P042 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G C C C T T C A G G C A G G I T G C A G C T 0 P043 I C A T G T T C C T C A G G C G G G I T G C A G T C I A A G T C C T C C C A G A C A A G I G A G A G C T 0 P044 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P045 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P046 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A [C] C T 0 P047 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P048 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P049 I C G T G C C C C T T G A A T A A A D T G C G G C T I C G T G C C C C T T G A A T A A A I T G C G G C T 0 P050 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P051 D C G T G C C C C T T G A A T A A A I T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P052 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P053 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P054 I C A T G T T C C T C A G G C G G G I T G C A G T C I A A G T C C T C C C A G A C A A G I G A G A G C T 0 P055 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P056 I C A T G C C C T T C A G G C A G G I T G C A [C] C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P057 I C A T T C C C C C C G A A C A A G I G A G A G C (T) I A A G T C C T C C C G A A C A A G I G A G A G C (C) 0 P058 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A I T G C G G C T 0 P059 I C A T G C C C T T C A G G C A G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P060 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P061 I C A T G C C C T T C A G G C A G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P062 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P063 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P064 I C A T G T T C C T C A G G C G G G I T G C A G C T I A A G T C C T C C C A G A C A A G I G A G A G C T 0 P065 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P066 I C A T G T T C C T C A G G C G G G I T G C A G T C I A A G T C C T C C C A G A C A A G I G A G A G C T 0 P067 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P068 D C G T G C C C C T T G A A T A A A D T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P069 I C A T G T T C C T C A G G C G G G I T G C A G C T I A A G T C C T C C C A G A C A [A] G I G A G A G C T 0 P070 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 0 P071 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P072 D C G T G C C C C T T G A A T A A A D T G C G G C T I A A G T C C T C C T G A A T A A A D T G C G G C T 0 P073 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A I T G C G G C T 0 P074 D C G T G C C C C T T G A A T A A A D T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P075 D C G T G C C C C T T G A A T A A A D T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P076 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P077 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P078 D C G T G C C C C T T G A A T A A A I T G C G G C T I A A G T C C T C C T G A A C A A G I G A G A G C T 0 P079 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P080 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G T T C C T C A G G C [G] G G I T G C A G C T 0 P081 I C A T G C C C T T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P082 I C A T G C C C T T C A G G C A G G I T G C A C C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P083 D C G T G C C C C T T G A A T A A A I T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P084 D C G T G C C C C T T G A A T A A A D T G C G G C T I C A T G C C C T T C A G G C A G G I T G C A C C T 0 P085 I C A T G T T C C T C A G G C G G G I T G C A G [T] [C] I A A G T C C T C C C A G A C A G G I G A G A G C T 0 P086 D C G T G C C C C T C G A A T A A A I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G [T] [C] 0 P087 I C A T G C C C T T C A G G C A G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P088 I C A T G T T C C T C A G G C G G G I T G C A G T C I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P089 I C A T G C C C T T C A G G C A G G I T G C A G C T I C A T G T T C C T C A G G C G G G I T G C A G T C 0 P090 D C G T G C C C C T T G A A T A A A D T G C G G C T D C G T G C C C C T T G A A T A A A D T G C G G C T 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 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 P002 = = = = = = = = = = ? = ? = = ? = = ? = = = = = = = = = = = = = = = = = ? = ? = = ? = = ? = = = = = = = 0 P003 ? = = = G = = = T T = = = G = = ? ? ? T G = = C = T ? = = = T = = = C C = = = A = = ? ? ? G A = = G = C 0 P004 = = = = = C C = T = = = = = = A = = ? ? = = = = C T = = = = = T T = C = = = = = = G = = ? ? = = = = T C 0 P005 D = ? ? = C C = = = ? G A A T A A A D = = = G ? C T I = ? ? = T T = = = ? A G G C G G G I = = = A ? T C 0 P006 = = = = = C C = T = = = = = = A = = ? = = = = C C T = = = = = T T = C = = = = = = G = = ? = = = = G T C 0 P007 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P008 D = G = = C C ? = = T ? ? A T ? ? ? D = = = G = C T I = A = = T T ? = = C ? ? G C ? ? ? I = = = A = T