************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 actbx.phase.inp actbx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST actbx.phase.out_freqs : haplotype frequency estimates actbx.phase.out_pairs : most likely haplotype pairs for each individual actbx.phase.out_recom : estimates of recombination parameters actbx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 20 Positions of loci: 28 174 541 1078 2038 2044 2219 2323 2339 2451 2839 3800 4570 5054 5495 5813 5972 6244 6308 6732 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file actbx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 CIAGGICGCCCCGATGGCTT 4.000000 2 CIAGGICGCCCCGGTGACTT 1.000000 3 CIAGGICGCCCCGGTGGCTT 1.000000 4 CIAGGICGCCCTGGCGACTT 2.000000 5 CIAGGICTCTTCAACAGCTT 2.000000 6 CIAGTDCGCCCCGATGGCTT 1.000000 7 CIAGTDCGCCCCGGCAGCTC 1.000000 8 CIAGTDCGCTCCAACAGCTT 1.000000 9 CIAGTDCTCTTCAATAGCTT 1.000000 10 CIAGTDCTCTTCAACAGCTT 10.000000 11 CIAGTDCTCTTCAACAGCTC 8.000000 12 CIAGTDCTCTTCAGCAGCTT 1.000000 13 CIATGICGCCCTGGTGACTT 1.000000 14 CIGTGICGCCCTGGTGACTT 1.000000 15 CDAGGDCGCCCCGACAGCTT 1.000000 16 CDGTGICGCCCTGGTGACTT 86.000000 17 CDGTGICGCCCTGGTAACTT 2.000000 18 CDGTGITGCCCCGGTGACTT 19.000000 19 CDGTTDCTCTTCAACAGCTT 2.000000 20 TIAGGDCGTTCCAACAGCAT 1.000000 21 TIAGGDCGTTTCAACAGCTT 3.000000 22 TIAGGDCGTTTCAACAGCAT 2.000000 23 TIAGGDCGTTTCAACAGTAT 12.000000 24 TIAGTDCTCTTCAACAGCTT 17.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (16,24) P002: (18,18) P003: (4,4) P004: (19,21) P005: (10,24) P006: (16,16) P007: (16,16) P008: (16,16) P009: (16,17) P010: (10,16) P011: (23,24) P012: (1,24) P013: (16,23) P014: (16,18) P015: (16,18) P016: (16,16) P017: (16,24) P018: (18,22) P019: (16,23) P020: (23,24) P021: (16,18) P022: (16,16) P023: (10,24) P024: (16,16) P025: (18,19) P026: (10,16) P027: (21,21) P028: (12,16) P029: (6,24) P030: (10,16) P031: (16,16) P032: (15,16) P033: (16,17) P034: (10,16) P035: (16,16) P036: (16,16) P037: (16,24) P038: (3,20) P039: (16,23) P040: (11,16) P041: (16,24) P042: (16,18) P043: (16,23) P044: (16,23) P045: (16,16) P046: (16,16) P047: (16,18) P048: (13,16) P049: (16,16) P050: (11,16) P051: (23,24) P052: (16,24) P053: (16,24) P054: (10,16) P055: (2,10) P056: (11,22) P057: (8,18) P058: (16,16) P059: (1,11) P060: (16,24) P061: (11,16) P062: (16,18) P063: (9,10) P064: (11,18) P065: (16,18) P066: (16,16) P067: (16,16) P068: (16,23) P069: (5,23) P070: (16,16) P071: (16,18) P072: (16,24) P073: (18,24) P074: (16,18) P075: (16,16) P076: (14,16) P077: (16,16) P078: (5,24) P079: (11,16) P080: (11,18) P081: (16,16) P082: (7,16) P083: (16,16) P084: (1,16) P085: (16,16) P086: (16,16) P087: (16,16) P088: (1,18) P089: (10,18) P090: (23,23) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 C D G T G I C G C C C T G G T G A C T T [T] I A G T D C T C T T C A A C A G C T T 0 P002 C D G T G I T G C C C C G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P003 C I A G G I C G C C C T G G C G A C T T C I A G G I C G C C C T G G C G A C T T 0 P004 C D G T (T) D C (T) (C) T T C A A C A G C T T T I A G (G) D C (G) (T) T T C A A C A G C [T] T 0 P005 [C] I A G T D C T C T T C A A C A G C T T [T] I A G T D C T C T T C A A C A G C T T 0 P006 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P007 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P008 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P009 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T A A C T T 0 P010 C I A G T D C T C T T C A A C A G C T [T] C D G T G I C G C C C T G G T G A C T T 0 P011 T I A G G D C G T T T C A A C A G T A T T I A G T D C T C T T C A A C A G C T T 0 P012 C I A G G I C G C C C C G A T G G C T T T I A G T D C T C T T C A A C A G C T T 0 P013 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P014 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P015 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P016 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P017 C D G T G I C G C C C T G G T G A C T T T I A G T D C T C T T C A A C