************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 prkrx.phase.inp prkrx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST prkrx.phase.out_freqs : haplotype frequency estimates prkrx.phase.out_pairs : most likely haplotype pairs for each individual prkrx.phase.out_recom : estimates of recombination parameters prkrx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 22 Positions of loci: 577 973 996 1355 8239 8837 9261 9588 9794 10182 11491 11649 13483 14182 14424 14794 14878 23140 31140 34603 39621 39881 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file prkrx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ICCCAADTACTCGGCAGCCCCA 3.000000 2 ICCTAAICTCTCGGCAGCCCTA 1.000000 3 ICCTAAICTCTCGGCAGCCCTC 3.000000 4 ICCTAAICTCCCGTCATCCCCA 5.000000 5 ICCTAAITACCCGTTATCCGTA 1.000000 6 ICCTAADTACCCATTATCCCTA 1.000000 7 ICCTAADTACCCATTATCCGTA 5.000000 8 ICCTAADTACCCATTATTCCTA 1.000000 9 ICCTGGICTCTCGGCAGCCCTA 3.000000 10 ICTCAAICTCTCGGCAGTCCTA 2.000000 11 ICTTAAICTCTCGGCAGCCCTA 2.000000 12 ICTTAAICTCTCGGCAGCCCCC 1.000000 13 ICTTAAICTCTCGGCAGTCCTA 1.000000 14 ICTTAAICTCTCGGCGGCCCTA 2.000000 15 ICTTAAICTCTCGGCGGTCCTA 3.000000 16 ICTTAAICTCTTGGCGGTCCTA 12.000000 17 ICTTGGICTCTCGGCAGCCCTA 43.000000 18 ICTTGGICTCTCGGCGGCCCTA 1.000000 19 IGCCAAICTCTCGGCAGCCCTA 7.000000 20 IGCCAAICTCTCGGCAGTCCTA 2.000000 21 IGCCAAICTCTCGGCAGTTCTA 1.000000 22 DCCCAAICTCTCGGCAGCCCTA 25.000000 23 DCCCAAICTCTCGGCAGCCCCA 1.000000 24 DCCCAAICTCTCGGCAGTCCTA 30.000000 25 DCCCAAICTCTCGGCAGTCCTC 4.000000 26 DCCCAAICTCCCGTCATCCCTA 1.000000 27 DCCCAAICTTTCGGCAGCCCTA 2.000000 28 DCCCAAICTTTCGGCAGTTCTA 11.000000 29 DCCCAADTACCCATTATCCGTA 1.000000 30 DCCCGGICTCTCGGCAGCCCTA 1.000000 31 DCCCGGICTCTCGGCAGCCGTC 2.000000 32 DCCTAAICTCTCGGCAGCCCTA 1.000000 33 DCCTAADTACCCATTATCCGTA 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (10,22) P002: (11,16) P003: (24,24) P004: (3,28) P005: (17,17) P006: (17,28) P007: (17,17) P008: (16,19) P009: (17,28) P010: (17,20) P011: (22,28) P012: (4,19) P013: (17,20) P014: (16,22) P015: (4,24) P016: (16,22) P017: (23,25) P018: (6,7) P019: (16,28) P020: (17,22) P021: (9,24) P022: (16,22) P023: (24,27) P024: (9,17) P025: (17,22) P026: (16,22) P027: (17,24) P028: (11,17) P029: (1,22) P030: (17,28) P031: (19,22) P032: (24,31) P033: (4,4) P034: (15,24) P035: (15,19) P036: (16,18) P037: (16,22) P038: (1,25) P039: (14,22) P040: (17,17) P041: (8,17) P042: (28,29) P043: (4,17) P044: (17,17) P045: (16,22) P046: (16,22) P047: (22,24) P048: (24,24) P049: (17,24) P050: (1,3) P051: (17,17) P052: (10,24) P053: (7,22) P054: (24,24) P055: (17,17) P056: (5,24) P057: (12,17) P058: (22,30) P059: (2,24) P060: (17,24) P061: (24,33) P062: (7,17) P063: (22,24) P064: (17,25) P065: (24,26) P066: (19,24) P067: (17,22) P068: (17,24) P069: (13,17) P070: (14,19) P071: (16,22) P072: (17,22) P073: (21,24) P074: (17,28) P075: (15,24) P076: (17,17) P077: (22,24) P078: (7,22) P079: (7,9) P080: (22,25) P081: (19,28) P082: (17,17) P083: (17,24) P084: (24,28) P085: (17,27) P086: (17,28) P087: (3,32) P088: (17,24) P089: (24,31) P090: (17,22) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 I C T C A A I C T C T C G G C A G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P002 I C T T A A I C T C T C G G C A G (C) C C T A I C T T A A I C T C T T G G C G G (T) C