************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 mybpc.phase.inp mybpc.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST mybpc.phase.out_freqs : haplotype frequency estimates mybpc.phase.out_pairs : most likely haplotype pairs for each individual mybpc.phase.out_recom : estimates of recombination parameters mybpc.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 90 Number of Loci: 44 Positions of loci: 113 328 664 763 1024 1219 1289 2420 3839 4373 4731 5259 6175 6773 8845 10121 10940 11017 11202 12931 13001 13751 13877 14359 14378 14427 15132 15804 16163 16510 16750 17219 18181 18800 19046 19346 21429 22148 22318 22719 23808 24079 24133 24457 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file mybpc.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DTCITTGCGDDTACGCTCGTCCCGTIAACGICGCCTGCGCCGIC 1.000000 2 DTCITTGCGDDTACACTCGCAGTACDGGCGICACTAATGTTADC 2.000000 3 DTCITTGCGDDGACGCTTGCACCGCIGACTICGCCTGCGCCGIC 33.000000 4 DTCITTGCGDDGACGCTTGCACCGCIGACTICGCCAGCGCCGIC 2.000000 5 DTCITTGCGDDGACGCTTGCACCGCIGACGICACTAATGTTADC 1.000000 6 DTCITTGCGDDGACGCTTGCAGCGCIGACTICGCCTGCGCCGIC 1.000000 7 DTCITTGCGDDGACGCCCGCACCGCIGGGGDTGTCAACGCTGIT 1.000000 8 DTCITTGCGDITACGCCCGCACCGCIGGCGICGCTAACGTTGDC 2.000000 9 DTCITTGCGDITACACTCGCAGTACDGGCGICACTAATGTTADC 2.000000 10 DTCITTGCGIITACGCCCGCACCGCIGGGGDTGTCAACGCTGIT 1.000000 11 DTCITTGCCIITACACTCGCAGTACDGGCGICACTAATGTTADC 1.000000 12 DCCITTGCGDDGACGCTTGCACCGCIGACTICGCCTGCGCCGIC 4.000000 13 DCCITTGCGDDGACGCTTGCACCGCIGACTICGCCTGCGCCGIT 1.000000 14 DCCITTGCGDDGACGCTTGCACCGCIGGCGICGCCAACGCTGIT 1.000000 15 DCCITTGCGDDGACGCTTGCAGTACDGGCGICACTAATGTTADC 1.000000 16 DCCITTGCGDDGACGCTTGCAGCACDGGCGICACTAATGTTADC 1.000000 17 DCCITTGCGDDGACGCTCGCACCGCIGACGICGCCTGCGCCGIC 1.000000 18 ITCICTGCCIITACACTCGCAGTACDGGCGICACTAATGTTADC 1.000000 19 ITCDCCCCCIITACGCTCGCACCGCIGGGGDCGCCAGCACCGIC 3.000000 20 ITCDCCCCCIITACGCTCGCAGTACDGGCGICACTAATGTTADC 5.000000 21 ITCDCCCCCIITACGCTCGCCCCGTIAACGICGCCTGCGCCGIC 6.000000 22 ITCDCCCCCIITACGCCCGCACCGCIGGGGDTGCCAACGCTGIT 1.000000 23 ITCDCCCCCIITACGCCCGCACCGCIGGGGDTGTCAACGCTGIT 1.000000 24 ITCDCCCCCIITACACTCGCAGTACDGGCGICACTAATGTTADC 27.000000 25 ITCDCCCCCIITACACTCGCAGTACDGGCGICGCCTGCGCCGIC 1.000000 26 ITCDCCCCCIITATGCTCGCAGTACDGGCGICACTAATGTTADC 1.000000 27 ITCDCCCCCIITGCGCTCGCACCGCIGGCGICGCTAACGTTGDC 1.000000 28 ITCDCCCCCIITGCGATTGCACCGTIGACGICGCCTGCGCCGIC 1.000000 29 ITCDCCGCCDDTACGCTTGCACCGCIGACTICGCCTGCGCCGIC 1.000000 30 ITCDCCGCCDDTACGCTTGTCCCGTIAACGICGCCTGCGCCGIC 1.000000 31 ITCDCCGCCDDTACGCTCGTACCGTIAACGICGCCTGCGCCGIC 1.000000 32 ITCDCCGCCDDTACGCTCGTCCCGTIAACGICGCCTGCGCCGIC 23.000000 33 ITCDCCGCCDDTACGCTCGTCCCGTIAACGICGCCTGCGCCGDT 1.000000 34 ITCDCCGCCDDTACGCCCGCACCGCIGGGGDTGCCAACGCTGIT 1.000000 35 ITCDCCGCCDDTACGCCCGCACCGCIGGGGDTGTCAACGCTGIT 4.000000 36 ITCDCCGCCDDTACACTCGCAGTACDGGCGICACTAATGTTADC 10.000000 37 ITCDCCGCCDDTATGACCACACCGCIGGCGICGCCAACACTGIT 1.000000 38 ITCDCCGCCDDGACACTCGCAGTACDGGCGICACTAATGTTADC 1.000000 39 ITCDCCGCCIITACGCTCGCAGTACDGGCGICACTAATGTTADC 4.000000 40 ITCDCCGGGDDTACGCCCGCACCGCIGGGGDCGTCAATGTTADC 2.000000 41 ITCDCCGGCIDTACGCTCGCACCGCIGGCGICGCTAACGTTGDC 2.000000 42 ITCDCCGGCIDGACGCTCGCCCCGTIAACGICGCCTGCGCCGIC 4.000000 43 ITCDCCGGCIITACGCTCGCAGTACDGGCGICACTAATGTTADC 1.000000 44 ITTDCCGCCIDGACGCTTGCACCGCIGACTICGCCTGCGCCGIC 1.000000 45 ITTDCCGCCIITACGCTCGCAGTACDGGCGICACTAATGTTADC 2.000000 46 ITTDCCGCCIITGTGACCACACCGCIGGCGICGCCTGCGCCGIC 3.000000 47 ITTDCCGCCIITGTGACCACACCGCIGGCGICGCCAACGCTGIT 8.000000 48 ITTDCCGCCIITGTGACCACACCGCIGGCGICGCCAACACTGIT 4.000000 49 ITTDCCGCCIITGTGACCACAGCGCIGGCGICGCCAACACTGIT 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY P001: (3,3) P002: (36,36) P003: (3,42) P004: (19,19) P005: (24,31) P006: (3,14) P007: (9,29) P008: (3,24) P009: (32,32) P010: (3,12) P011: (21,39) P012: (24,46) P013: (24,42) P014: (35,36) P015: (32,32) P016: (3,24) P017: (3,48) P018: (3,24) P019: (11,24) P020: (24,32) P021: (21,39) P022: (3,3) P023: (3,24) P024: (3,24) P025: (35,44) P026: (3,24) P027: (16,32) P028: (47,48) P029: (21,10) P030: (7,21) P031: (3,9) P032: (20,28) P033: (32,32) P034: (24,42) P035: (3,48) P036: (24,37) P037: (3,24) P038: (8,40) P039: (3,12) P040: (32,32) P041: (3,19) P042: (8,20) P043: (2,47) P044: (22,32) P045: (35,35) P046: (15,24) P047: (36,47) P048: (32,46) P049: (3,18) P050: (47,49) P051: (3,24) P052: (1,3) P053: (3,17) P054: (3,47) P055: (24,36) P056: (39,48) P057: (20,39) P058: (34,46) P059: (21,45) P060: (3,32) P061: (21,45) P062: (32,32) P063: (3,24) P064: (26,42) P065: (23,27) P066: (24,32) P067: (5,24) P068: (3,24) P069: (3,24) P070: (3,38) P071: (24,36) P072: (3,32) P073: (32,33) P074: (32,47) P075: (36,36) P076: (6,24) P077: (3,12) P078: (3,32) P079: (2,24) P080: (41,43) P081: (13,36) P082: (24,47) P083: (4,32) P084: (3,12) P085: (32,36) P086: (4,32) P087: (30,41) P088: (20,40) P089: (20,47) P090: (24,25) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 P001 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P002 I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P003 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C G G C I D G A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C 0 P004 I T C D C C C C C I I T A C G C T C G C A C C G C I G G G G D C G C C A G C A C C G I C I T C D C C C C C I I T A C G C T C G C A C C G C I G G G G D C G C C A G C A C C G I C 0 P005 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C G C T C G T A C C G T I A A C G I C G C C T G C G C C G I C 0 P006 D (T) C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D (C) C I T T G C G D D G A C G C T T G C A C C G C I G G C G I C G C C A A C G C T G I T 0 P007 (D) T C (I) (T) (T) G C (G) D (I) T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C (I) T C (D) (C) (C) G C (C) D (D) T A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P008 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P009 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P010 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D C C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P011 I T C D C C (C) C C I I T A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C (G) C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P012 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C T G C G C C G I C 0 P013 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G G C I D G A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C 0 P014 I T C D C C G C C D D T A C G C C C G C A C C G C I G G G G D T G T C A A C G C T G I T I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P015 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P016 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P017 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C A C T G I T 0 P018 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P019 D T C I [T] T G C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P020 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P021 I T C D C C C C C I I T A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P022 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P023 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P024 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P025 I T C D C C G C C D D T A C G C C C G C A C C G C I G G G G D T G T C A A C G C T G I T I T T D C C G C C I D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P026 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P027 D C C I T T G C G D D G A C G C T T G C A G C A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P028 I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C A C T G I T 0 P029 (I) T C (D) (C) (C) (C) C (C) I I T A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C (D) T C (I) (T) (T) (G) C (G) I I T A C G C [C] C G C A C C G C I G G G G D T G T C A A C G C T G I T 0 P030 (D) T C (I) (T) (T) (G) C (G) (D) (D) (G) A C G C C C G C A C C G C I G G G G D T G T C A A C G C T G I T (I) T C (D) (C) (C) (C) C (C) (I) (I) (T) A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C 0 P031 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D T C I T T G C G D I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P032 I T C D C C C C C I I T (A) C G (C) T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C C C C I I T (G) C G (A) T T G C A C C G T I G A C G I C G C C T G C G C C G I C 0 P033 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P034 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G G C I D G A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C 0 P035 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C A C T G I T 0 P036 I T C D C C (C) C C (I) (I) T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C (G) C C (D) (D) T [A] [T] G A C C A C A C C G C I G G C G I C G C C A A C A C T G I T 0 P037 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P038 D T C I T T G C G D I T A C G C C C G C A C C G C I G G C G I C G C T A A C