A G C T T 0 P018 C D G T G I T G C C C C G G T G A C T T T I A G G D C G T T T C A A C A G C A T 0 P019 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P020 T I A G G D C G T T T C A A C A G T A T T I A G T D C T C T T C A A C A G C T T 0 P021 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P022 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P023 C I A G T D C T C T T C A A C A G C T [T] T I A G T D C T C T T C A A C A G C T T 0 P024 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P025 C D G T G I T G C C C C G G T G A C T T C D G T [T] [D] C T C T T C A A C A G C T T 0 P026 C I A G T D C T C T T C A A C A G C T T C D G T G I C G C C C T G G T G A C T T 0 P027 T I A G G D C G T T T C A A C A G C T T T I A G G D C G T T T C A A C A G C T T 0 P028 C I A G T D C T C T T C A G C A G C T T C D G T G I C G C C C T G G T G A C T T 0 P029 [C] I A G T D C G C C C C G A T G G C T T [T] I A G T D C T C T T C A A C A G C T T 0 P030 C I A G T D C T C T T C A A C A G C T T C D G T G I C G C C C T G G T G A C T T 0 P031 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P032 C D A G G (D) C G C C C C G A C A G C T T C D G T G (I) C G C C C T G G T G A C T T 0 P033 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T A A C T T 0 P034 C I A G T D C T C T T C A A C A G C T T C D G T G I C G C C C T G G T G A C T T 0 P035 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P036 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P037 C D G T G I C G C C C T G G T G A C T T [T] I A G T D C T C T T C A A C A G C T T 0 P038 C I A G G I C G C C C C G G T G G C T T T I A G G D C G T T C C A A C A G C A T 0 P039 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P040 C I A G T D C T C T T C A A C A G C T C C D G T G I C G C C C T G G T G A C T T 0 P041 C D G T G I C G C C C T G G T G A C T T T I A G T D C T C T T C A A C A G C T T 0 P042 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P043 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P044 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P045 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P046 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P047 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P048 C I A T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P049 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P050 C I A G T D C T C T T C A A C A G C T C C D G T G I C G C C C T G G T G A C T T 0 P051 T I A G G D C G T T T C A A C A G T A T T I A G T D C T C T T C A A C A G C T T 0 P052 C D G T G I C G C C C T G G T G A C T T [T] I A G T D C T C T T C A A C A G C T T 0 P053 C D G T G I C G C C C T G G T G A C T T [T] I A G T D C T C T T C A A C A G C T T 0 P054 C I A G T D C T C T T C A A C A G C T T C D G T G I C G C C C T G G T G A C T T 0 P055 C I A G (G) (I) C G C C C C G G T G A C T T C I A G (T) (D) C T C T T C A A C A G C T T 0 P056 C I A G T D C T C T T C A A C A G C T C T I A G G D C G T T T C A A C A G C A T 0 P057 C I A G [T] [D] C G C (T) C C A A C A G C T T C D G T G I T G C (C) C C G G T G A C T T 0 P058 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P059 C I A G G I C G C C C C G A T G G C T T C I A G T D C T C T T C A A C A G C T C 0 P060 C D G T G I C G C C C T G G T G A C T T T I A G T D C T C T T C A A C A G C T T 0 P061 C I A G T D C T C T T C A A C A G C T C C D G T G I C G C C C T G G T G A C T T 0 P062 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P063 C I A G T D C T C T T C A A T A G C T T C I A G T D C T C T T C A A C A G C T T 0 P064 C I A G T D C T C T T C A A C A G C T C C D G T G I T G C C C C G G T G A C T T 0 P065 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P066 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P067 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P068 C D G T G I C G C C C T G G T G A C T T T I A G G D C G T T T C A A C A G T A T 0 P069 C I A G G I C T C T T C A A C A G C T T T I A G G D C G T T T C A A C A G T A T 0 P070 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P071 