C T A 0 P003 D C C C A A I C T [C] T C G G C A G T [C] C T A D C C C A A I C T C T C G G C A G T C C T A 0 P004 I C C T A A I C T C T C G G C A G C C C T [C] D C C C A A I C T T T C G G C A G T [T] C T A 0 P005 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P006 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G T [T] C T A 0 P007 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P008 I C T T A A I C T C T [T] G G C [G] G [T] C C T A I G C C A A I C T C T C G G C A G [C] C C T A 0 P009 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G T T C T A 0 P010 I C T T G G I C T C T C G G C A G (C) C C T A I G C C A A I C T C T C G G C A G (T) C C T A 0 P011 D C C C A A I C T (C) T C G G C A G C C C T A D C C C A A I C T (T) T C G G C A G T [T] C T A 0 P012 I C C T A A I C T C C C G T C A T C C C C A I G C C A A I C T C T C G G C A G C C C T A 0 P013 I C T T G G I C T C T C G G C A G C C C T A I G C C A A I C T C T C G G C A G T C C T A 0 P014 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P015 I C C T A A I C T C C C G T C A T C C C C A D C C C A A I C T C T C G G C A G T C C T A 0 P016 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P017 D C C C A A I C T C T C G G C A G C C C (C) (A) D C C C A A I C T C T C G G C A G T C C (T) (C) 0 P018 I C C T A A D T A C C C A T T A T C C C T A I C C T A A D T A C C C A T T A T C C G T A 0 P019 I C T T A A I C T C T T G G C G G T C C T A D C C C A A I C T T T C G G C A G T T C T A 0 P020 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P021 I C C T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P022 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P023 D C C C A A I C T (C) T C G G C A G T C C T A D C C C A A I C T (T) T C G G C A G C C C T A 0 P024 I C C T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P025 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P026 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P027 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P028 I C T T A A I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P029 I C C C A A D T A C T C G G C A G C C C C A D C C C A A I C T C T C G G C A G C C C T A 0 P030 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G T T C T A 0 P031 I G C C A A I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P032 D C C C A A I C T C T C G G C A G T C (C) T (A) D C C C G G I C T C T C G G C A G C C (G) T (C) 0 P033 I C C T A A I C T C C C G T C A T C C C C A I C C T A A I C T C C C G T C A T C C C C A 0 P034 I C T T A A I C T C T C G G C G G T C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P035 I C T T A A I C T C T C G G C G G (T) C C T A I G C C A A I C T C T C G G C A G (C) C C T A 0 P036 I C T T (A) (A) I C T C T T G G C G G T C C T A I C T T (G) (G) I C T C T C G G C G G C C C T A 0 P037 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P038 I C C C A A D T A C T C G G C A G C C C C (A) D C C C A A I C T C T C G G C A G T C C T (C) 0 P039 I C T T A A I C T C T C G G C G G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P040 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P041 I C C T A A D T A C C C A T T A T (T) C C T A I C T T G G I C T C T C G G C A G (C) C C T A 0 P042 D C C C A A I C T T T C G G C A G T T C T A D C C C A A D T A C C C A T T A T C C G T A 0 P043 I C