G T T G D C I T C D C C G G G D D T A C G C C C G C A C C G C I G G G G D C G T C A A T G T T A D C 0 P039 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D C C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P040 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P041 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C G C T C G C A C C G C I G G G G D C G C C A G C A C C G I C 0 P042 D T C I T T G C G D I T A C G C C C G C A C C G C I G G C G I C G C T A A C G T T G D C I T C D C C C C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P043 D T C I T T G C G D D [T] A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T [T] D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P044 I T C D C C (C) C C (I) (I) T A C G C C C G C A C C G C I G G G G D T G C C A A C G C T G I T I T C D C C (G) C C (D) (D) T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P045 I T C D C C G C C D D T A C G C C C G C A C C G C I G G G G D T G T C A A C G C T G I T I T C D C C G C C D D T A C G C C C G C A C C G C I G G G G D T G T C A A C G C T G I T 0 P046 D C C I T T G C G D D G A C G C T T G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P047 I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P048 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C T G C G C C G I C 0 P049 (D) T C I (T) T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C (I) T C I (C) T G C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P050 I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T I T T D C C G C C I I T G T G A C C A C A G C G C I G G C G I C G C C A A C A C T G I T 0 P051 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P052 D T C I T T G C [G] D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P053 D (T) C I T T G C G D D G A C G C T (T) G C A C C G C I G A C (T) I C G C C T G C G C C G I C D (C) C I T T G C G D D G A C G C T (C) G C A C C G C I G A C (G) I C G C C T G C G C C G I C 0 P054 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P055 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P056 I T C D C C G C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C A C T G I T 0 P057 I T C D C C C C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P058 I T C D C C G C C D D T A C G C C C G C A C C G C I G G G G D T G C C A A C G C T G I T I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C T G C G C C G I C 0 P059 I T (C) D C C (C) C C I I T A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C I T (T) D C C (G) C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P060 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P061 I T (C) D C C (C) C C I I T A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C I T (T) D C C (G) C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P062 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P063 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P064 I T C D C C [C] C C I I T A T G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G G C I D G A C G C T C G C C C C G T I A A C G I C G C C T G C G C C G I C 0 P065 I T C D C C C C C I I T (A) C G C (C) C G C A C C G C I G G G G D T G T C A A C G C T G I T I T C D C C C C C I I T (G) C G C (T) C G C A C C G C I G G C G I C G C T A A C G T T G D C 0 P066 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P067 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C G I C A C T A A T G T T A D C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P068 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P069 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P070 (D) T C (I) (T) (T) G C (G) D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C (I) T C (D) (C) (C) G C (C) D D G A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P071 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P072 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P073 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G (I) C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C [C] G (D) T 0 P074 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P075 I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P076 D T C I T T G C G D D G A C G C T T G C A G C G C I G A C T I C G C C T G C G C C G I C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P077 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D C C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P078 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C 0 P079 D T C I T