C 0 P009 = = = = = = = = = = = = ? = = = = = D = = = = = = = = = = = = = = = = = = = ? = = = = = I = = = = = = = 0 P010 = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = = = = = I = = = = = = = 0 P011 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P012 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P013 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P014 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P015 D C G T G = = C = T = ? ? = T = = A D T G C G = = = I A A G T = = T = C = ? ? = C = = G I G A G A = = = 0 P016 D = G = = = = = C = T G A A T = A A D = = = G = = = I = A = = = = = T = C A G G C = G G I = = = A = = = 0 P017 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P018 D = G = = = = = C = = G A A T = A A = = = = = = = = I = A = = = = = T = = A G G C = G G = = = = = = = = 0 P019 = C = T G T T C = T = = = G = G G = = T G C = = T C = A = G T C C T = C = = = A = A A = = G A G = = C T 0 P020 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P021 = = = = = = = = ? = = = = = = = = = = = = = = = C T = = = = = = = = ? = = = = = = = = = = = = = = = T C 0 P022 = = = = = C C = T = = = = = = A = = = = = = = C C T = = = = = T T = C = = = = = = G = = = = = = = G T C 0 P023 D = G = = C C = = = T G A A T A A A ? = = = G = C T I = A = = T T = = = C A G G C G G G ? = = = A = T C 0 P024 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P025 D C G T G = = C = T = = = = T = = A = T G C G ? = = I A A G T = = T = C = = = = C = = G = G A G A ? = = 0 P026 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P027 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P028 = = = = = C C = T = = = = = = A = = ? = = = = C C T = = = = = T T = C = = = = = = G = = ? = = = = G T C 0 P029 D = G = = C C = = = = G A A T A A A = = = = = = C T I = A = = T T = = = = A G G C G G G = = = = = = T C 0 P030 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P031 D = G = = C C = = = T G A A T A A A = = = = G = = = I = A = = T T = = = C A G G C G G G = = = = A = = = 0 P032 D = G = = C C = = = T G A A T A A ? = = = = G = C T I = A = = T T = = = C A G G C G G ? = = = = A = T C 0 P033 D = G = = = = = C = T G A A T = A A D = = = G G = = I = A = = = = = T = C A G G C = G G I = = = A C = = 0 P034 D = G = = C C = = = T G A A T A A A ? ? = = G = ? ? I = A = = T T = = = C A G G C G G G ? ? = = A = ? ? 0 P035 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 P036 D = G = = C C = = = T G A A T A A A D = ? ? G = C T I = A = = T T = = = C A G G C G G G I = ? ? A = T C 0 P037 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P038 = = = = = = = = = = = = = = = (A) = = = = = = = = C T = = = = = = = = = = = = = = = (G) = = = = = = = = T C 0 P039 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P040 D = G = = = = = C = = G A A ? = A A = = = = = G = = I = A = = = = = T = = A G G ? = G G = = = = = C = = 0 P041 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P042 D = G = = = = = C = = G A A T = A A = = = = = = = = I = A = = = = = T = = A G G C = G G = = = = = = = = 0 P043 = C = T G T T C = T = = = G = G G = = T G C = = T C = A = G T C C T = C = = = A = A A = = G A G = = C T 0 P044 D = G = = = = = C = T G A A T ? ? A = = = = G G = = I = A = = = = = T = C A G G C ? ? G = = = = A C = = 0 P045 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P046 D = G = = = = = C = T G A A T = A A = = = = G ? = = I = A = = = = = T = C A G G C = G G = = = = A ? = = 0 P047 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P048 D = G = = C C = = = T G A A T A A A D = = = G = ? T I = A = = T T = = = C A G G C G G G I = = = A = ? C 0 P049 = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = = = = = I = = = = = = = 0 P050 D = G = = C C = = = = G A A T A A A ? ? = = = = C T I = A = = T T = = = = A G G C G G G ? ? = = = = T C 0 P051 D C G T G = = C = T = = = = T = = A = T G C G = = = I A A G T = = T = C = = = = C = = G = G A G A = = = 0 P052 D = G = = C C = = = T G A A T A A A D = = ? G = C T I = A = = T T = = = C A G G C G G G I = = ? A = T C 0 P053 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P054 = C = T G T T C = T = = = G = G G = = T G C = = T C = A = G T C C T = C = = = A = A A = = G A G = = C T 0 P055 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P056 = = = = = C C = T = = = = = = A = = = = = = = ? C T = = = = = T T = C = = = = = = G = = = = = = = ? T C 0 P057 = C = T = = = C = = = = = = = = = = = = = = = = = (T) = A = G = = = T = = = = = = = = = = = = = = = = = (C) 0 P058 = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = = = = = I = = = = = = = 0 P059 = = = = = C C = T = = = = = = A = = = = = = = = C T = = = = = T T = C = = = = = = G = = = = = = = = T C 0 P060 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P061 = = = = = C C = T = = = = = = A = = = = = = = = C T = = = = = T T = C = = = = = = G = = = = = = = = T C 0 P062 D = G = = = = = C = T G A A T = A A D = = = G G = = I = A = = = = = T = C A G G C = G G I = = = A C = = 0 P063 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P064 = C = T G T T C = T = = = G = G G = = T G C = = = ? = A = G T C C T = C = = = A = A A = = G A G = = = ? 