C T A A I C T C C C G T C A T C C C C A I C T T G G I C T C T C G G C A G C C C T A 0 P044 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P045 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P046 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P047 D C C C A A I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P048 D C C C A A I C T C T C G G C A G T C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P049 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P050 I C C C A A D T A C T C G G C A G C C C C (A) I C C T A A I C T C T C G G C A G C C C T (C) 0 P051 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P052 I C T C A A I C T C T C G G C A G T C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P053 I C C T A A D T A C C C A T T A T C C G T A D C C C A A I C T C T C G G C A G C C C T A 0 P054 D C C C A A I C T C T C G G C A G T C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P055 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P056 I C C T A A I T A C C C G T T A T C C G T A D C C C A A I C T C T C G G C A G T C C T A 0 P057 I C T T (A) (A) I C T C T C G G C A G C C C (C) (C) I C T T (G) (G) I C T C T C G G C A G C C C (T) (A) 0 P058 D C C C A A I C T C T C G G C A G C C C T A D C C C G G I C T C T C G G C A G C C C T A 0 P059 I C C T A A I C T C T C G G C A G (C) C C T A D C C C A A I C T C T C G G C A G (T) C C T A 0 P060 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P061 D C C C A A I C T C T C G G C A G T C C T A D C C T A A D T A C C C A T T A T C C G T A 0 P062 I C C T A A D T A C C C A T T A T C C G T A I C T T G G I C T C T C G G C A G C C C T A 0 P063 D C C C A A I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P064 I C T T G G I C T C T C G G C A G C C C T (A) D C C C A A I C T C T C G G C A G T C C T (C) 0 P065 D C C C A A I C T C T C G G C A G (T) C C T A D C C C A A I C T C C C G T C A T (C) C C T A 0 P066 I G C C A A I C T C T C G G C A G (C) C C T A D C C C A A I C T C T C G G C A G (T) C C T A 0 P067 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P068 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P069 I C T T A A I C T C T C G G C A G (T) C C T A I C T T G G I C T C T C G G C A G (C) C C T A 0 P070 I C T T A A I C T C T C G G C G G C C C T A I G C C A A I C T C T C G G C A G C C C T A 0 P071 I C T T A A I C T C T T G G C G G (T) C C T A D C C C A A I C T C T C G G C A G (C) C C T A 0 P072 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A 0 P073 I G C C A A I C T C T C G G C A G T (T) C T A D C C C A A I C T C T C G G C A G T (C) C T A 0 P074 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G T T C T A 0 P075 I C T T A A I C T C T C G G C G G T C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P076 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P077 D C C C A A I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P078 I C C T A A D T A C C C A T T A T C C G T A D C C C A A I C T C T C G G C A G C C C T A 0 P079 I C C T A A D T A C C C A T T A T C C G T A I C C T G G I C T C T C G G C A G C C C T A 0 P080 D C C C A A I C T C T C G G C A G (C) C C T A D C C C A A I C T C T C G G C A G (T) C C T C 0 P081 I G C C A A I C T C T C G G C A G (C) C C T A D C C C A A I C T T T C G G C A G (T) [T] C T A 0 P082 I C T T G G I C T C T C G G C A G C C