T G C G D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P080 I T C D C C G G C I D T A C G C T C G C A C C G C I G G C G I C G C T A A C G T T G D C I T C D C C G G C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P081 D C C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C [C] G I (T) I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D (C) 0 P082 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P083 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C (A) G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C (T) G C G C C G I C 0 P084 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C D C C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C T G C G C C G I C 0 P085 I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G C C D D T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C 0 P086 D T C I T T G C G D D G A C G C T T G C A C C G C I G A C T I C G C C (A) G C G C C G I C I T C D C C G C C D D T A C G C T C G T C C C G T I A A C G I C G C C (T) G C G C C G I C 0 P087 I T C D C C G C C D D T A C G C T (T) G T C C C G T I A A C G I C G C C T G C G C C G I C I T C D C C G G C I D T A C G C T (C) G C A C C G C I G G C G I C G C T A A C G T T G D C 0 P088 I T C D C C C C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C G G G D D T A C G C C C G C A C C G C I G G G G D C G T C A A T G T T A D C 0 P089 I T C D C C [C] C C I I T A C G C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T T D C C G C C I I T G T G A C C A C A C C G C I G G C G I C G C C A A C G C T G I T 0 P090 I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C A C T A A T G T T A D C I T C D C C C C C I I T A C A C T C G C A G T A C D G G C G I C [G] C C T G C G C C G I C 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 D = ? ? ? ? ? C G ? = = = = = = = ? = = A ? ? = C = G = = T = = = = = = = = = = = = = = I = ? ? ? ? ? G C ? = = = = = = = ? = = C ? ? = T = A = = G = = = = = = = = = = = = = = 0 P004 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P005 = = = = = = C = = ? I = ? ? A = = = = C = G T A C D G G = = = = A = T A A T = T T A D = = = = = = = G = = ? D = ? ? G = = = = T = C C G T I A A = = = = G = C T G C = C C G I = 0 P006 = (T) ? ? ? ? ? = = = = = ? ? = = = = = = = = = = = = = A = T = = = = = T G ? = = C = = C = (C) ? ? ? ? ? = = = = = ? ? = = = = = = = = = = = = = G = G = = = = = A A ? = = T = = T 0 P007 (D) = = (I) (T) (T) = = (G) = (I) = = = A ? ? C = = = ? ? A = D = G = G = = A = T A A ? = ? T A D = (I) = = (D) (C) (C) = = (C) = (D) = = = G ? ? T = = = ? ? G = I = A = T = = G = C T G ? = ? C G I = 0 P008 D = ? ? ? ? ? = G D D G = ? G = = T = = = C ? G = ? = A = T = = G = C T G C = C C G I = I = ? ? ? ? ? = C I I T = ? A = = C = = = G ? A = ? = G = G = = A = T A A T = T T A D = 0 P009 = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? 0 P010 = T = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = 0 P011 = = = = = = (C) = = = = = = = = = = = = = C C C G T I A A = = = = G = C T G C = C C G I = = = = = = = (G) = = = = = = = = = = = = = A G T A C D G G = = = = A = T A A T = T T A D = 0 P012 = = C = = = C = = = = = A C A C T = G = = G T A = D = = = = = = A = T A ? T = T ? A D = = = T = = = G = = = = = G T G A C = A = = C C G = I = = = = = = G = C T ? C = C ? G I = 0 P013 = = = = = = C C = = I T = = A = = = = = A G T A C D G G = = = = A = T A A T = T T A D = = = = = = = G G = = D G = = G = = = = = C C C G T I A A = = = = G = C T G C = C C G I = 0 P014 = = = = = = = = = = = ? = = G = C = = ? ? C C G = I ? ? G = ? T ? T C = = C = C = G I T = = = = = = = = = = = ? = = A = T = = ? ? G T A = D ? ? C = ? C ? C T = = T = T = A D C 0 P015 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 P016 D = = I T T G = G D D G = = G = = T = = = C C G = I = A = T = = G = C ? G ? = C C G I = I = = D C C C = C I I T = = A = = C = = = G T A = D = G = G = = A = T ? A ? = T T A D = 0 P017 ? ? C I ? T = = G ? ? ? A C = C T T G = = = = = = = = A = T = = = = = T G = G = ? ? ? ? ? ? T D ? C = = C ? ? ? G T = A C C A = = = = = = = = G = G = = = = = A A = A = ? ? ? ? 