************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 cochx.phase.inp cochx.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST cochx.phase.out_freqs : haplotype frequency estimates cochx.phase.out_pairs : most likely haplotype pairs for each individual cochx.phase.out_recom : estimates of recombination parameters cochx.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 36 Positions of loci: 1690 1807 2235 3039 3087 4706 4762 5205 5208 5269 5905 7133 7668 7792 9983 11445 12113 12322 12572 13294 13752 14305 15416 15930 16084 16577 16796 16802 16821 17228 17608 17685 17914 18051 18485 19516 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file cochx.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 GCAITCCDICGACATCCTTCDGCDCTACDTCIITTI 1.000000 2 GCAITCCDICAACACCCTACDTTDCTATIACIIATI 1.000000 3 GCAITCCDICAACACCCTACDTTDTTACDACIIACI 1.000000 4 GCAITCCDICAAAACACTACDTTICCCTDACIIATI 1.000000 5 GCAITCCDICACCACACTTGDTTDTTCTDTCIITTI 1.000000 6 GCAITCCDICACCACACTACDGCICTATDTCIITTI 1.000000 7 GCAITCCDITACCACACTAGDTTITTATDTCIITTI 1.000000 8 GCAITCCDDCAACACCCTACDTTDCTATDACIIATI 1.000000 9 GCAITCCDDTAACACCCCACDTTDCTATDTCIITTI 1.000000 10 GCAITCGDICGACATCCTTCDGTDTTACDTCIITTI 1.000000 11 GCAITCGDICGACATCCTTCDGCDCTCTDACIIATD 1.000000 12 GCAITCGDICGACATCCTACDGCICTATDTCIITTI 6.000000 13 GCAITCGDICGACACCCTACDTTDTTCTDACIIACI 1.000000 14 GCAITCGDICAACATCCTTCDGCDCTACDTCIITTI 1.000000 15 GCAITCGDICAACATCCTTCDGCDCTCTDACIIACI 1.000000 16 GCAITCGDICAACATCCTTCDGCDCTCTDACDIATI 1.000000 17 GCAITCGDICAACACCCTACDGTDTTACDTCIITTI 2.000000 18 GCAITCGDICAACACCCTACDTTDCTATIACIIATI 2.000000 19 GCAITCGDICAACACCCCACDTTDTTATIACDITTI 2.000000 20 GCAITCGDICAACACCCCACDTTDTTATIACDIATI 1.000000 21 GCAITCGDICAACACACTACDGTDTTACDACIIATI 1.000000 22 GCAITCGDICAACGCCGTACITTDTTCTDACIIACI 1.000000 23 GCAITCGDICAAAACACTACDTTDTTCTDACIIATI 1.000000 24 GCAITCGDICAAAACACTACDTTICCCTDACIIATI 1.000000 25 GCAITCGDICACCACACTTCDTTICTATDACIIACI 3.000000 26 GCAITCGDICACCACACTTGDTTDTTCTDTCIITTI 1.000000 27 GCAITCGDICACCACACTTGDTTDTTCTDACIIATD 1.000000 28 GCAITCGDICACCACACTTGDTTICTCTDACIITTI 1.000000 29 GCAITCGDICACCACACTACDGTDTTCTDACDIATI 1.000000 30 GCAITCGDICACCACACTACDGTDTTCTDATIDACI 1.000000 31 GCAITCGDICACCACACTACDGTICTCTDACIIACI 2.000000 32 GCAITCGDICACCACACTACDGCICTATDTCIITTI 1.000000 33 GCAITCGDICACCACACTACDTTDTTCTDACIIATI 1.000000 34 GCAITCGDICACCACACTACDTTDTTCTDACIIATD 1.000000 35 GCAITCGDICACCACACTAGDTTDCTCTDACIIATD 2.000000 36 GCAITCGDICACCACACTAGDTTDCTCTDACIIACI 1.000000 37 GCAITCGDICACCACACTAGDTTDTTCCDATIDACI 1.000000 38 GCAITCGDICACCACACTAGDTTICTCTDACIIATD 5.000000 39 GCAITCGDITGACGCCGTACITTDTTATDACIIATI 1.000000 40 GCAITCGDITACCACACTAGDTTITTATDTCIITTI 1.000000 41 GCAITCGDDCGACACCCTACDTTDTTCTDATIDACI 2.000000 42 GCAITCGDDCAACATCCTTCDGCDCTCTDACIIACI 1.000000 43 GCAITCGDDCAACACCCCACDTTDTTATIACIIATI 1.000000 44 GCAITCGDDCACCACACTAGDTTICTCTDACIIATI 1.000000 45 GCAITCGIICACCACACTACDGCICTATDTCIITTI 1.000000 46 GCAITCGIDCGACACACTACDGTDTTACDATIDACI 1.000000 47 GCAITCGIDCGACGCCGTACITTDTTATDACIIATI 1.000000 48 GCAITCGIDCAACGCCGTACITTDTTCTDTCIITTI 