C T A I C T T G G I C T C T C G G C A G C C C T A 0 P083 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P084 D C C C A A I C T C T C G G C A G T C C T A D C C C A A I C T [T] T C G G C A G T T C T A 0 P085 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G C C C T A 0 P086 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T T T C G G C A G T [T] C T A 0 P087 (I) C C T A A I C T C T C G G C A G C C C T C (D) C C T A A I C T C T C G G C A G C C C T A 0 P088 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G T C C T A 0 P089 D C C C A A I C T C T C G G C A G T C (C) T (A) D C C C G G I C T C T C G G C A G C C (G) T (C) 0 P090 I C T T G G I C T C T C G G C A G C C C T A D C C C A A I C T C T C G G C A G C C C T A END BESTPAIRS1 Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in [] with phase known positions indicated by = BEGIN BESTPAIRS2 0 P001 I = T = = ? = ? ? ? = = ? ? ? = = (T) = = = = D = C = = ? = ? ? ? = = ? ? ? = = (C) = = = = 0 P002 = = = = = = = = ? ? = C = = = A = (C) = = = = = = = = = = = = ? ? = T = = = G = (T) = = = = 0 P003 = = = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = ? = = = 0 P004 I = = T = = = = = C = = = = = = = C ? = ? ? D = = C = = = = = T = = = = = = = T ? = ? ? 0 P005 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = 0 P006 I = T T G G = = = C = = = = = = = C ? = = = D = C C A A = = = T = = = = = = = T ? = = = 0 P007 = = = = = = = = ? ? = = = = = = = = ? = = = = = = = = = = = ? ? = = = = = = = = ? = = = 0 P008 = C T T = = ? ? ? ? ? ? ? ? ? ? ? ? ? = = = = G C C = = ? ? ? ? ? ? ? ? ? ? ? ? ? = = = 0 P009 I = T T G ? = = = C = = = = = = = C C = = ? D = C C A ? = = = T = = = = = = = T T = = ? 0 P010 = C T T G G = = = = = = = = = = = (C) = = = = = G C C A A = = = = = = = = = = = (T) = = = = 0 P011 = = = = = = = = = (C) = = = = = = = C ? = = = = = = = = = = = = (T) = = = = = = = T ? = = = 0 P012 ? C = T = = = = = = C = = ? ? ? ? = ? = C = ? G = C = = = = = = T = = ? ? ? ? = ? = T = 0 P013 = C T T G G = = = = = = = = = = = C ? = = = = G C C A A = = = = = = = = = = = T ? = = = 0 P014 I ? ? T = = = = ? = = T = = = G = (T) = = = = D ? ? C = = = = ? = = C = = = A = (C) = = = = 0 P015 ? = = T = = = = = = C = = ? ? ? ? C ? = C = ? = = C = = = = = = T = = ? ? ? ? T ? = T = 0 P016 I = T T = = = = = = = T = = = G = (T) ? = = = D = C C = = = = = = = C = = = A = (C) ? = = = 0 P017 = = = = = = = = ? ? = = = = = = = C ? = (C) (A) = = = = = = = = ? ? = = = = = = = T ? = (T) (C) 0 P018 = = = = = = = = ? ? = = = = = ? = = = C = = = = = = = = = = ? ? = = = = = ? = = = G = = 0 P019 I = T T = = = = = C = T = = = G = = C = = = D = C C = = = = = T = C = = = A = = T = = = 0 P020 I = T T G G = = = = = = = = = = = = ? = = = D = C C A A = = = = = = = = = = = = ? = = = 0 P021 I = = T G G = = = = = = = = = = = C = = = = D = = C A A = = = = = = = = = = = T = = = = 0 P022 I = T T = = = = = = = T = = = G = (T) ? = = = D = C C = = = = = = = C = = = A = (C) ? = = = 0 P023 = = = = = = = = = (C) = = = = = = = T = = = = = = = = = = = = = (T) = = = = = = = C = = = = 0 P024 = = C = = ? = = = = = = = = = = = = ? = = = = = T = = ? = = = = = = = = = = = = ? = = = 0 P025 I = T T G G = = = = = = = = = = = = ? = = = D = C C A A = = = = = = = = = = = = ? = = = 0 P026 I = T T = = = = ? = = T = = = G = (T) = = = = D = C C = = = = ? = = C = = = A = (C) = = = = 0 P027 I = T T G G = = = = = = = = = = = C = = = = D = C C A A = = = = = = = = = = = T = = = = 0 P028 = = = = A A = = = = = = = = = = = = = = = = = = = = G G = = = = = = = = = = = = = = = = 0 P029 I = = = = = D T A = = = = = = = = = = = C = D = = = = = I C T = = = = = = = = = = = T = 0 P030 I = T T G G = = = C = = = = = = = C C = = = D = C C A A = = = T = = = = = = = T T = = = 0 P031 I G = = = = = = = = = = = = = = = = ? = = = D C = = = = = = = = = = = = = = = = ? = = = 0 P032 = = = ? A A = = = = = = = = = = = T = (C) = (A) = = = ? G G = = = = = = = = = = = C = (G) = (C) 0 P033 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = 0 P034 I = T T = = = = = = = = = = = G = = = = = = D = C C = = = = = = = = = = = A = = = = = = 0 P035 = C T T = = = = = = = = = = = G = (T) ? = = = = G C C = = = = = = = = = = = A = (C) ? = = = 0 P036 = = = = (A) (A) = = ? = = T = = = = = T = = = = = = = = (G) (G) = = ? = = C = = = = = C = = = = 0 P037 I = T T = = = = = = = T = = = G = (T) ? = = = D = C C = = = = = = = C = = = A = (C) ? = = = 0 P038 I = = = = = D T A = = = = = = = = C ? = C (A) D = = = = = I C T = = = = = = = = T ? = T (C) 0 P039 I = T T = = = = = = = = = = = G = = = = = = D = C C = = = = = = = = = = = A = = = = = = 0 P040 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = 0 P041 = = C = A A D T A = C = A T T = T (T) ? = = = = = T = G G I C T = T = G G C = G (C) ? = = = 0 P042 = = = = = = I C T T T = G G C = G T T C = = = = = = = = D T A C C = A T T = T C C G = = 0 P043 ? = C = A A = = = = C = = ? ? ? ? = ? = C = ? = T = G G = = = = T = = ? ? ? ? = ? = T = 0 P044 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 0 P045 I = T T = = = = = = = T = = = G = (T) = = = = D = C C = = = = = = = C = = = A = (C) = = = = 0 P046 I = T T = = = = = = = T = = = G = (T) = = = = D = C C = = = = = = = C = = = A = (C) = = = = 0 P047 = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = 0 P048 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P049 I = T ? G ? ? ? = = = = = = = = = C ? = = = D = C ? A ? ? ? = = = = = = = = = T ? = = = 0 P050 = = = C = = D T A = = = = = = = = = = = C (A) = = = T = = I C T = = = = = = = = = = = T (C) 0 P051 = = = ? = = = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = = = ? = = = 0 P052 I = T = = = = = = = = = = = = = = = = = = = D = C = = = = = = = = = = = = = = = = = = = 0 P053 I = = ? = = D T A = C = A T T = T = = G = = D = = ? = = I C T = T = G G C = G = = C = = 0 P054 = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = 0 P055 = = = ? = = = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = = = ? = = = 0 P056 I = = T = = = T A = C = = T T = T C = G = = D = = C = = = C T = T = = G C = G T = C = = 0 P057 = = = = (A) (A) = = = = = = = = = = = = ? = (C) (C) = = = = (G) (G) = = = = = = = = = = = = ? = (T) (A) 0 P058 = = = = A A ? ? = = = = = = = = = = = = = = = = = = G G ? ? = = = = = = = = = = = = = = 0 P059 I = = T = = = = ? ? = = = = = = = (C) ? = = = D = = C = = = = ? ? = = = = = = = (T) ? = = = 0 P060 I = T T G G = = = = = = = = = = = C = = = = D = C C A A = = = = = = = = = = = T = = = = 0 P061 = = = C = = ? C T = T = G G C = G T ? C = = = = = T = = ? T A = C = A T T = T C ? G = = 0 P062 = = C = A A D T A = C = A T T = T = = G = = = = T = G G I C T = T = G G C = G = = C = = 0 