0 P018 D = = I T T G = G D D G = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I T = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P019 D = = I ? T G = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = = D ? C C = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P020 = = = = = = C = ? ? I = = = A = = = = C A G T ? ? ? G G = = = = A = T A A ? = T T A D = = = = = = = G = ? ? D = = = G = = = = T C C C ? ? ? A A = = = = G = C T G ? = C C G I = 0 P021 = = = = = = C = = = = = = = = = = = = = C C C G T I ? A = = = = G ? ? ? G C = C C G I = = = = = = = G = = = = = = = = = = = = = A G T A C D ? G = = = = A ? ? ? A T = T T A D = 0 P022 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P023 D = = I T T G = G D D ? = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I ? = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P024 D = = I T T G = G D D G = = G ? ? T = = = C C G = I = A = T = = G = C ? G C = C C G I = I = = D C C C = C I I T = = A ? ? C = = = G T A = D = G = G = = A = T ? A T = T T A D = 0 P025 = = C = = = = = ? D = ? = = = = C C = = = = = = = = = G G G D T = T = A A = = = ? ? ? ? = = T = = = = = ? I = ? = = = = T T = = = = = = = = = A C T I C = C = T G = = = ? ? ? ? 0 P026 D = = I T T G = G D D ? = = G = = T = = = C C G = I = A = T = = G ? C T G C = C C G I = I = = D C C C = C I I ? = = A = = C = = = G T A = D = G = G = = A ? T A A T = T T A D = 0 P027 D C = I T T = = G = = G = = = = = T = C A G = A C D G G = = = = A ? T A A T = T T A D = I T = D C C = = C = = T = = = = = C = T C C = G T I A A = = = = G ? C T G C = C C G I = 0 P028 = = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = = = = A = = = = = 0 P029 (I) = = (D) (C) (C) (C) = (C) = = = = = = ? ? = = = C = = = T = A A C = I C = C = T G = = = C = = C (D) = = (I) (T) (T) (G) = (G) = = = = = = ? ? = = = A = = = C = G G G = D T = T = A A = = = T = = T 0 P030 (D) = = (I) (T) (T) (G) = (G) (D) (D) (G) = = = = C = = = A = = = C = G G G = D T = T = A A = = = T = = T (I) = = (D) (C) (C) (C) = (C) (I) (I) (T) = = = = T = = = C = = = T = A A C = I C = C = T G = = = C = = C 0 P031 = = ? ? ? ? ? = = = D G = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = = = ? ? ? ? ? = = = I T = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P032 = = = = = = = = = = = = (A) = = (C) = C = = = G T A C D = G = = = = A ? ? ? A ? = T T A D = = = = = = = = = = = = = (G) = = (A) = T = = = C C G T I = A = = = = G ? ? ? G ? = C C G I = 0 P033 = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? 0 P034 = = = = = = C C = = I T = = A = = = = = A G T A C D G G = = = = A = T A A T = T ? A D = = = = = = = G G = = D G = = G = = = = = C C C G T I A A = = = = G = C T G C = C ? G I = 0 P035 D = C I T T = = G D D G A C = C T T G = = = = = = = = A = T = = = = = T G = G = C = = C I = T D C C = = C I I T G T = A C C A = = = = = = = = G = G = = = = = A A = A = T = = T 0 P036 = = = = = = (C) = = (I) (I) = ? ? A C T = G = = G T A = D = = = = = = A = T = = T G T = A D C = = = = = = (G) = = (D) (D) = ? ? G A C = A = = C C G = I = = = = = = G = C = = C A C = G I T 0 P037 D = = I T T G = G D D G = ? G = = T = = = C C ? = I = A = T = = G = C ? G C = C C G I = I = = D C C C = C I I T = ? A = = C = = = G T ? = D = G = G = = A = T ? A T = T T A D = 0 P038 D = = I T T = C = = I = = = = = = = = = = = = = = = = = C = I = = C T = = C = = = G = = I = = D C C = G = = D = = = = = = = = = = = = = = = = = G = D = = T C = = T = = = A = = 0 P039 = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P040 = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = ? ? = = = = = 0 P041 D = = I T T G = ? D D G = = = = = T = = = = = = = = = A C T I = = = = T = = G = ? ? ? ? I = = D C C C = ? I I T = = = = = C = = = = = = = = = G G G D = = = = A = = A = ? ? ? ? 0 P042 D = = I ? T G = G D = = = = = = C = = = = C C G = I = = = = = = G = = = = ? ? ? = G = = I = = D ? C C = C I = = = = = = T = = = = G T A = D = = = = = = A = = = = ? ? ? = A = = 0 P043 D = ? ? ? ? ? = G D D ? A C A C T = G = = G T A = D = = = = = = A = T = = T = T = A D C I = ? ? ? ? ? = C I I ? G T G A C = A = = C C G = I = = = = = = G = C = = C = C = G I T 0 P044 = = = = = = (C) = = (I) (I) = ? ? = = C = = C A = = = C = G G G = D T = = = A A = = = T = = T = = = = = = (G) = = (D) (D) = ? ? = = T = = T C = = = T = A A C = I C = = = T G = = = C = = C 0 P045 = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = 0 P046 D C = I T T G = G D D G = = G = = T = = = = = = = = = = = = = = = = = ? = = = = = = = = I T = D C C C = C I I T = = A = = C = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 P047 = = C = = = = = = D D = A C A C T = G = = G T A = D ? = = = = = A ? ? ? = T = T = A D C = = T = = = = = = I I = G T G A C = A = = C C G = I ? = = = = = G ? ? ? = C = C = G I T 0 P048 = = C = = = = = = D D = ? ? = C T = G T C = = = T = A A = = = = = = = = = = = = = = = = = = T = = = = = = I I = ? ? = A C = A C A = = = C = G G = = = = = = = = = = = = = = = = 0 P049 (D) = = = (T) = = = G D D G = = G = = T = = = C C G = I = A = T = = G = C T G ? ? ? ? ? ? ? (I) = = = (C) = = = C I I T = = A = = C = = = G T A = D = G = G = = A = T A A ? ? ? ? ? ? ? 