************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 aqpn1.phase.inp aqpn1.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST aqpn1.phase.out_freqs : haplotype frequency estimates aqpn1.phase.out_pairs : most likely haplotype pairs for each individual aqpn1.phase.out_recom : estimates of recombination parameters aqpn1.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 39 Positions of loci: 444 1237 1239 3280 3544 3545 3961 4612 5294 5460 5475 5612 5618 5623 5812 5862 6034 6718 6946 6984 8197 8359 8903 9281 9497 9665 9979 10059 11490 12913 13805 14269 14322 14389 14645 16693 17287 17316 17453 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file aqpn1.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCCTAITTGIAGGGG 3 ACACCCCTAT 2 GIDCCACTCDG 2.000000 2 ACCCTAITTGIAGGGT 3 GCGCCTTCAT 2 GIICCGTCTDG 1.000000 3 ACCCTAITTGIAGGGT 3 GCGCTTTCAT 2 GIICCGCCTDG 1.000000 4 ACCCTAITTGIAGGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 5 ACCCTAITTGIAGGAG 3 ACACCTCTAT 2 GIICCGTCCIC 1.000000 6 ACCCTAITTGDGAGGT 4 GCGTCTCCCT 2 GDDTCACCCDC 3.000000 7 ACCCTAITTADGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 1.000000 8 ACCCTAICTGDAGGGT 3 GCGCCTCTAT 2 GIDTCACCCIC 2.000000 9 ACCCTADTTGIGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 1.000000 10 ACCCTADTTGIAGGGT 3 ATACTTTCCA 3 AIICCGTCTDG 1.000000 11 ACCCTADTTADGAGGG 3 GCGCCTCTAT 2 GIDTCACCCIC 1.000000 12 ACCCCADTTGIAGGGG 3 ACACCCCTAT 2 GIDTGACCCDC 1.000000 13 ACCCCTITTADGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 1.000000 14 ACCGTAITTGIGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 2.000000 15 ACCGTAITTGIAGGGT 1 ATACTTTCCA 3 GIICCGTCTDG 2.000000 16 ACCGTAICTGDGAGGG 3 GCGCCCTCCA 3 GIDCCACCTDG 1.000000 17 ACCGTAICTGDGAGGG 3 GCGCCCTCCA 3 GIICCGCTTDG 1.000000 18 ACTCTAITTGIAGGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 19 ACTCTAITTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 3.000000 20 ACTCTADTTGIGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 2.000000 21 ACTCTADTTGIAGGGT 3 ATACTTTCCA 3 AIICCGTCTDG 3.000000 22 ACTCTADTTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 2.000000 23 ACTCTADTTGDGAGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 24 ACTCTADTTGDAGGGT 3 GCGCCTCTAT 2 GIDTCACCCIC 1.000000 25 ACTCCAITTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 4.000000 26 ACTCCAITTGDGAGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 27 ACTCCAITCGIAGAAT 3 ACACCCCCCT 2 GDDTCACCCDC 1.000000 28 ACTCCADTTGIGAGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 29 ACTCCADTTGIAGGGG 3 ACACCCCTAT 2 GIDTGACCCDC 2.000000 30 ACTCCADTTGDGAGGG 3 GCGCCTTCCA 3 GIICCGCCTDG 1.000000 31 ACTCCADTTGDAGGGT 3 ATACTTTCCA 3 AIICCGTCTDG 1.000000 32 ACTCCTITTGIAGGGT 3 ATACCCCTAT 2 GIDTGACCCDC 1.000000 33 ACTCCTITTGIAGGGT 3 ATACTTTCCA 3 GIICCGTCTDG 1.000000 34 ACTCCTITTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 1.000000 35 ACTCCTDTTGIGGAAT 3 GCACCCCTAT 2 GIDTGACCCDC 1.000000 36 ACTCCTDTTGIAGGGG 3 ACACCCCTAT 2 GIDTGACCCDC 2.000000 37 ACTCCTDTTGIAGGGT 3 ATACTTTCCA 3 AIICCGTCTDG 1.000000 38 ACTCCTDTCGIAGGGG 3 GCGCTTTCAT 2 GIICCGTCTDG 1.000000 39 AGCCCAITTGIAGAAT 3 ACACCCTCCA 3 AIICCGTCTDG 1.000000 40 AGCCCAITTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 4.000000 41 AGCCCAITTGIAGAAT 3 ACACCCCTAT 2 GDDTCACCCDC 3.000000 42 AGCCCAITCGIAGAAT 3 ACACCCCCCT 2 GDDTCACCCDC 2.000000 43 AGCCCADTTGIAGGGT 3 ACACCCCTAT 2 GIDTGACCCDC 3.000000 44 AGCCCADTTGIAGAGT 