************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 hspa2.phase.inp hspa2.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST hspa2.phase.out_freqs : haplotype frequency estimates hspa2.phase.out_pairs : most likely haplotype pairs for each individual hspa2.phase.out_recom : estimates of recombination parameters hspa2.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 95 Number of Loci: 21 Positions of loci: 135 291 1355 1684 2120 2862 3006 3319 3568 3981 4343 5721 7389 8682 9499 10071 10159 10272 10300 10363 10546 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file hspa2.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 DGCIATCCDCTATICAGDGIC 1.000000 2 DGCIATCCDCTATIGCADGIT 2.000000 3 DGCIATCCDCTATIGCADCIT 102.000000 4 DGCIATCCDCTATDGCADCIT 3.000000 5 DGGDGAAADTCACICAGDGDC 1.000000 6 DGGDGAAAITCACIGCADCIT 1.000000 7 DGGDGAAAITCACDCAGIGDC 24.000000 8 DGGDGAAAITCACDCAGDGIC 1.000000 9 DGGDGAAAITCACDCAGDGDC 12.000000 10 DGGIGAACITCGCDGAGDGDC 1.000000 11 DAGIGAAADTCGCDCAGIGDC 1.000000 12 DAGIGAAADTCGCDCAGDGDC 5.000000 13 DAGIGAAAITCACDCAGDGDC 8.000000 14 IGCIATCCDCTATIGCADCIT 1.000000 15 IACIATCCDCTATIGCADCIT 24.000000 16 IACIATCCDCTGTIGCADCIT 3.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY D001: (1,3) D002: (7,8) D003: (3,3) D004: (7,15) D005: (3,15) D006: (7,9) D007: (3,7) D008: (9,9) D009: (3,7) D010: (7,15) D011: (3,3) D012: (3,9) D013: (7,12) D014: (3,7) D015: (3,9) DY01: (3,9) DY02: (3,9) DY03: (3,13) DY04: (3,9) DY05: (3,3) DY06: (7,13) DY07: (3,15) DY08: (7,9) DY09: (9,13) DY10: (3,9) DY11: (7,15) DY12: (3,9) E101: (3,15) E102: (3,3) E103: (12,16) E104: (3,15) E105: (15,16) E106: (3,3) E107: (3,15) E108: (3,11) E109: (4,15) E110: (3,12) E111: (3,3) E112: (3,7) E113: (3,3) E114: (2,15) E115: (3,12) E116: (7,10) E117: (3,3) E118: (15,16) E119: (3,13) E120: (3,3) E121: (7,15) E122: (12,15) H101: (3,3) H102: (3,7) H103: (3,3) H104: (3,3) H105: (3,3) H106: (3,3) H107: (3,3) H108: (3,7) H109: (3,3) H110: (3,3) H111: (3,15) H112: (13,15) H113: (3,7) H114: (3,3) H115: (3,3) H116: (3,3) H117: (3,3) H118: (3,3) H119: (3,7) H120: (3,7) H121: (3,3) H122: (7,13) X101: (2,3) X102: (3,3) X103: (3,3) X104: (3,14) X105: (3,3) X106: (7,15) X107: (3,7) X108: (3,15) X109: (3,3) X110: (4,4) X111: (3,15) X112: (5,6) X113: (3,3) X114: (3,15) X115: (7,15) X116: (3,13) X117: (3,15) X118: (3,15) X119: (7,13) X120: (3,15) X121: (3,3) X122: (3,3) X123: (3,3) X124: (3,3) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 D001 D G C I A T C C D C T A T I C [A] [G] [D] [G] [I] [C] D G C I A T C C D C T A T I G C A D C I T 0 D002 D G G D G A A A I T C A C D C A G (I) G D C D G G D G A A A I T C A C D C A G (D) G I C 0 D003 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 D004 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 D005 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 D006 D G G D G A A A I T C A C D C A G I G D C D G G D G A A A I T C A C D C A G [D] G D C 0 D007 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 D008 D G G D G A A A I T C A C D C A G D G D C D G G D G A A A I T C A C D C A G D G D C 0 D009 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G [I] G D C 0 D010 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 D011 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 D012 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 D013 D G G D G A A A I T C A C D C A G (I) G D C D A G I G A A A D T C G C D C A G (D) G D C 0 D014 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 D015 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 DY01 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 DY02 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 DY03 D G C I A T C C D C T A T I G C A D C I T D A G I G A A A I T C A C D C A G D G D C 0 DY04 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 DY05 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 DY06 D G G D G A A A I T C A C D C A G I G D C D A G I G A A A I T C A C D C A G D G D C 0 DY07 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 DY08 D G G D G A A A I T C A C D C A G I G D C D G G D G A A A I T C A C D C A G D G D C 0 DY09 D G G D G A A A I T C A C D C A G D G D C D A G I G A A A I T C A C D C A G D G D C 0 DY10 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 DY11 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 DY12 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G D G D C 0 E101 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 E102 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E103 D A G I G A A A D T C G C D C A G D G D C I A C I A T C C D C T G T I G C A D C I T 0 E104 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 E105 I A C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T G T I G C A D C I T 0 E106 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E107 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 E108 D G C I A T C C D C T A T