0 P050 = = ? = ? ? ? = = = = = = = = = = = = = = C = = = = = = = = = ? = = = = = = G = = = = = = = ? = ? ? ? = = = = = = = = = = = = = = G = = = = = = = = = ? = = = = = = A = = = = = 0 P051 D = = I T T G = G D D G = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I T = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P052 = = = = = = = = ? ? = T = = = = = C = T C = = = T = A = = G = = = = = = = = = = = = = = = = = = = = = = ? ? = G = = = = = T = C A = = = C = G = = T = = = = = = = = = = = = = = 0 P053 = (T) = = ? ? ? = = = = = = = = = = (T) = = = = = = = = = = = (T) = = = = = = = = = = = = = = = (C) = = ? ? ? = = = = = = = = = = (C) = = = = = = = = = = = (G) = = = = = = = = = = = = = = 0 P054 D = ? ? ? ? ? = G D D G A C = C T T G = = = = = = = = A = T = = = = = T G = = = C = = C I = ? ? ? ? ? = C I I T G T = A C C A = = = = = = = = G = G = = = = = A A = = = T = = T 0 P055 = = = = = = C = = I I = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = G = = D D = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 P056 = = C = = = = = = = = = A C = C T = G = = G T A = D = = = = = = A = T = = T G T = A D C = = T = = = = = = = = = G T = A C = A = = C C G = I = = = = = = G = C = = C A C = G I T 0 P057 = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? = = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? 0 P058 = = C = = = = = = D D = ? C = C = = G = = = = = = = ? ? ? = D T ? = = A A = = = T = = T = = T = = = = = = I I = ? T = A = = A = = = = = = = ? ? ? = I C ? = = T G = = = C = = C 0 P059 = = (C) = = = (C) = = = = = = = = = = = = = C C C G T I A ? = = = = G = C T G ? ? ? C G I = = = (T) = = = (G) = = = = = = = = = = = = = A G T A C D G ? = = = = A = T A A ? ? ? T A D = 0 P060 D = = I T T = = G = = G = = = = = T = C A = = = C = G ? = T = = = = = = = = = = = = = = I = = D C C = = C = = T = = = = = C = T C = = = T = A ? = G = = = = = = = = = = = = = = 0 P061 = = (C) = = = (C) = = = = = = ? = = = = = = C C C ? ? I A A = = = = G ? ? ? G ? ? ? C G I = = = (T) = = = (G) = = = = = = ? = = = = = = A G T ? ? D G G = = = = A ? ? ? A ? ? ? T A D = 0 P062 = = = = = = = = = = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = 0 P063 D = = I T T G = G D D G = ? G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I T = ? A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P064 = = = = ? ? ? C = = I T ? T = = = = = = A G T ? ? ? G G = = = = A = T A A T = T T A D = = = = = ? ? ? G = = D G ? C = = = = = = C C C ? ? ? A A = = = = G = C T G C = C C G I = 0 P065 = = = = ? ? ? = = = = = (A) = = = (C) = = = = = = = = = ? = G = D T = T C = = = = C ? ? ? T = = = = ? ? ? = = = = = (G) = = = (T) = = = = = = = = = ? = C = I C = C T = = = = T ? ? ? C 0 P066 = = = = = = C = ? ? I = = = A = = = = C A G T A C D G G = = = = A = T A A T = T T A D = = = = = = = G = ? ? D = = = G = = = = T C C C G T I A A = = = = G = C T G C = C C G I = 0 P067 D = = I T T G = G D D G = = G = = T = = = C C G = I = A = = = = = = = = = = = = = = = = I = = D C C C = C I I T = = A = = C = = = G T A = D = G = = = = = = = = = = = = = = = = 0 P068 D = = I T T G = G D D G = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I T = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P069 D = = I T T G = G D D G = = G = = T = = = C C ? = I = A = T = = G = C T G C = C C G I = I = = D C C C = C I I T = = A = = C = = = G T ? = D = G = G = = A = T A A T = T T A D = 0 P070 (D) = = (I) (T) (T) = = (G) = = = = = G = = T = = = C C G = I = A = T = = G = C T G C = C C G I = (I) = = (D) (C) (C) = = (C) = = = = = A = = C = = = G T A = D = G = G = = A = T A A T = T T A D = 0 P071 = = = = = = C = = I I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = D D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P072 D = = I T T = = G = = G = = = = = T = C A = = = C = G = = T = = = = = = = = = = = = = = I = = D C C = = C = = T = = = = = C = T C = = = T = A = = G = = = = = = = = = = = = = = 0 P073 = = = = ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = ? = (I) C = = = = ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = ? = (D) T 0 P074 = = C = = = = = = D D = A ? = C T ? G T C = = = T = A A ? = = = ? = = T