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P072 C D G T G I C G C C C T G G T G A C T T T I A G T D C T C T T C A A C A G C T T 0 P073 C D G T G I T G C C C C G G T G A C T T T I A G T D C T C T T C A A C A G C T T 0 P074 C D G T G I C G C C C T G G T G A C T T C D G T G I T G C C C C G G T G A C T T 0 P075 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P076 C I G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P077 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P078 (C) I A G G I C T C T T C A A C A G C T T (T) I A G T D C T C T T C A A C A G C T T 0 P079 C I A G T D C T C T T C A A C A G C T C C D G T G I C G C C C T G G T G A C T T 0 P080 C I A G T D C T C T T C A A C A G C T C C D G T G I T G C C C C G G T G A C T T 0 P081 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P082 C I A G T D C G C C C C G G (C) (A) (G) C T (C) C D G T G I C G C C C T G G (T) (G) (A) C T (T) 0 P083 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P084 C I A G G I C G C C C C G A T G G C T T C D G T G I C G C C C T G G T G A C T T 0 P085 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P086 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P087 C D G T G I C G C C C T G G T G A C T T C D G T G I C G C C C T G G T G A C T T 0 P088 C I A G G I C G C C C C G A T G G C T T C D G T G I T G C C C C G G T G A C T T 0 P089 C I A G T D C T C T T C A A C A G C T T C D G T G I T G C C C C G G T G A C T T 0 P090 T I A G G D C G T T T C A A C A G T A T T I A G G D C G T T T C A A C A G T A 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 ? D G T G I = G = ? ? T ? G ? ? ? ? = = ? I A G T D = T = ? ? C ? A ? ? ? ? = = 0 P002 = = = = = = = = = = = = ? = = = ? ? ? = = = = = = = = = = = = = ? = = = ? ? ? = 0 P003 = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = ? = = ? ? = = = = = = 0 P004 C D G T (T) = = (T) (C) = = = ? = = = = = ? = T I A G (G) = = (G) (T) = = = ? = = = = = ? = 0 P005 ? ? = = = = = = = = = = ? = = = = = ? = ? ? = = = = = = = = = = ? = = = = = ? = 0 P006 = = = = = = = = = = = = ? = = ? ? = = = = = = = = = = = = = = = ? = = ? ? = = = 0 P007 ? = = = = = = ? = ? = = ? = = = = = = = ? = = = = = = ? = ? = = ? = = = = = = = 0 P008 ? = = = ? ? = = = = ? = ? = ? ? = = = = ? = = = ? ? = = = = ? = ? = ? ? = = = = 0 P009 ? = = = = = = = = = = = ? = = G = = = = ? = = = = = = = = = = = ? = = A = = = = 0 P010 = I A G T D = T = T T C A A C A G = = ? = D G T G I = G = C C T G G T G A = = ? 0 P011 = = = = G = = G T = = = ? = = = = T A = = = = = T = = T C = = = ? = = = = C T = 0 P012 C = = = G I = G = C C = ? = T G = = ? ? T = = = T D = T = T T = ? = C A = = ? ? 0 P013 ? ? ? T = I = = C C C T G G T G A C ? = ? ? ? G = D = = T T T C A A C A G T ? = 0 P014 = = = = = = C = = ? = T ? = = = = = ? = = = = = = = T = = ? = C ? = = = = = ? = 0 P015 = = = = = = C = = = = T = = = = = = = = = = = = = = T = = = = C = = = = = = = = 0 P016 ? = = = = = = = = = = = = ? = = = = = = ? = = = = = = = = = = = = ? = = = = = = 0 P017 C D G T ? ? = G = C C T ? G T G A = = = T I A G ? ? = T = T T C ? A C A G = = = 0 P018 C D G T = I T = C C C = ? G T G A = T = T I A G = D C = T T T = ? A C A G = A = 0 P019 C D G T = I = = C C C T G G T G A C T = T I A G = D = = T T T C A A C A G T A = 0 P020 = = = = G = = G T = = = = = = = = T A ? = = = = T = = T C = = = = = = = = C T ? 0 P021 ? ? ? = = = C = = = = T = = = = = = = = ? ? ? = = = T = = = = C = = = = = = = = 0 P022 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 C = = = = = = = = = = = = = = = = = = ? T = = = = = = = = = = = = = = = = = = ? 