I G C A (D) C I T D A G I G A A A D T C G C D C A G (I) G D C 0 E109 D G C I A T C C D C T A T (D) G C A D C I T I A C I A T C C D C T A T (I) G C A D C I T 0 E110 D G C I A T C C D C T A T I G C A D C I T D A G I G A A A D T C G C D C A G D G D C 0 E111 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E112 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 E113 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E114 D G C I A T C C D C T A T I G C A D (G) I T I A C I A T C C D C T A T I G C A D (C) I T 0 E115 D G C I A T C C D C T A T I G C A D C I T D A G I G A A A D T C G C D C A G D G D C 0 E116 D G G (D) G A A A I T C A C D (C) A G [I] G D C D G G (I) G A A C I T C G C D (G) A G [D] G D C 0 E117 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E118 I A C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T G T I G C A D C I T 0 E119 D G C I A T C C D C T A T I G C A D C I T D A G I G A A A I T C A C D C A G D G D C 0 E120 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 E121 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 E122 D A G I G A A A D T C G C D C A G D G D C I A C I A T C C D C T A T I G C A D C I T 0 H101 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H102 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 H103 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H104 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H105 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H106 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H107 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H108 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 H109 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H110 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H111 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 H112 D A G I G A A A I T C A C D C A G D G D C I A C I A T C C D C T A T I G C A D C I T 0 H113 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 H114 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H115 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H116 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H117 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H118 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H119 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 H120 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 H121 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 H122 D G G D G A A A I T C A C D C A G I G D C D A G I G A A A I T C A C D C A G D G D C 0 X101 D G C I A T C C D C T A T I G C A D G I T D G C I A T C C D C T A T I G C A D C I T 0 X102 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X103 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X104 D G C I A T C C D C T A T I G C A D C I T I G C I A T C C D C T A T I G C A D C I T 0 X105 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X106 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 X107 D G C I A T C C D C T A T I G C A D C I T D G G D G A A A I T C A C D C A G I G D C 0 X108 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X109 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X110 D G C I A T C C D C T A T D G C A D C I T D G C I A T C C D C T A T D G C A D C I T 0 X111 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X112 D G G D G A A A (D) T C A C I C A G D G D C D G G D G A A A (I) T C A C I G C A D C I T 0 X113 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X114 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X115 (D) (G) G D G A A A I T C A C D C A G I G D C (I) (A) C I A T C C D C T A T I G C A D C I T 0 X116 D G C I A T C C D C T A T I G C A D C I T D A G I G A A A I T C A C D C A G D G D C 0 X117 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X118 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X119 D G G D G A A A I T C A C D C A G I G D C D A G I G A A A I T C A C D C A G D G D C 0 X120 D G C I A T C C D C T A T I G C A D C I T I A C I A T C C D C T A T I G C A D C I T 0 X121 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X122 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X123 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I T 0 X124 D G C I A T C C D C T A T I G C A D C I T D G C I A T C C D C T A T I G C A D C I 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 D001 = = = ? ? = = = = = = ? = = C ? ? ? ? ? ? = = = ? ? = = = = = = ? = = G ? ? ? ? ? ? 0 D002 = = = = = = = = = = = = = = = = = (I) = D = = = = = = = = = = = = = = = = = = (D) = I = 0 D003 = = = = ? = = ? ? = = = = = = = = = = = = = = = = ? = = ? ? = = = = = = = = = = = = 0 D004 (D) (G) G D G A A A I T C = C D C A G I G D C (I) (A) C I A T C C D C T = T I G C A D C I T 0 D005 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 D006 = = = = = ? = = = = = = = = = = ? ? ? ? ? = = = = = ? = = = = = = = = = = ? ? ? ? ? 