P063 = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = T = = = = 0 P064 I = T T G G = = = = = = = = = = = C = = = (A) D = C C A A = = = = = = = = = = = T = = = (C) 0 P065 = = = = = = = = = = T = = G = = G (T) ? = = = = = = = = = = = = = C = = T = = T (C) ? = = = 0 P066 I G = = = = = = ? = = = = = = = = (C) = = = = D C = = = = = = ? = = = = = = = = (T) = = = = 0 P067 I = T T G G = = = = = = = = = = = = ? = = = D = C C A A = = = = = = = = = = = = ? = = = 0 P068 I = T T G G = = = = = = = = = = = C = = = = D = C C A A = = = = = = = = = = = T = = = = 0 P069 = = = = A A = = = = = = = = = = = (T) = = = = = = = = G G = = = = = = = = = = = (C) = = = = 0 P070 = C T T = = = = = = = = = = = G = = ? = = = = G C C = = = = = = = = = = = A = = ? = = = 0 P071 I = T T = = = = = = = T = = = G = (T) ? = = = D = C C = = = = = = = C = = = A = (C) ? = = = 0 P072 I = T T G G = = = = = = = = = = = = = = = = D = C C A A = = = = = = = = = = = = = = = = 0 P073 I G = = = = = = ? = = = = = = = = = (T) = = = D C = = = = = = ? = = = = = = = = = (C) = = = 0 P074 I = T T G G = = = C = = = = = = = C C = = = D = C C A A = = = T = = = = = = = T T = = = 0 P075 I = T T = = = = = = = = = = = G = = ? = = = D = C C = = = = = = = = = = = A = = ? = = = 0 P076 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P077 = = = = = = = = = = = = = = = = = C ? ? = = = = = = = = = = = = = = = = = = = T ? ? = = 0 P078 I = = T = = D T A = C = A T T = T = = G = ? D = = C = = I C T = T = G G C = G = = C = ? 0 P079 = = = = A A D T A = C = A T T = T = ? G = = = = = = G G I C T = T = G G C = G = ? C = = 0 P080 = = = = = = = = ? = = = = = = = = (C) = = = A = = = = = = = = ? = = = = = = = = (T) = = = C 0 P081 I G = = = = = = = C = = = = = = = (C) ? = ? = D C = = = = = = = T = = = = = = = (T) ? = ? = 0 P082 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P083 I = T T G G = = = = = = = = = = = C ? = = = D = C C A A = = = = = = = = = = = T ? = = = 0 P084 = = = = = = = = ? ? = = = = = = = = C = = = = = = = = = = = ? ? = = = = = = = = T = = = 0 P085 I = T T G G = = = C = = = = = = = = ? = = = D = C C A A = = = T = = = = = = = = ? = = = 0 P086 I = T T G G = ? = C = = = = = = = C ? = = = D = C C A A = ? = T = = = = = = = T ? = = = 0 P087 (I) = = = = = = = ? ? = = = = = = = = ? = = C (D) = = = = = = = ? ? = = = = = = = = ? = = A 0 P088 I = T T G G = = = = = = = = = = = C ? = = = D = C C A A = = = = = = = = = = = T ? = = = 0 P089 = = = = A A = = = = = = = = = = = T ? (C) = (A) = = = = G G = = = = = = = = = = = C ? (G) = (C) 0 P090 I = T T G G = = = = = = = = = = = = ? = = = D = C C A 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 = = ? = ? ? ? = = ? ? ? = = 0.88 = = = = = = = = = = = = ? ? = 1.00 = = = 1.00 = 0.89 = = = = = = = = = = = = ? ? = = = = = = = = ? = = = 0.92 = = 0.92 = = = = = 0.98 = = = = = = = 1.00 ? = ? ? = = = = = = = = = = = = = = = = = = ? = = = 1.00 = 1.00 1.00 1.00 1.00 = = = 0.99 = = = = = = = 0.98 ? = = = = = = = = = = = ? ? = = = = = = = = ? = = = = 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 = = = = = = = = = = = 0.86 = = = = = = = = = = = = = 0.80 = = = = = = = 0.99 ? = = = ? 