1.000000 49 GCAITCGIDCACCACACTACDTTDTTCTDACIITTI 1.000000 50 GCAITCGIDCACCACACTAGDTTICTCTDACIIATI 1.000000 51 GCAITACDITAAAACACTACDTTDTTACDACIIACI 1.000000 52 GCAICCGDICGACATCCTAGDTTICTCTDACIITTI 1.000000 53 GCAICCGDICACCACACTTCDTTDCCCTDACIIATD 1.000000 54 GCAICCGDICACCACACTTGDTTICTCTDTCIITTI 1.000000 55 GCAICCGDICACCACACTAGDTTITTATDTCIITTI 1.000000 56 GCAICCGDDCACCACACTAGDTTICTCTDTCIITTI 1.000000 57 GCADTACDITACCACACTAGDTTDCTCTDACIIATD 1.000000 58 GCGITCCDICAACATCCTACDGTDTTACDACIIACI 1.000000 59 GCGITCCDICAACACACTACDGTDTTACDATIDACI 1.000000 60 GCGITCCDITGACGCCGTACITTDTTATDACIIATI 1.000000 61 GCGITCGDICGACGCCGTACITTICTCTDACIIATI 1.000000 62 GCGITCGDICACCACACTTGDTTDTTCTDTCIITTI 1.000000 63 GCGITCGDICACCACACTACDTTDTTCTDACDIACI 1.000000 64 GCGITCGDDCGACATACTTCDTTICTACDACIIACI 1.000000 65 GCGITACDICACCACACTACDGTDTTCTDACDITTI 1.000000 66 GTAITCCIDCACCACACTTGDTTICCCTDACIIATD 1.000000 67 GTAITCGDICAACACCCTACDGTDTTACDTCIITTI 1.000000 68 GTAITCGDICAAAACACTACDTTICCCTDACIIATI 1.000000 69 GTAITCGDDCAAAACACTACDTTDTTCTDACIIATI 1.000000 70 GTAITCGDDCACCACACTAGDTTDCTCTDACIIATI 2.000000 71 GTAITCGDDCACCACACTAGDTTICCCTDACIIATD 1.000000 72 ACGDTCCDICACCACACTAGDTTDTTATDACIIATI 1.000000 73 ACGDTCGDICAACATCCTTCDGCDCTCTDTCIITTI 1.000000 74 ACGDTCGDICACCACACTAGDTTDTTACDATIDACI 1.000000 75 ACGDTCGDICACCACACTAGDTTICTCTDACIIATD 2.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (10,1) DY02: (18,29) DY03: (30,60) DY04: (47,64) DY05: (17,51) DY06: (8,49) DY07: (21,31) DY08: (9,43) DY09: (18,61) DY10: (19,72) DY11: (24,69) DY12: (39,48) DY13: (59,44) DY14: (4,17) DY15: (3,20) DY16: (14,16) DY17: (22,37) DY18: (19,31) DY19: (58,65) DY20: (2,67) DY21: (41,46) DY22: (23,41) DY23: (33,74) DY24: (12,63) E101: (11,32) E102: (57,5) E103: (62,34) E104: (26,68) E105: (38,75) E106: (12,66) E107: (12,42) E108: (7,50) E109: (27,38) E110: (53,70) E111: (12,28) E112: (45,75) E113: (38,71) E114: (36,56) E115: (15,55) E116: (38,54) E117: (12,38) E118: (25,35) E119: (25,73) E120: (13,6) E121: (12,25) E122: (35,70) E123: (40,52) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 G C A I T C (G) D I C G A C A T C C T T C D G [T] D T T A C D T C I I T T I G C A I T C (C) D I C G A C A T C C T T C D G C D C T A C D T C I I T T I 0 DY02 G C A I T C [G] D I C A A C A C C C T A C D (T) T D (C) T A T I A C (I) I A T I G C A I T C [G] D I C A C C A C A C T A C D (G) T D (T) T C T D A C (D) I A T I 0 DY03 G C A I T C [G] D I C A C C A C A C T A C D G T D T T C T D A (T) I (D) A (C) I G C G I T [C] [C] D I T G A C G C C G T A C I T T D T T A T D A (C) I (I) A (T) I 0 DY04 G C (A) I T C G (I) D C G A C G C C G T A C I T T D T T A T D A C I I A T I G C (G) I T C G (D) D C G A C A T A C T T C D [T] T I C T A C D A C I I A C I 0 DY05 G C A I T (C) (G) D I (C) A A (C) A C (C) C T A C D (G) T D T T A C D T C I I T T I G C A I T (A) (C) D I (T) A A (A) A C (A) C T A C D (T) T D T T A C D A C I I A C I 0 DY06 G C A I T C (C) (D) D C A A C A C C C T A C D [T] T D (C) T (A) T D A C I I (A) T I G C A I T C (G) (I) D C A C C A C A C T A C D [T] T D (T) T (C) T D A C I I (T) T I 0 DY07 G C A I T C G D I C A (A) C A C A C T A C D G T D T T A C D A C I I A (T) I G C A I T C G D I C A (C) C A C A C T A C D G T [I] [C] T C T D A C I I A (C) I 0 DY08 G C A I T C C D D (T) A A C A C C C C A C D T T D C T A T D (T) C I I (T) T I G C A I T C G D D (C) A A C A C C C C A C D T T D T T A T I (A) C I I (A) T I 0 DY09 G C A I T C [G] D I C A A C A C C C [T] A C D T T D [C] T A T I A C I I A T I G C G I T C [G] D I C [G] A C G C C G T A C [I] T T I C T C T D A C I I A T I 0 DY10 (G) C (A) (I) T C (G) D I C A A C A C C C C A C D T T D T T A T I A C D I (T) T I (A) C (G) (D) T C (C) D I C A C C A C A C T A G D T T D T T A T D A C I I (A) T I 0 DY11 G (C) A I T C [G] D I C A A A A C A C T A C D T T [I] [C] [C] C T D A C I I A T I G (T) A I T C [G] D D C A A A A C A C T A C D T T [D] [T] [T] C T D A C I I A T I 0 DY12 G C A I T C [G] (D) (I) (T) G A C G C C G T A C I T T D T T A T D A C I I A T I G C A I T C [G] (I) (D) (C) A A C G C C G T A C I T T D T T C T D T C I I T T I 0 DY13 G C (G) I T C C D (I) C A A C A C A C T A C D G T D [T] T A C D A T I D A C I G C (A) I T C G D (D) C A C C A C A C T A G D T T I C T C T D A C I I [A] T I 0 DY14 G C A I T C (C) D I C A A A A C A C T A C D T T I C C C T D A C I I A T I G C A I T C (G) D I C A A C A C C C T A C D G T D T T A C D T C I I T T I 0 DY15 G C A I T C C D I C A A C A C C C T A C D T T D [T] T A C D A C I I A C I G C A I T C G D I C A A C A C C C C A C D T T D T T A T I A C D I A T I 0 DY16 G C A I T C [G] D I C A A C A T C C T T C D G C D [C] T A C D T C I I T T I G C A I T C [G] D I C A A C A T C C T T C D G C D C T C T D A C D I A [T] I 0 DY17 G C A I T C [G] D I C A A C G C C G T A C I T T D T T C (T) D A (C) I (I) A C I G C A I T C [G] D I C A C C A C A C T A [G] D T T D T T C (C) D A (T) I (D) A C I 0 DY18 G C A I T C G D I C A A C A C C C C A C D T T D T T A T I A C D I (T) (T) I G C A I T C G D I C A C C A C A C T A C D G T I C T C T D A C I I (A) (C) I 0 DY19 G C G I T (C) C D I C A A C A (T) C C T A C D G T D T T A C D A C (I) I (A) (C) I G C G I T (A) C D I C A C C A (C) A C T A C D G T D T T C T D A C (D) I (T) (T) I 0 DY20 G C A I T C C D I C A A C A C C C T A C D T T D C T A T I A C I I A T I G T A I T C G D I C A A C A C C C T A C D G T D T T A C D T C I I T T I 0 DY21 G C A I T C [G] D D C G A C A C C C T A C D T T D T T C T D A T I D A C I G C A I T C [G] I D C G A C A C A C T A C D G T D [T] T A C D A T I D A C I 0 DY22 G C A I T C [G] D (I) C A A A A C A C T A C D T T D T T C T D A C I I [A] T I G C A I T C [G] D (D) C G A C A C C C T A C D T T D T T C T D A T I D A C I 0 DY23 G C A I T C [G] D I C A C C A C A C T A C D T T D [T] T C T D A C I I [A] T I A C G D T C [G] D I C A C C A C A C T A G D T T [D] [T] T A C D A T I D A C I 0 DY24 G C (A) I T C [G] D I C G A C A T C C T A C D G C I C T A T D T C I I T T I G C (G) I T C [G] D I C A C C A C A C T A C D T T D [T] T C T D A C D I A C I 0 E101 G C A I T C [G] D I C (G) (A) C A (T) (C) C T T C D G C D C T C T D A C I I A T D G C A I T C [G] D I C (A) (C) C A (C) (A) C T A