0 P065 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P066 = C = T G T T C = T = = = G = G G = = T G C = = T C = A = G T C C T = C = = = A = A A = = G A G = = C T 0 P067 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = 0 P068 ? C G T G = = C = T = = ? = T = = A D T G C G = = = ? A A G T = = T = C = = ? = C = = G I G A G A = = = 0 P069 = C = T G T T C = T = = = G = G ? = = T G C = = = = = A = G T C C T = C = = = A = A ? = = G A G = = = = 0 P070 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P071 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P072 D C G T G = = C = T = = = = = = = = = = = = = = = = I A A G T = = T = C = = = = = = = = = = = = = = = = 0 P073 = = = = = = = = = = = = = = = = = = D = = = = ? = = = = = = = = = = = = = = = = = = = = I = = = = ? = = 0 P074 D C G T G = = C = T = = ? = T = = A D T G C ? = = = I A A G T = = T = C = = ? = C = = G I G A G ? = = = 0 P075 D C G T G = = C = T = = = = T = ? A D T G C G = = = I A A G T = = T = C = = = = C = ? G I G A G A = = = 0 P076 D = G = = C C = = = T G A A T A A A D = = = G = C T I = A = = T T = = = C A G G C G G G I = = = A = T C 0 P077 D = G = = C C = = = T G A A T A A A = = = = G = C T I = A = = T T = = = C A G G C G G G = = = = A = T C 0 P078 D C G T G = = C = T ? = = = T = ? A = T G C G = = = I A A G T = = T = C ? = = = C = ? G = G A G A = = = 0 P079 = = = = = C C = T = = = = = = A = = = = = = = C C T = = = = = T T = C = = = = = = G = = = = = = = G T C 0 P080 D = G = = C C = = = T G A A T ? ? A D = = = G = = = I = A = = T T = = = C A G G C ? ? G I = = = A = = = 0 P081 = = = = = C C = T = = = = = = = = = = = = = = = = = = = = = = T T = C = = = = = = = = = = = = = = = = = 0 P082 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P083 D = G = = = = = C = T G A A T = ? A = = = = G G = = I = A = = = = = T = C A G G C = ? G = = = = A C = = 0 P084 D ? G = = = = ? ? = ? ? ? A T = ? A D = = = G G = = I ? A = = = = ? ? = ? ? ? G C = ? G I = = = A C = = 0 P085 = C = T G ? T C = T = = = G = ? = ? = T ? ? ? = ? ? = A = G T ? C T = C = = = A = ? = ? = G ? ? ? = ? ? 0 P086 D = G = = C C = = = = G A A T ? ? A = = ? ? = ? ? ? I = A = = T T = = = = A G G C ? ? G = = ? ? = ? ? ? 0 P087 = = = = = C C = T = = = = = = ? = = = = = = = = C T = = = = = T T = C = = = = = = ? = = = = = = = = T C 0 P088 = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = 0 P089 = = = = = C C = T = = = = = = A = = = = = = = = C T = = = = = T T = C = = = = = = G = = = = = = = = T C 0 P090 = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = = = = = = ? = = = = = = = ? = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = ? = = ? = = ? = = = = = = = ? = = = 1.00 = = = 1.00 1.00 = = = 1.00 = = ? ? ? 1.00 1.00 = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = ? ? = = = = 1.00 1.00 1.00 = ? ? = 1.00 1.00 = = = ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 ? 1.00 1.00 = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = ? = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 ? = = 1.00 ? ? 1.00 1.00 ? ? ? 1.00 = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = ? = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = ? ? = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = = = = = = ? = = = = = = = = = = = = = = = 1.00 1.00 = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = ? = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = = 1.00 = ? ? = = = = = = = = = = = = = = = = = = ? = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = = = 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 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 ? = 1.00 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 = = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = 1.00 ? = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = ? 1.00 = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = ? 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 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 = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 1.00 = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = ? = = = = = = = = = ? 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = ? = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = 1.00 ? = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = ? = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = ? = 1.00 = = 1.00 1.00 1.00 1.00 1.00 ? = = = 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = 1.00 = ? 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 ? = = = 1.00 = ? 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 ? ? 1.00 1.00 = = = 1.00 = = = = = = = = 1.00 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = ? 1.00 = = = = 1.00 1.00 = = 1.00 ? 1.00 = = = = ? ? = ? ? ? 1.00 1.00 = ? 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = 1.00 1.00 ? 1.00 1.00 = 1.00 = = = 1.00 = ? = ? = 1.00 ? ? ? = ? ? 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 = = = = = = = = = = = = = = = = ? = = = = = = = ? = END PHASEPROBS