0 D007 = = C I ? T C C D C T = T I G C A D C I T = = G D ? A A A I T C = C D C A G I G D C 0 D008 = = = ? = ? = = = ? ? = = = = = = = = = = = = = ? = ? = = = ? ? = = = = = = = = = = 0 D009 = = C I A T C C ? C T ? T I G ? ? ? ? ? ? = = G D G A A A ? T C ? C D C ? ? ? ? ? ? 0 D010 (D) (G) G D G A A A I T C = C D C A G I G D C (I) (A) C I A T C C D C T = T I G C A D C I T 0 D011 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 D012 = = C I A T C C D C T = T I G C A = C I T = = G D G A A A I T C = C D C A G = G D C 0 D013 = G = D = = = = I = = A = = = = = (I) = = = = A = I = = = = D = = G = = = = = (D) = = = 0 D014 = = C ? A T C ? ? ? T = T I G C A D ? I T = = G ? G A A ? ? ? C = C D C A G I ? D C 0 D015 = = C I A T C C D C T = ? I G C A = C I T = = G D G A A A I T C = ? D C A G = G D C 0 DY01 = = C I A T C C D C T = T I G ? A = C I T = = G D G A A A I T C = C D C ? G = G D C 0 DY02 = = C I A T C C D C T = T I G C A = C I T = = G D G A A A I T C = C D C A G = G D C 0 DY03 = G C = A T C C D C T = T I G C A = C I T = A G = G A A A I T C = C D C A G = G D C 0 DY04 = = C I A T C C D C T = T I G C A = C I T = = G D G A A A I T C = C D C A G = G D C 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY06 = G = D = = = = = = = = = = = = = I = = = = A = I = = = = = = = = = = = = = D = = = 0 DY07 D G = = = = = = = = = = = = ? = ? ? ? ? ? I A = = = = = = = = = = = = ? = ? ? ? ? ? 0 DY08 = = = = = = = = = = = = = = = = = I = = = = = = = = = = = = = = = = = = = = D = = = 0 DY09 = G = D = = = = = = = = = ? = = = = = = = = A = I = = = = = = = = = ? = = = = = = = 0 DY10 = = C I A T C C D C T = T I G C A = C I T = = G D G A A A I T C = C D C A G = G D C 0 DY11 (D) (G) G D G A A A I T C = C D C A G I G D C (I) (A) C I A T C C D C T = T I G C A D C I T 0 DY12 = = C I A T C C D C T = T I G C A = C I T = = G D G A A A I T C = C D C A G = G D C 0 E101 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 D = G = G A A A = T C = C D C A G = G D C I = C = A T C C = C T = T I G C A = C I T 0 E104 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 E105 = = = = = = = = = = = A ? ? = = = = = = = = = = = = = = = = = = G ? ? = = = = = = = 0 E106 = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = 0 E107 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 E108 = G C = A T C C = C T A T I G C A (D) C I T = A G = G A A A = T C G C D C A G (I) G D C 0 E109 D G = = = = = = = = = = = (D) = = = = = = = I A = = = = = = = = = = = (I) = = = = = = = 0 E110 = G C = A T C C = C T A T I G C A = C I T = A G = G A A A = T C G C D C A G = G D C 0 E111 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 E112 = = C I A T C C D C T = T I G C A D C I T = = G D G A A A I T C = C D C A G I G D C 0 E113 = = = = = = = = = = = = ? ? = = = = = = ? = = = = = = = = = = = = ? ? = = = = = = ? 0 E114 D G = = ? = = = = ? ? = = = = = = = (G) = = I A = = ? = = = = ? ? = = = = = = = (C) = = 0 E115 = G C = A T C C = C T A T I G C A = C I T = A G = G A A A = T C G C D C A G = G D C 0 E116 = = = (D) = = = A = = = A ? ? (C) = ? ? ? ? ? = = = (I) = = = C = = = G ? ? (G) = ? ? ? ? ? 0 E117 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = G = = = = = = = = = 0 E119 = G C = A T C C D C T = T ? G C A = C I T = A G = G A A A I T C = C ? C A G = G D C 0 E120 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E121 (D) (G) G D G A A A I T C = ? ? C A G I G D ? (I) (A) C I A T C C D C T = ? ? G C A D C I ? 0 E122 D = G = G A A A = T C G C D C A G = G D C I = C = A T C C = C T A T I G C A = C I T 0 H101 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 H102 = = C I A T C C D C T = T I G C A D ? I T = = G D G A A A I T C = C D C A G I ? D C 0 H103 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 H104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H105 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H107 = = = = = = = = = = = = = ? = = = = ? = ? = = = = = = = = = = = = = ? = = = = ? = ? 0 H108 = = C I A T C C D C T = T I G C A D C I T = = G D G A A A I T C = C D C A G I G D C 0 H109 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H110 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H111 D G = = = = = = = = = = = ? = = = = = = = I A = = = = = = = = = = = ? = = = = = = = 0 H112 D = G = G A A A I T C = C D C A G = G D C I = C = A T C C D C T = T I G C A = C I T 0 H113 = = C I A T C C D C T = T I G C A D C I ? = = G D G A A A I T C = C D C A G I G D ? 0 H114 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H115 = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = 0 H116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H117 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H118 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 H119 = = C I A T C C D C T = T I G C A D C I T = = G D G A A A I T C = C D C A G I G D C 0 H120 = = C I A T C C D C T = T ? G C A D C I ? = = G D G A A A I T C = C ? C A G I G D ? 0 H121 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = 0 H122 = G = D = = = = = = = = = ? = = = I = = = = A = I = = = = = = = = = ? = = = D = = = 0 X101 = = = = = = = = = = = = = ? = = = = G = ? = = = = = = = = = = = = = ? = = = = C = ? 