C D G C I C T A T D T C I I T T I 0 E102 G C A (D) T (A) C D I (T) A C C A C A C T A G D T T D C T C T D A C I I A T (D) G C A (I) T (C) C D I (C) A C C A C A C T T G D T T D T T C T D T C I I T T (I) 0 E103 G C (G) I T C [G] D I C A C C A C A C T (T) (G) D T T D T T C T D T C I I T T I G C (A) I T C [G] D I C A C C A C A C T (A) (C) D T T D T T C T D A C I I A T D 0 E104 G (C) A I T C [G] D I C A C C A C A C T T G D T T [D] [T] T C T D T C I I T T I G (T) A I T C [G] D I C A A A A C A C T A C D T T [I] [C] [C] C T D A C I I A T I 0 E105 G C A I T C [G] D I C A C C A C A C T A G D T T [I] C T C T D A C I I A T D A C G D T C [G] D I C A C C A C A C T A G D T T [I] C T C T D A C I I A T D 0 E106 G (C) A I T C (G) (D) (I) C G A C A T C C T (A) C D G C I C T A T D T C I I T T I G (T) A I T C (C) (I) (D) C A C C A C A C T (T) G D T T I C C C T D A C I I A T D 0 E107 G C A I T C [G] D (I) C G A C A T C C T A C D G C I C T A T D T C I I T T I G C A I T C [G] D (D) C A A C A T C C T T C D G C D C T C T D A C I I A C I 0 E108 G C A I T C [C] D I T A C C A C A C T A G D T T I T T A T D T C I I T T I G C A I T C [G] I D C A C C A C A C T A G D T T I C T C T D A C I I A T I 0 E109 G C A I T C [G] D I C A C C A C A C T (T) [G] D T T D [T] T C T D A C I I A T D G C A I T C [G] D I C A C C A C A C T (A) G D T T I C T C T D A C I I A T D 0 E110 G (C) A I (C) C [G] D (I) C A C C A C A C T (T) (C) D T T D C (C) C T D A C I I A T (D) G (T) A I (T) C [G] D (D) C A C C A C A C T (A) (G) D T T D C (T) C T D A C I I A T (I) 0 E111 G C A I T C [G] D I C G A C A T C C T (A) (C) D (G) (C) I C T (A) T D (T) C I I T T I G C A I T C [G] D I C A C C A C A C T (T) (G) D (T) (T) I C T (C) T D (A) C I I T T I 0 E112 (G) C (A) (I) T C [G] (I) I C A C C A C A C T A C D G C I C T A T D T C I I T T I (A) C (G) (D) T C [G] (D) I C A C C A C A C T A G D T T I C T C T D A C I I A T D 0 E113 G (C) A I T C [G] D (I) C A C C A C A C T A G D T T I C (T) C T D A C I I A T D G (T) A I T C [G] D (D) C A C C A C A C T A G D T T I C (C) C T D A C I I A T D 0 E114 G C A I (T) C [G] D (I) C A C C A C A C T A G D T T (D) C T C T D A C I I A C I G C A I (C) C [G] D (D) C A C C A C A C T A G D T T (I) C T C T D T C I I T T I 0 E115 G C A I (T) C [G] D I C A A C A T C C T T C D G C D C T C T D A C I I A C I G C A I (C) C [G] D I C A C C A C A C T A G D T T [I] [T] T A T D T C I I T T I 0 E116 G C A I (T) C [G] D I C A C C A C A C T (A) G D T T I C [T] C T D A C I I A T D G C A I (C) C [G] D I C A C C A C A C T (T) G D T T I C T C T D T C I I T T I 0 E117 G C A I T C G D I C G A C A T C C T A C D G C I C T A T D T C I I T T I G C A I T C G D I C A C C A C A C T A G D T T I C T C T D A C I I A T D 0 E118 G C A I T C [G] D I C A C C A C A C T T C D T T (I) C T A T D A C I I A C I G C A I T C [G] D I C A C C A C A C T A [G] D T T (D) C T C T D A C I I A T D 0 E119 (G) C (A) (I) T C G D I C A C C A C A C T T C D T T [I] C T A T D (A) C I I (A) (C) I (A) C (G) (D) T C [G] D I C [A] A C A T C C T T C D G C D C T C T D (T) C I I (T) (T) I 0 E120 G C A I T C (G) D I C G