0 P024 = = = = = = = ? = = = = ? = = = = = = = = = = = = = = ? = = = = ? = = = = = = = 0 P025 ? = = = ? ? T G = C C = G G T G A = = = ? = = = ? ? C T = T T = A A C A G = = = 0 P026 = I A G T D = T = T T C A A C A G = = = = D G T G I = G = C C T G G T G A = = = 0 P027 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P028 = I A G T D = T = T T C ? = ? A G = = = = D G T G I = G = C C T ? = ? G A = = = 0 P029 ? ? ? = = = = G = C C = G = T G = = = = ? ? ? = = = = T = T T = A = C A = = = = 0 P030 = I A G T D = T = T T C ? A C A G = = = = D G T G I = G = C C T ? G T G A = = = 0 P031 ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0 P032 ? = A G = (D) = = = = = C = A C A G = = = ? = G T = (I) = = = = = T = G T G A = = = 0 P033 ? = = = ? ? = = = = = = ? = = G = = = = ? = = = ? ? = = = = = = ? = = A = = = = 0 P034 = I A G T D = T = T T C A A C A G = = = = D G T G I = G = C C T G G T G A = = = 0 P035 = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = ? ? ? ? 0 P036 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P037 ? ? ? T G I = G = C C T G G T G A = = = ? ? ? G T D = T = T T C A A C A G = = = 0 P038 C = = = = I = = C C = = G G T G = = T = T = = = = D = = T T = = A A C A = = A = 0 P039 ? ? ? T = I = = C C C T G G T G A C T = ? ? ? G = D = = T T T C A A C A G T A = 0 P040 = I A G T D = T = T T C ? A C A G = = C = D G T G I = G = C C T ? G T G A = = T 0 P041 C D G T ? ? = G = ? C T G G T G A = = ? T I A G ? ? = T = ? T C A A C A G = = ? 0 P042 = = = = = = C = = = = T = = = = ? ? ? ? = = = = = = T = = = = C = = = = ? ? ? ? 0 P043 C D G T = I = = C C C T G G T G A C T ? T I A G = D = = T T T C A A C A G T A ? 0 P044 C D G T = I = = C C C T G G T G A C T ? T I A G = D = = T T T C A A C A G T A ? 0 P045 ? ? ? = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = = = = = = = = = = = ? ? ? ? 0 P046 = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = ? ? ? ? 0 P047 ? ? ? = = = C = = = = T = = = = = = = ? ? ? ? = = = T = = = = C = = = = = = = ? 0 P048 = I A = = = = = = = = = ? = = = ? ? ? ? = D G = = = = = = = = = ? = = = ? ? ? ? 0 P049 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P050 = I A G T D = T = T T C ? A C A G = = C = D G T G I = G = C C T ? G T G A = = T 0 P051 = = = = G = = G T = = = = = = = = T A = = = = = T = = T C = = = = = = = = C T = 0 P052 ? D G T G I = G = C C T G G ? G A = = = ? I A G T D = T = T T C A A ? A G = = = 0 P053 ? ? ? T G I = G = C C T ? G ? G A = ? = ? ? ? G T D = T = T T C ? A ? A G = ? = 0 P054 = I A G T D = T = T T C ? A C A G = = = = D G T G I = G = C C T ? G T G A = = = 0 P055 = = = = (G) (I) = G = C C = ? G T G A = = = = = = = (T) (D) = T = T T = ? A C A G = = = 0 P056 C = = = T = = T C = = = ? = = = = = T C T = = = G = = G T = = = ? = = = = = A T 0 P057 = I A G ? ? C = = (T) = = A A C A G = = = = D G T ? ? T = = (C) = = G G T G A = = = 0 P058 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P059 = = = = G I = G = C C = G = T G = = = T = = = = T D = T = T T = A = C A = = = C 0 P060 C D G T G I = G = C C T ? G T G A = = = T I A G T D = T = T T C ? A C A G = = = 0 P061 ? ? ? G T D = T = T T C ? A C A G = = C ? ? ? T G I = G = C C T ? G T G A = = T 0 P062 = = = = = = C = = = = T = = = = = = = = = = = = = = T = = = = C = = = = = = = = 0 P063 = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = C = = = = = 0 P064 = I A G T D C T = T ? = ? A C A G = = C = D G T G I T G = C ? = ? G T G A = = T 0 P065 = = = = = = C = = = = T ? = = = = = = = = = = = = = T = = = = C ? = = = = = = = 0 P066 = = = = = = = = = = = = ? = = = ? ? ? ? = = = = = = = = = = = = ? = = = ? ? ? ? 0 P067 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P068 C D G T = I = = C C C T ? G T G A C T = T I A G = D = = T T T C ? A C A G T A = 0 P069 ? ? ? = = I = T C = = = = = = = = C T = ? ? ? = = D = G T = = = = = = = = T A = 0 P070 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 P071 = = = = = = C = = = = T ? = = = = = = = = = = = = = T = = = = C ? = = = = = = = 0 P072 C D G T G I = G = C C T ? G T G ? = ? = T I A G T D = T = T T C ? A C A ? = ? = 0 P073 C D G T G I T G = C C = ? G ? G A = = = T I A G T D C T = T T = ? A ? A G = = = 0 P074 = = = = = = C = = = = T ? = ? = = = = = = = = = = = T = = = = C ? = ? = = = = = 0 P075 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 P076 = I = = = = = = = = = = ? = = = = = = = = D = = = = = = = = = = ? = = = = = = = 0 P077 ? ? ? = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = 0 P078 (C) = = = G I = = = = = = = = = = = = = = (T) = = = T D = = = = = = = = = = = = = = 0 P079 = I A G T D = ? = T T C ? A C A G = = C = D G T G I = ? = C C T ? G T G A = = T 0 P080 = I A G T D C T = T T = ? A C A ? = = C = D G T G I T G = C C = ? G T G ? = = T 0 P081 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P082 = I A G T D = = = = = C ? = (C) (A) (G) = = (C) = D G T G I = = = = = T ? = (T) (G) (A) = = (T) 0 P083 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 P084 = I A G = = = = = = = C = A = = G = = = = D G T = = = = = = = T = G = = A = = = 0 P085 ? ? ? = = = = = = = = = ? = = = = = = = ? ? ? = = = = = = = = = ? = = = = = = = 0 P086 = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = ? = = = ? = = = 0 P087 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P088 = I A G = = C = = = = = ? A = = G = = = = D G T = = T = = = = = ? G = = A = = = 0 P089 = I A G T D C T = T T = ? A C ? G = = = = D G T G I T G = C C = ? G T ? A = = = 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 0.78 = = 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 1.00 1.00 = = ? = = = = 1.00 = = 1.00 1.00 = = = ? = = = = 1.00 1.00 = 0.98 = = = 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 = = = = 1.00 = = = = = = = = ? = = = = = = = = = = = = ? = = = = = = 1.00 1.00 1.00 1.00 ? ? = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 1.00 = = = = = = = = 1.00 1.00 ? ? ? ? = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = ? = = = = = = = ? = = = = ? = = = = = = = ? = = = ? ? 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? = ? 1.00 1.00 = = = ? ? ? = = = = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = = ? = = = = = = = = = = = = = = = = = = = ? = 1.00 1.00 = 0.75 = = = = = 1.00 = 1.00 0.96 0.92 1.00 = = = ? = = = ? ? = = = = = = ? = = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = ? ? ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = = 1.00 = ? ? ? 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 ? ? = 1.00 = ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = ? = = = = = = 1.00 = = = = 1.00 = = = = ? ? ? ? 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? ? ? ? = = = = = = = = = = = = = ? ? ? ? = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = 1.00 = = = = 1.00 = = = = = = = ? = 0.96 1.00 = = = = = = = = = ? = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 = = = = 1.00 = = 1.00 1.00 = = = = = = = = 1.00 1.00 = ? 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 = = = ? ? ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 ? 1.00 1.00 = ? = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = = = = = = 0.66 0.66 = 0.99 = 0.99 0.99 = ? 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 = = 0.80 = = 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = = ? ? ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? = ? 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = 1.00 = = = = 1.00 ? = = = = = = = = = = = = = = = = = = = ? = = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = ? ? ? = = 1.00 = 1.00 1.00 = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = 1.00 = = = = 1.00 ? = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 1.00 ? = ? = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? 1.00 ? 1.00 1.00 = = = = = = = = = 1.00 = = = = 1.00 ? = ? = = = = = = = = = = = = = = = = = ? = = = = = = = = 1.00 = = = = = = = = = = ? = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = 0.80 = = = 1.00 1.00 = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = ? = 1.00 1.00 1.00 ? 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? 1.00 1.00 1.00 ? = = 1.00 = = = = = = = = = = = = = = = = = = = = = 0.99 0.99 0.99 0.99 0.99 = = = = = 0.99 ? = 0.55 0.55 0.55 = = 0.55 = = = = = = = = = = = = ? = = = = = = = = 1.00 1.00 1.00 = = = = = = = 1.00 = 1.00 = = 1.00 = = = ? ? ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 = = 1.00 = = = = = ? 1.00 = = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = ? 1.00 1.00 ? 1.00 = = = = = = = = = = ? = = = = ? = = = = = = = END PHASEPROBS