G ? = = C = = C = = T = = = = = = I I = G ? = A C ? A C A = = = C = G G ? = = = ? = = A A ? = = T = = T 0 P075 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = 0 P076 D = = I T T G = G D D G = ? G = = T = = = = C G = I = A = T = = ? = C T G C = C C G I = I = = D C C C = C I I T = ? A = = C = = = = T A = D = G = G = = ? = T A A T = T T A D = 0 P077 = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P078 D = = I T T = = G = = G = = = = = T = C A = = = C = G = = T = = ? = = = = = = = = = = = I = = D C C = = C = = T = = = = = C = T C = = = T = A = = G = = ? = = = = = = = = = = = 0 P079 D = ? ? ? ? ? = G D D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = I = ? ? ? ? ? = C I I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P080 = = = = ? ? = = = = D = = = = = = = = = = ? ? G = I = = = = = = G = = = = C = = = G = = = = = = ? ? = = = = I = = = = = = = = = = ? ? A = D = = = = = = A = = = = T = = = A = = 0 P081 D C = I ? ? ? = G = = G = = G = = T = = = C C G = I = A = T = = G = C T G ? ? ? ? ? I (T) I T = D ? ? ? = C = = T = = A = = C = = = G T A = D = G = G = = A = T A A ? ? ? ? ? D (C) 0 P082 = = ? ? ? ? ? = = = = = A C A C T = G = = G T A = D = = = = = = ? = T = = T = ? = A D C = = ? ? ? ? ? = = = = = G T G A C = A = = C C G = I = = = = = = ? = C = = C = ? = G I T 0 P083 D = = I ? T = = G = = G = = = = = T = C A ? ? = C = G ? = T = = = = = (A) = ? ? ? = = = = I = = D ? C = = C = = T = = = = = C = T C ? ? = T = A ? = G = = = = = (T) = ? ? ? = = = = 0 P084 = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 P085 = = = = = = = = = = = = = = G = = = = T C C C G T I A A = = = = G = C T G ? ? C C G I = = = = = = = = = = = = = = = A = = = = C A G T A C D G G = = = = A = T A A ? ? T T A D = 0 P086 D = = I T T = = ? ? = G = = = = = T = C A = = = C = G = = T = = = = = (A) = = = = = = = = I = = D C C = = ? ? = T = = = = = C = T C = = = T = A = = G = = = = = (T) = = = = = = = = 0 P087 = = = = = = = C = ? = = = = = = = (T) = T C ? ? = T = A A = = = = = = C T G ? = C C = I = = = = = = = = G = ? = = = = = = = (C) = C A ? ? = C = G G = = = = = = T A A ? = T T = D = 0 P088 ? ? = = = = C C C I I = = = = = T = = = = G T A = D = = C = I = A C T = = = = = = = = = ? ? = = = = G G G D D = = = = = C = = = = C C G = I = = G = D = G T C = = = = = = = = = 0 P089 = = C = ? ? ? = = = = = A C = C T = G = = G ? A = D = = = = = = ? = T = = T = T ? A D C = = T = ? ? ? = = = = = G T = A C = A = = C ? G = I = = = = = = ? = C = = C = C ? G I T 0 P090 = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = ? = T A A T = T T A D = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = ? = C T G C = C C G I = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = ? ? ? = = = = ? = = = = = = = = = = ? = = = = = = = = = ? = = = = ? = = ? ? ? ? = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = ? ? ? 1.00 = ? ? ? ? ? 1.00 1.00 ? = = = = = = = ? = = 1.00 ? ? = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.98 = = ? 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 = = 0.57 ? ? ? ? ? = = = = = ? ? = = = = = = = = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 ? = = 1.00 = = 1.00 0.54 = = 0.54 0.54 0.54 = = 0.54 = 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 = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = ? = = = = = = = = = = = = = = = = = 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 = = = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 = 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 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = ? = = 1.00 = 1.00 = = ? ? 1.00 1.00 1.00 = 1.00 ? ? 1.00 = ? 1.00 ? 1.00 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 ? 1.00 ? = 1.00 1.00 1.00 1.00 = ? ? 1.00 1.00 ? 1.00 = = 1.00 ? ? ? 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 = ? ? ? ? 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 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 = = = = = = = 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 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 ? ? 1.00 = = = 1.00 1.00 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 = = = = = ? 0.97 = ? = = = = 1.00 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = ? ? ? ? 