A C A C C C T A C D T T D [T] T C T D A C I I A C I G C A I T C (C) D I C A C C A C A C T A C D G C I C T A T D T C I I T T I 0 E121 G C A I T C [G] D I C G A C A T C C T A C D G C I C T A T D T C I I T T I G C A I T C [G] D I C A C C A C A C T T C D T T [I] C T A T D A C I I A C I 0 E122 G (C) A I T C [G] D (I) C A C C A C A C T A G D T T D C T C T D A C I I A T (D) G (T) A I T C [G] D (D) C A C C A C A C T A G D T T D C T C T D A C I I A T (I) 0 E123 G C A I (T) C [G] D I T A C C A C A C T A G D T T I T T A T D T C I I T T I G C A I (C) C [G] D I C G A C A T C C T A G D T T [I] C T C T D A C I I T T I 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 DY01 = = = = = = (G) = = = = = = = = = = = = ? ? ? ? = T = = = = = = = = = = = = = = = = = (C) = = = = = = = = = = = = ? ? ? ? = C = = = = = = = = = = = 0 DY02 = = = = = ? ? = = = = A = = = C = = = = = (T) = = (C) = A = I = = (I) = = = = = = = = = ? ? = = = = C = = = A = = = = = (G) = = (T) = C = D = = (D) = = = = 0 DY03 = = A = = ? ? = = C A C = A = A C = = = D G = = = = C = = = (T) = (D) ? (C) = = = G = = ? ? = = T G A = G = C G = = = I T = = = = A = = = (C) = (I) ? (T) = 0 DY04 = = (A) = = = = (I) = = = = = G C C G = A = I ? = D ? = = T = = = = = = T = = = (G) = = = = (D) = = = = = A T A C = T = D ? = I ? = = C = = = = = = C = 0 DY05 = = = = = (C) (G) = = (C) = = (C) = = (C) = = = = = (G) = = = = = = = T = = = T T = = = = = = (A) (C) = = (T) = = (A) = = (A) = = = = = (T) = = = = = = = A = = = A C = 0 DY06 = = = = = = (C) (D) = = = A = = = C = = = = = ? = = (C) = (A) = = = = = = (A) = = = = = = = = (G) (I) = = = C = = = A = = = = = ? = = (T) = (C) = = = = = = (T) = = 0 DY07 = = = = = = = = = = = (A) = = ? = = = = = = = = ? ? ? A C = = = = = = (T) = = = = = = = = = = = = (C) = = ? = = = = = = = = ? ? ? C T = = = = = = (C) = 0 DY08 = = ? = = = C = = (T) = = = = = ? = = = = = ? = = C = = = D (T) = = = (T) = = = = ? = = = G = = (C) = = = = = ? = = = = = ? = = T = = = I (A) = = = (A) = = 0 DY09 = = A = = ? ? ? ? ? ? = = A = = ? ? = ? ? = = D ? = A = I = = = = = = = = = G = = ? ? ? ? ? ? = = G = = ? ? = ? ? = = I ? = C = D = = = = = = = 0 DY10 (G) = (A) (I) = = (G) = = = = A = = = C = C = C = = = = = = = = I = = D = (T) = = (A) = (G) (D) = = (C) = = = = C = = = A = T = G = = = = = = = = D = = I = (A) = = 0 DY11 = (C) = = = ? ? = I = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = = (T) = = = ? ? = D = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = 0 DY12 = = = = = ? ? (D) (I) (T) G = = = = = = = = = = = = = = = A = = A = = = A = = = = = = = ? ? (I) (D) (C) A = = = = = = = = = = = = = = = C = = T = = = T = = 0 DY13 = = (G) = = = C = (I) = = A = = = = = = = C = ? = D ? = A C = = T = D ? C = = = (A) = = = G = (D) = = C = = = = = = = G = ? = I ? = C T = = C = I ? T = 0 DY14 = = = = = = (C) = = = = = A = = A = = = = = T = I ? C C T = A = = = A = = = = = = = = (G) = = = = = C = = C = = = = = G = D ? T A C = T = = = T = = 0 DY15 = = = = = = C ? ? ? = = = = ? ? = T = = = = ? ? ? ? = C D = = I = = C = = = = = = = G ? ? ? = = = = ? ? = C = = = = ? ? ? ? = T