0 X102 = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = 0 X103 = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = 0 X104 D = = = = = = = = = = = = = ? = = = = = = I = = = = = = = = = = = = = ? = = = = = = 0 X105 = = = = = = = = = = = = ? = = = = = = = ? = = = = = = = = = = = = ? = = = = = = = ? 0 X106 (D) (G) G D G A A A I T C = C D C A G I G D C (I) (A) C I A T C C D C T = T I G C A D C I T 0 X107 = = C I A T C C D C T = T ? G C A D C I T = = G D G A A A I T C = C ? C A G I G D C 0 X108 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 X109 = = = = = = = = = = = = = ? = = ? ? ? ? ? = = = = = = = = = = = = = ? = = ? ? ? ? ? 0 X110 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 X111 D G = = = = = = = = = = = = = = = = = = = I A = = = = = = = = = = = = = = = = = = = 0 X112 = = = ? = = = = (D) = = = = = C A G = G D C = = = ? = = = = (I) = = = = = G C A = C I T 0 X113 = = = = = = = = = = = ? = ? = = ? ? ? ? ? = = = = = = = = = = = ? = ? = = ? ? ? ? ? 0 X114 D G = = = = = = = = = = ? ? = = = = = = = I A = = = = = = = = = = ? ? = = = = = = = 0 X115 (D) (G) G D G A A A I T C = C D C A G I G D C (I) (A) C I A T C C D C T = T I G C A D C I T 0 X116 = G C = A T C C D C T = ? I G C A = C I T = A G = G A A A I T C = ? D C A G = G D C 0 X117 D G = = = = = = = = = = ? ? = = = = = = = I A = = = = = = = = = = ? ? = = = = = = = 0 X118 D G = = = = = = = = = = ? = = = = = = = = I A = = = = = = = = = = ? = = = = = = = = 0 X119 = G = D = = = = = = = = = = = = = I = = = = A = I = = = = = = = = = = = = = D = = = 0 X120 D G = = = = = = = = = = = = = = = = = = = I A = = = = = = = = = = = = = = = = = = = 0 X121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 X122 = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = 0 X123 = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = = ? = = = = ? = = = 0 X124 = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = = = ? ? = = = = = = ? = = 1.00 ? ? ? ? ? ? = = = = = = = = = = = = = = = = = 0.51 = 1.00 = = = = = ? = = ? ? = = = = = = = = = = = = 0.68 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 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = ? = = = = = = = = = = = = = ? = = = = = = = = = = ? ? ? ? ? = = 1.00 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = ? = ? = = = ? ? = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 ? 1.00 1.00 1.00 ? ? ? ? ? ? 0.67 0.67 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = = ? = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 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 = = = = = 0.88 = = = = = 1.00 ? 1.00 1.00 1.00 ? ? ? 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = ? 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 ? 1.00 = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 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 = = = = = = = = = = = = = = = = = = = = = = 0.99 = 1.00 = = = = = = = = = = = = = 0.96 = = = 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 0.68 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 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 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 = = = = = = = = = = ? = = = = = = = = = 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 0.79 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = = 0.71 = = = = = = = = 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 = = ? = = = = ? ? = = = = = = = 0.73 = = = 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 = = = 0.65 = = = 0.94 = = = 0.94 ? ? 0.82 = ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 = = = = = = = = = = = = = = = = = = = = = 0.67 0.67 1.00 1.00 1.00 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 1.00 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 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 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 = = = = = = = = = ? = = = 0.96 = = = = = = = = = = = = = = = = ? = = = = 1.00 = ? = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = 1.00 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = = = = ? 0.69 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 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = ? ? ? ? ? = = = = = = = = = = = = = = ? = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = ? = = = = 0.65 = = = = = 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = = = = = = = = ? = ? = = ? ? ? ? ? 1.00 1.00 = = = = = = = = = = ? ? = = = = = = = 0.68 0.67 1.00 1.00 1.00 1.00 1.00 1.00 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 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 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 = = = = = = = = = = = = = 0.96 = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = = = = ? = = = = = = = = = = = = = = ? = = = = = = = = = END PHASEPROBS