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = = = = = ? = ? = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = 0.50 = = 0.50 0.50 0.50 0.50 = 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 0.60 = = 0.60 0.60 0.60 0.60 = 0.60 0.60 0.60 0.60 = = = = 1.00 = = = 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = = ? ? ? ? ? = = = 0.92 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 = = = = = = = = = = = = = 0.88 = = 0.69 = 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 = = = ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = = = = 0.95 1.00 = = 1.00 1.00 = = 1.00 = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = 0.60 = = 0.60 0.60 = ? ? 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = ? 1.00 = = 1.00 = = = 1.00 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 1.00 = = = = = 1.00 = = = = = = = = = 1.00 1.00 1.00 1.00 = = = = 1.00 = = 1.00 = ? ? ? ? 1.00 = = 1.00 ? 1.00 1.00 = 1.00 1.00 = = = = = = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = = = = ? ? ? = 1.00 = = 0.92 = ? ? ? ? ? = 0.92 0.93 0.93 ? 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = 0.52 = = 0.52 0.52 = ? ? = = 1.00 = = 1.00 1.00 = = = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = = 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 1.00 = = = = = = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 ? = = = = = 1.00 ? ? ? = 1.00 = 1.00 = 1.00 1.00 1.00 = = 1.00 = = = = = = 1.00 1.00 = ? ? = 1.00 1.00 = 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = 0.53 = = = 0.63 = = = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 ? ? ? ? ? ? ? = = ? = ? ? ? = = = = = = = = = = = = = = 1.00 = = = = = = = = = ? = = = = = = 1.00 = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = = ? ? = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = 0.70 = = ? ? ? = = = = = = = = = = 0.81 = = = = = = = = = = = 0.82 = = = = = = = = = = = = = = 1.00 = ? ? ? ? ? = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = = = = 1.00 = 1.00 = = = = = 1.00 1.00 = = = 1.00 = = 1.00 = = = = = = 1.00 = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = 1.00 = = = = = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? ? = = 1.00 = = = = = = 1.00 1.00 = ? 1.00 = 1.00 = = 1.00 = = = = = = = ? ? ? = 1.00 1.00 ? = = 1.00 1.00 = = = 1.00 = = 1.00 = = 0.52 = = = 0.52 = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = = = 1.00 = 1.00 1.00 1.00 ? ? ? 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 ? = 1.00 = = = = = = = = = = = = = = = = 0.53 = = = 0.53 = = = = = = ? = = = = = = 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 = = = = 1.00 ? ? ? 1.00 ? ? ? 1.00 1.00 1.00 = = = = = = = = = = = = = = ? = = = = = = = = = = = = ? = = = = = = = = = = ? = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = ? 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = ? ? ? 1.00 = = 1.00 1.00 ? 1.00 = = = = = = 1.00 1.00 1.00 ? ? ? 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = = = = ? ? ? = = = = = 0.73 = = = 0.89 = = = = = = = = = ? = 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 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 ? = 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 = = 0.80 0.80 0.80 = = 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 = = = = = = = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = ? = = = = = = = ? = 0.62 1.00 = = 1.00 = = = = = = 1.00 1.00 = 1.00 ? = 1.00 1.00 ? 1.00 1.00 1.00 = = = 1.00 = 1.00 1.00 ? = = = ? = = 1.00 1.00 ? = = 1.00 = = 1.00 = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = ? 1.00 = = 1.00 = = = = 1.00 1.00 = 1.00 = 1.00 = 1.00 = = ? = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = = ? = = = = = = = = = = = 1.00 = ? ? ? ? ? = 1.00 0.93 0.91 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = 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 0.54 = = ? ? ? ? ? = = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = = = = = = ? = 1.00 = = 1.00 = ? = 1.00 1.00 1.00 1.00 = = 1.00 ? 1.00 = = 1.00 = = 1.00 = = = = = 1.00 = 1.00 1.00 ? ? = 1.00 = 1.00 ? = 1.00 = = = = = 0.61 = ? ? ? = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = = ? ? = 1.00 = = = = = 1.00 = 1.00 1.00 = = = 1.00 = 1.00 = = 1.00 = = = = = 0.62 = = = = = = = = = = = = = = = 1.00 = ? = = = = = = = 0.52 = 1.00 1.00 ? ? = 1.00 = 1.00 1.00 = = = = = = 1.00 1.00 1.00 ? = 1.00 1.00 = 1.00 = ? ? = = = = 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = 1.00 1.00 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = 1.00 = ? ? ? = = = = = 1.00 1.00 = 1.00 1.00 = 1.00 = = 1.00 ? 1.00 = 1.00 = = = = = = ? = 1.00 = = 1.00 = 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