I = = D = = T = 0 DY16 = = = = = ? ? = = = = = = = ? ? = = ? = = = = ? ? ? A C = T = I = T ? = = = = = = ? ? = = = = = = = ? ? = = ? = = = = ? ? ? C T = A = D = A ? = 0 DY17 = = = = = ? ? = = = = A = G = C G = = ? ? = = = = = = (T) = = (C) = (I) ? = = = = = = = ? ? = = = = C = A = A C = = ? ? = = = = = = (C) = = (T) = (D) ? = = 0 DY18 = = = = = = = = = = = A = = = C = C = = = T = D ? = A = I = = D = (T) (T) = = = = = = = = = = = = C = = = A = T = = = G = I ? = C = D = = I = (A) (C) = 0 DY19 = = = = = (C) = = = = = A = = (T) C = = = = = = = = = = A C = = = (I) = (A) (C) = = = = = = (A) = = = = = C = = (C) A = = = = = = = = = = C T = = = (D) = (T) (T) = 0 DY20 = C = = = = C = = = = = = = = = = = = = = T = ? ? ? = T I A = = = A = = = T = = = = G = = = = = = = = = = = = = = G = ? ? ? = C D T = = = T = = 0 DY21 = = = = = ? ? D = = = = = = = C = = = = = T = ? ? ? C T = = = = = = = = = = = = = ? ? I = = = = = = = A = = = = = G = ? ? ? A C = = = = = = = = 0 DY22 = = ? = = ? ? = (I) = A = A = = A = = = = = = ? = = = = = = = C = I ? T = = = ? = = ? ? = (D) = G = C = = C = = = = = = ? = = = = = = = T = D ? C = 0 DY23 G = A I = ? ? = = = = = = = = = = = = C = = = ? ? ? C T = = C = I ? T = A = G D = ? ? = = = = = = = = = = = = G = = = ? ? ? A C = = T = D ? C = 0 DY24 = = (A) = = ? ? = = = G A = = ? C = = = = = G C ? ? ? A = = T = I = T T = = = (G) = = ? ? = = = A C = = ? A = = = = = T T ? ? ? C = = A = D = A C = 0 E101 = = = ? ? ? ? = = = (G) (A) = = (T) (C) = = T ? ? = = D ? = C = = A = = = A = D = = = ? ? ? ? = = = (A) (C) = = (C) (A) = = A ? ? = = I ? = A = = T = = = T = I 0 E102 = = = (D) = (A) = = = (T) = = = = ? = = = A = ? = = = C = = = = A = = = A = (D) = = = (I) = (C) = = = (C) = = = = ? = = = T = ? = = = T = = = = T = = = T = (I) 0 E103 = = (G) = = ? ? = = = ? = = = = = = = (T) (G) = = = = = = = = = T = = = T = I = = (A) = = ? ? = = = ? = = = = = = = (A) (C) = = = = = = = = = A = = = A = D 0 E104 = (C) = = = ? ? = = = = C C = = = = = T G = = = ? ? ? = = = T = = = T = = = (T) = = = ? ? = = = = A A = = = = = A C = = = ? ? ? = = = A = = = A = = 0 E105 G = A I = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = A = G D = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = 0 E106 = (C) = = = = (G) (D) (I) = G ? = = T C = = (A) C = G C = = T A = = T = = = T = I = (T) = = = = (C) (I) (D) = A ? = = C A = = (T) G = T T = = C C = = A = = = A = D 0 E107 = = = = = ? ? = (I) = G = = = = = = = A = = = = ? ? ? A = = T = = = T T = = = = = = ? ? = (D) = A = = = = = = = T = = = = ? ? ? C = = A = = = A C = 0 E108 = = ? = = ? ? D I T = = = = = = = = = = = = = = T ? A = = T = = = T = = = = ? = = ? ? I D C = = = = = = = = = = = = = = C ? C = = A = = = A = = 0 E109 = = = = = ? ? = = = = = = = ? = = = (T) ? ? = = D ? = = = = = = = = = = = = = = = = ? ? = = = = = = = ? = = = (A) ? ? = = I ? = = = = = = = = = = = 0 E110 = (C) = = (C) ? ? ? (I) = = = = = = = = = (T) (C) = = = = = (C) = = = = = = = = = (D) = (T) = = (T) ? ? ? (D) = = = = = = = = = (A) (G) = = = = = (T) = = = = = = = = = (I) 0 E111 = = = = = ? ? = = = G ? = = T C = = (A) (C) = (G) (C) = = = (A) = = (T) = = = = = = = = = = = ? ? = = = A ? = = C A = = (T) (G) = (T) (T) = = = (C) = = (A) = = = = = = 0 E112 (G) = (A) (I) = ? ? (I) = ? = = = = ? = = = = C = G C = = = A = = T = = = T = I (A) = (G) (D) = ? ? (D) = ? = = = = ? = = = = G = T T = = = C = = A = = = A = D 0 E113 = (C) = = = ? ? = (I) = = = = = = = = = = = = = = = = (T) = = = = = = = = = = = (T) = = = ? ? = (D) = = = = = = = = = = = = = = = = (C) = = = = = = = = = = 0 E114 = = = = (T) ? ? ? (I) = = = = = = = = = = = = = = (D) ? = = = = A = = = A C = = = = = (C) ? ? ? (D) = = = = = = = = = = = = = = (I) ? = = = = T = = = T T = 0 E115 = = = = (T) ? ? = = = = A = = T C = = T C = G C ? ? ? C = = A = = = A C = = = = = (C) ? ? = = = = C = = C A = = A G = T T ? ? ? A = = T = = = T T = 0 E116 = = ? = (T) ? ? = = = = = = = = = = = (A) = = = = = = ? = = = A = = = A = D = = ? = (C) ? ? = = = = = = = = = = = (T) = = = = = = ? = = = T = = = T = I 0 E117 = = = ? ? = = = = = G A = = T C = = = ? ? G C = = = A = = T = = = T = I = = = ? ? = = = = = A C = = C A = = = ? ? T T = = = C = = A = = = A = D 0 E118 = = = ? = ? ? = = ? = = = = ? = = = T ? ? = = (I) ? = A = = = = = = = C I = = = ? = ? ? = = ? = = = = ? = = = A ? ? = = (D) ? = C = = = = = = = T D 0 E119 (G) = (A) (I) = ? ? = = = ? C = = ? A = = = = = T T ? ? ? A = = (A) = = = (A) (C) = (A) = (G) (D) = ? ? = = = ? A = = ? C = = = = = G C ? ? ? C = = (T) = = = (T) (T) = 0 E120 = = = = = = (G) = = = G A = = = C = = ? = = T T D ? = C = = A = = = A C = = = = = = = (C) = = = A C = = = A = = ? = = G C I ? = A = = T = = = T T = 0 E121 = = = = = ? ? = = = G ? = = T C = = A = = G C ? ? ? = = = T = = = T T = = = = = = ? ? = = = A ? = = C A = = T = = T T ? ? ? = = = A = = = A C = 0 E122 = (C) = = = ? ? = (I) = = ? = = = = ? ? = = = = = = = = = = = = = = = = = (D) = (T) = = = ? ? = (D) = = ? = = = = ? ? = = = = = = = = = = = = = = = = = (I) 0 E123 = = = = (T) ? ? = = T A ? = = ? A = = = = = = = ? ? ? A = = T = = = = = = = = = = (C) ? ? = = C G ? = = ? C = = = = = = = ? ? ? C = = A = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = = = = 0.51 = = = = = = = = = = = = ? ? ? ? = 0.94 = = = = = = = = = = = = = = = = ? ? = = = = 1.00 = = = 1.00 = = = = = 0.86 = = 0.82 = 0.95 = 0.95 = = 0.82 = = = = = = 1.00 = = ? ? = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = = 1.00 = = = 0.87 = 0.87 ? 0.87 = = = 0.51 = = = = 0.59 = = = = = 1.00 1.00 0.93 1.00 = 1.00 = 1.00 ? = 1.00 ? = = 1.00 = = = = = = 1.00 = = = = = = 0.61 0.61 = = 0.57 = = 0.87 = = 0.88 = = = = = 0.90 = = = = = = = 0.93 = = = 0.93 0.93 = = = = = = = 0.64 0.56 = = = 0.93 = = = 0.93 = = = = = ? = = 0.79 = 0.86 = = = = = = 0.64 = = = = = = = = = = = = = 0.90 = = ? = = = = = = = = ? ? ? 0.94 0.94 = = = = = = 0.54 = = = ? = = = 0.90 = = 0.67 = = = = = ? = = = = = ? = = 0.99 = = = 0.99 0.70 = = = 0.70 = = = = 1.00 = = ? ? ? ? ? ? = = 1.00 = = ? ? = ? ? = = 1.00 ? = 1.00 = 1.00 = = = = = = = 0.60 = 0.60 0.60 = = 0.57 = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = = = = = = = = 0.99 = = 0.99 = 0.60 = = = 0.75 = = = ? ? = 1.00 = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = = = = = = ? ? 