1.00 = 1.00 = = = = = = 1.00 = = ? ? ? ? = ? = 1.00 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.92 ? = = = 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 = 0.85 ? = = = = = = = = = = = ? ? = = = = = = = 1.00 ? = 0.86 0.62 = = = = = = = = ? ? = = = = = ? = = = 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 = = = = = = = = = = = = ? = = = 0.98 = = 0.98 1.00 1.00 = = = = = = = = = = = 0.98 = = = = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = 0.85 ? = = = = = = = = = = = = 0.67 = = = = = = = 1.00 = = = = = = 1.00 = = ? = = = = = = = = = = = = ? = = = 1.00 = 1.00 1.00 0.99 0.99 = = = = = = = = = = = = ? = = = 1.00 = 1.00 1.00 = = = = ? = = 1.00 = = = 1.00 = 0.85 = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.96 = = = = = = = = 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 = = = = = = = 0.99 0.99 = = = 1.00 1.00 = = = = = = = = = = = = = = = = ? = = = = = = ? 1.00 1.00 = = = = = = = = = = = 0.99 = 0.69 = 0.69 = = = = = = = = = = = = = = = = = = ? = = = 1.00 = 1.00 1.00 = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = 0.99 = 0.57 ? = = = = = = = 0.85 0.85 = = ? = = 0.97 = = = = = 0.92 = = = = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = 0.85 ? = = = 1.00 = = = = = 1.00 1.00 1.00 = = = = = = = = 1.00 ? = 0.99 0.87 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 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 = = = = 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 = 0.85 = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 ? 1.00 ? ? ? = = = = = = = = = 0.96 ? = = = = = = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = 1.00 0.88 = = = ? = = = = = = = = = = = = = = ? = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = 0.96 = = ? = = 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 = = = = = = 0.88 0.88 = = = = = = = = = = = = ? = 0.71 0.81 = = = = 1.00 1.00 ? ? = = = = = = = = = = = = = = 1.00 = = 1.00 = = = = ? ? = = = = = = = 0.75 ? = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.96 = = = = = = = 0.91 = = ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 ? 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 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 = = = 0.88 = = = = = = = = = = 1.00 = = 1.00 = = 1.00 0.84 ? = = = 1.00 1.00 = = = = = = ? = = = = = = = = 0.65 = = = = 1.00 = 1.00 1.00 0.99 0.99 = = = = = = = = = = = = ? = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.96 = = = = = = = = 1.00 1.00 = = = = = = = = = = = 0.84 = = = = = 1.00 1.00 1.00 = = = = = = = = = = = 0.99 = = ? = = = 1.00 = 1.00 1.00 = = = = = = = 1.00 = = = 1.00 = 0.85 ? = = = 1.00 = 1.00 1.00 0.99 0.99 = = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = ? = = = = = = = = = 0.54 = = = 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 ? ? = = 0.96 = = 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 = = = = = = = = = = ? = = = = = = = = 0.89 = = = 1.00 0.94 0.94 = = = = = = = 0.96 = = = = = = = 0.87 ? = ? = = = = = = = = = = = = = = = = = = = = = = = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.96 ? = = = = = = = = = = = ? ? = = = = = = = = 1.00 = = = 1.00 = 1.00 1.00 1.00 1.00 = = = 0.96 = = = = = = = = ? = = = 1.00 = 1.00 1.00 1.00 1.00 = ? = 0.99 = = = = = = = 0.99 ? = = = 0.83 = = = = = = = ? ? = = = = = = = = ? = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.95 ? = = = = = = = 1.00 1.00 = = = = = = = = = = = 0.99 ? 0.69 = 0.69 1.00 = 1.00 1.00 0.99 0.99 = = = = = = = = = = = = ? = = = END PHASEPROBS