0.65 0.65 0.65 0.93 = = = = = = = = = = = = = = = 0.93 = = 0.94 = = = 0.94 = = = = 0.56 = = = 1.00 = 0.66 = = 1.00 = = = = = = = 1.00 = ? = 0.99 ? = 1.00 1.00 = = 1.00 = 1.00 ? 1.00 = = = = = = = 0.50 = = = = = 0.99 = = 0.99 = = = = = 1.00 = 1.00 ? 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = = 1.00 ? ? ? = = = = ? ? = 1.00 = = = = ? ? ? ? = 1.00 1.00 = = 1.00 = = 1.00 = = = = = = ? ? = = = = = = = ? ? = = ? = = = = ? ? ? 1.00 1.00 = 1.00 = 1.00 = 1.00 ? = = = = = = ? ? = = = = 1.00 = 1.00 = 1.00 1.00 = = ? ? = = = = = = 0.59 = = 0.52 = 0.52 ? = = = = = = = = = = = = = 0.99 = = = 1.00 = 1.00 = = = 1.00 = 1.00 ? = 1.00 = 1.00 = = 0.95 = 0.68 0.83 = = = = = = 0.55 = = = = = 0.94 = = 0.81 0.92 = = = = = = = = = = 0.94 0.94 = = = 0.65 = 0.58 0.68 = = 1.00 = = = = 1.00 = = = = = = = = = = = = = = 1.00 = ? ? ? = 1.00 1.00 1.00 = = = 1.00 = = = = = = = ? ? 1.00 = = = = = = = 1.00 = = = = = 1.00 = ? ? ? 1.00 1.00 = = = = = = = = = = ? = = ? ? = 0.82 = 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 = = = 0.62 = = ? ? = = = 1.00 1.00 = = ? 1.00 = = = = = 1.00 1.00 ? ? ? 1.00 = = 1.00 = 1.00 = 1.00 1.00 = = = = ? ? ? ? = = = 0.62 0.63 = = 0.63 0.63 = = 0.95 ? ? = = 0.98 ? = 0.98 = = 0.98 = = = 0.98 = 0.98 = = = 0.52 = 0.56 = = = 0.60 = = = = ? = = = 0.94 = ? = = = 0.99 = = = = 0.92 = = = 0.92 = 0.88 = = 0.51 = = ? ? = = = ? = = = = = = = 0.71 0.78 = = = = = = = = = 1.00 = = = 1.00 = 0.94 = 0.50 = = = ? ? = = = = 0.98 0.98 = = = = = 0.98 0.98 = = = ? ? ? = = = 0.98 = = = 0.98 = = 1.00 = 1.00 1.00 = ? ? = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = 0.53 = = = = 0.50 0.54 0.54 = 1.00 ? = = 1.00 1.00 = = 0.51 1.00 = 1.00 1.00 = = 1.00 1.00 = = 1.00 = = = 1.00 = 1.00 = = = = = ? ? = 0.65 = 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 = = = = = = = ? ? = = = = = = = ? = = = 0.74 ? ? = = 0.99 ? = = = = = = = = = = = = 0.81 = = 0.82 ? ? ? 0.86 = = = = = = = = = 0.90 0.90 = = = = = 0.73 = = = = = = = = = 0.66 = = = = = ? ? = = = 1.00 ? = = 1.00 1.00 = = 0.65 0.86 = 0.86 0.86 = = = 0.86 = = 0.86 = = = = = = 0.60 = 0.60 0.60 = ? ? 0.51 = ? = = = = ? = = = = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 = = = 1.00 = 1.00 = 0.85 = = = ? ? = 0.85 = = = = = = = = = = = = = = = = 0.74 = = = = = = = = = = = = = = 0.50 ? ? ? 0.53 = = = = = = = = = = = = = = 0.59 ? = = = = 1.00 = = = 1.00 1.00 = = = = = 0.52 ? ? = = = = 1.00 = = 1.00 1.00 = = 1.00 1.00 = 1.00 1.00 ? ? ? 0.91 = = 0.91 = = = 0.91 0.91 = = = ? = 0.61 ? ? = = = = = = = = = = = 0.61 = = = = = = ? = = = 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 ? ? = = 0.78 ? = 1.00 = = = = = = = 1.00 1.00 0.68 = 0.68 0.68 = ? ? = = = ? 0.94 = = ? 0.94 = = = = = 0.94 0.94 ? ? ? 0.92 = = 0.52 = = = 0.52 0.52 = = = = = = = 0.52 = = = 0.90 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 = = 0.83 = = = ? ? = 0.87 = = ? = = = = ? ? = = = = = = = = = = = = = = = = = 0.77 = = = = 0.70 ? ? = = 1.00 1.00 ? = = ? 1.00 = = = = = = = ? ? ? 1.00 = = 1.00 = = = = = = END PHASEPROBS