4 GCGCCCCTAT 2 GIDTCACCCDC 2.000000 45 AGCCCADTTGIAGAAT 3 ACACCCCCAT 2 GIDTGACCCDC 1.000000 46 AGCCCADTTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 5.000000 47 AGCCCADTTGDGAGGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 48 AGCGTAITTGIAGGGT 3 ACACCCCCAT 4 GIICCGTCTDG 1.000000 49 TCCCTAITTGIGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 1.000000 50 TCCCTADTTGIGAGGG 3 ACACCCCTAT 2 GDDTCACCCDC 1.000000 51 TCCCCADTTGIAGGGG 3 ACACCCCTAT 2 GIDTGACCCDC 1.000000 52 TCCCCTITTADGAGGG 3 GCGCCTCTAT 2 GIDTCACCCIC 1.000000 53 TCCGTAITTGIGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 2.000000 54 TCCGTAITTGIGAGGG 3 ATACTTTCCA 3 AIICCGTCTDG 2.000000 55 TCCGTAITTGIGAGGG 3 ATACTCTCCA 3 AIICCGTCTDG 2.000000 56 TCCGTAITTGIAGGGT 3 ATACTTTCCA 3 AIICCGTCTDG 1.000000 57 TCCGTAITTADGAGGG 3 GCGCCTTCCA 3 GIDCCACTTDG 1.000000 58 TCCGTAICCGIGAGGG 3 ATACCCCCAT 2 GIICCGTCTDG 1.000000 59 TCCGTADTTGIAGGGG 3 ACACCCCTAT 2 GIDTGACCCDC 1.000000 60 TCCGTADTTGIAGAGT 4 GCGTCCCCCT 2 GDDTCACCCDC 1.000000 61 TCCGTADTTGIAGAAT 3 ACACCCCTAT 2 GIDTGACCCDC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (14,20) DY02: (6,38) DY03: (7,46) DY04: (4,28) DY05: (17,18) DY06: (15,57) DY07: (21,58) DY08: (3,53) DY09: (2,9) DY10: (11,53) DY11: (20,54) DY12: (16,50) DY13: (37,49) DY14: (6,55) DY15: (10,15) DY16: (8,52) DY17: (26,33) DY18: (14,54) DY19: (1,5) DY20: (21,21) DY21: (8,48) DY22: (1,55) DY23: (30,13) DY24: (6,24) E101: (19,25) E102: (25,25) E103: (23,29) E104: (29,59) E105: (40,46) E106: (31,60) E107: (40,46) E108: (19,43) E109: (25,40) E110: (44,61) E111: (35,46) E112: (41,47) E113: (40,41) E114: (22,41) E115: (36,44) E116: (32,39) E117: (12,45) E118: (19,51) E119: (34,42) E120: (22,36) E121: (27,56) E122: (42,46) E123: (43,43) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 [A] C C G T A I T T G I G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G A C T C T A D T T G I G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY02 A C (C) C (T) (A) (I) T T G D (G) (A) G G T 4 G C G T C [T] C C C T 2 G D D T C A C C C D C A C (T) C (C) (T) (D) T C G I (A) (G) G G G 3 G C G C T T T C A T 2 G I I C C G T C T D G 0 DY03 A C C C T A (I) T T A D G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G A G C C C A (D) T T G I A G [A] [A] [T] 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 DY04 A C (C) C (T) A (I) T T G I (A) (G) G G T 4 G C G T C C C C C T 2 G D D T C A C C C D C A C (T) C (C) A (D) T T G I (G) (A) G G T 4 G C G T C C C C C T 2 G D D T C A C C C D C 0 DY05 A C (C) (G) T A I (C) T G D G A G G G 3 G C G C C C T C C A 3 G I I C C G C (T) T D G A C (T) (C) T A I (T) T G I A G G G T 4 G C G T C C C C C T 2 G D D T C A C (C) C D C 0 DY06 A C C G T A I T T G I A G G G T [1] A T A C T T T C C A 3 G I I C C G T C T D G [T] C C G T A I T T A D G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY07 (A) C (T) (C) T A (D) (T) (T) G I (A) (G) G G (T) 3 A T A C (T) (T) (T) C C (A) (3) (A) I I C C G T C T D G (T) C (C) (G) T A (I) (C) (C) G I (G) (A) G G (G) 3 A T A C (C) (C) (C) C [A] (T) (2) (G) I I C C G T C T D G 0 DY08 (A) C C [C] T A I T T G I (A) (G) G G (T) 3 G C G C T T T C A T 2 G I I C C G C C T D G (T) C C [G] T A I T T G I (G) (A) G G (G) 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY09 A C C C T A (I) T T G I (A) (G) G G (T) 3 G C G C C T T C A T 2 G I I C C G T C T D G A C C C T A (D) T T G I (G) (A) G G (G) 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY10 (A) C C (C) T A (D) T T (A) (D) [G] [A] G G [G] 3 G C G C C T C T A T 2 G I D T C A C C C I C (T) C C (G) T A (I) T T (G) (I) G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY11 (A) C (T) (C) T A (D) T T G I G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G (T) C (C) (G) T A (I) T T G I G A G G G 3 A T A C T T T C C A 3 A I I C C G T C T D G 0 DY12 (A) C C (G) T A (I) (C) T G (D) G A G G G 3 G C G C C C T C C A 3 G I D C C A C C T D G (T) C C (C) T A (D) (T) T G (I) G A G G G 3 A C A C C C C T A T 2 G D D T C A C C C D C 0 DY13 (A) C (T) C (C) (T) (D) T T G I A G G G T 3 A T A C T T T C C A 3 A I I C C G T C T D G (T) C (C) C (T) (A) (I) T T G I G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G 0 DY14 A C C C T A I T T G D G A G G T 4 G C G T C (T) C C C T 2 G D D T C A C C C D C T C C G T A I T T G I G A G G G 3 A T A C T (C) T C C A 3 A I I C C G T C T D G 0 DY15 A C C (C) T A D T T G I A G G G T (3) A T A C T T T C C A 3 A I I C C G T C T D G A C C (G) T A I T T G I A G G G T (1) A T A C T T T C C A 3 G I I C C G T C T D G 0 DY16 A C C C (T) (A) I (C) T G D A G G G T 3 G C G C C T C T A T 2 G I D T C A C C C I C [T] C C C (C) (T) I (T) T A D [G] [A] G G [G] 3 G C G C C T C T A T 2 G I D T C A C C C I C 0 DY17 A C T C C (A) I T T G D G A G G T 4 G C G T C C C C C T 2 G D D T C A C C C D C A C T C C (T) I T T G I A G G G T 3 A T A C T T T C C A 3 G I I C C G T C T D G 0 DY18 (A) C C G T A I T T G I G A G G G 3 G C G C C T T C C A 3 G I D C C A C T T D G (T) C C G T A I T T G I G A G G G 3 A T A C T T T C C A 3 A I I C C G T C T D G 0 DY19 A C C C T A I T T G I A G G (G) G 3 A C A C C (C) C T A T 2 G I D C C A C T C D G A C C C T A I T T G I A G G (A) G 3 A C A C C (T) C T A T 2 G I I C C G [T] C C I C 0 DY20 A C T C T A D T T G I A G G G T 3 A T A C T T T C C A 3 A I I C C G T C T D G A C T C T A D T T G I A G G G T 3 A T A C T T T C C A 3 A I I C C G T C T D G 0 DY21 A (C) C (C) T A I (C) T G D A G G G T 3 G C G C C T C T A T (2) G I D T C A C C C I C A (G) C (G) T A I (T) T G I A G G G T 3 A C A C C C C C A T (4) G I I C C G [T] C T D G 0 DY22 A C C C T A I T T G I A G G G G 3 A C A C C C C T A T 2 G I D C C A C T C D G T C C G T A I T T G I G A G G G 3 A T A C T C T C C A 3 A I I C C G T C T D G 0 DY23 A C (T) C C (A) (D) T T (G) D G A G G [G] 3 G C G C C T T C C A 3 G I (I) C C (G) C (C) T D G [A] C (C) C C (T) (I) T T (A) D G A G G G 3 G C G C C T T C C A 3 G I (D) C C (A) C (T) T D G 0 DY24 A C (C) C T A (I) T T G D G A G G T 4 G C G T C T C C C T 2 G D D T C A C C C D C A C (T) C T A (D) T T G D A G G G T 3 G C G C C T C T A T 2 G I D T C A C C C I C 0 E101 A C T C T A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A C T C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E102 A C T C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A C T C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E103 A C T C (T) A D T T G D G A G G T 4 G C G T C C C C C T 2 G D D T C A C C C D C A C T C (C) A D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E104 A C T C C A D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C T C C G T A D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E105 A G C C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A G C C C A D T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E106 (A) C (T) (C) (C) A D T T G (D) A G (G) G T 3 A T A C T T T C C A 3 [A] I I C C G T C T D G (T) C (C) (G) (T) A D T T G (I) A G (A) G T 4 G C G T C C C C C T 2 G D D T C A C C C D C 0 E107 A G C C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A G C C C A D T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E108 A (C) (T) C (T) A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A (G) (C) C (C) A D T T G I A G G G T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E109 A C T C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A G C C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E110 (A) (G) C (C) (C) A D T T G I A G A G T 4 G C G C C C C T A T 2 G I D T C A C C C D C (T) (C) C (G) (T) A D T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E111 A C T C C T D T T G I (G) G A A T 3 (G) C A C C C C T A T 2 G I D T G A C C C D C A G C C C A D T T G I (A) G A A T 3 (A) C A C C C C T A T 2 G I D T G A C C C D C 0 E112 A G C C C A (I) T T G I A G A A T 3 A C A C C C C T A T 2 G D D T C A C C C D C A G C C C A (D) T T G D G A G G T 4 G C G T C C C C C T 2 G D D T C A C C C D C 0 E113 A G C C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A G C C C A I T T G I A G A A T 3 A C A C C C C T A T 2 G D D T C A C C C D C 0 E114 A (C) (T) C (T) A (D) T T G I A G A A T 3 A C A C C C C T A T 2 G (I) D T (G) A C C C D C A (G) (C) C (C) A (I) T T G I A G A A T 3 A C A C C C C T A T 2 G (D) D T (C) A C C C D C 0 E115 A (C) (T) C C (T) D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C A (G) (C) C C (A) D T T G I A G A G T 4 G C G C C C C T A T 2 G I D T C A C C C D C 0 E116 A C T C C T I T T G I A G G G T 3 A T A C C C C T A T 2 G I D T G A C C C D C A G C C C A I T T G I A G A A T 3 A C A C C C T C C A 3 A I I C C G T C T D G 0 E117 [A] (C) C C C A D T T G I A G G G G 3 A C A C C C C (T) A T 2 G I D T G A C C C D C A (G) C C C A D T T G I A G A A T 3 A C A C C C C (C) A T 2 G I D T G A C C C D C 0 E118 (A) C (T) C (T) A I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C (T) C (C) C (C) A D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E119 A (C) (T) C C (T) I T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A (G) (C) C C (A) I T C G I A G A A T 3 A C A C C C C C C T 2 G D D T C A C C C D C 0 E120 A C T C (T) (A) D T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C A C T C (C) (T) D T T G I A G G G G 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E121 (A) C (T) (C) (C) A I T C G I A G A A T 3 A C A C C C C C C T 2 G D D T C A C C C D C (T) C (C) (G) (T) A I T T G I A G G G T 3 A T A C T T T C C A 3 A I I C C G T C T D G 0 E122 A G C C C A (I) T C G I A G A A T 3 A C A C C C C C C T 2 G D D T C A C C C D C A G C C C A (D) T T G I A G A A T 3 A C A C C C C T A T 2 G I D T G A C C C D C 0 E123 A G C C C A D T T G I A G G G T 3 A C A C C C C T A T 2 G I D T G A C C C D C A G C C C A D T T G I A G G G T 3 A C A C C C C T A T 2 G I D T G A C C C D 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 DY01 ? = C G = = I = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = ? = T C = = D = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = 0 DY02 = = (C) = (T) (A) (I) = T = D (G) (A) = = T 4 = = = ? C ? ? = C = = = D D T = A C = C = C = = (T) = (C) (T) (D) = C = I (A) (G) = = G 3 = = = ? T ? ? = A = = = I I C = G T = T = G 0 DY03 = C = = T = (I) = = A D ? ? ? ? ? ? G = G = = T T C C A 3 = = = C C = = T T = G = G = = C = (D) = = G I ? ? ? ? ? ? A = A = = C C T A T 2 = = = T G = = C C = C 0 DY04 = = (C) = (T) = (I) = = = = (A) (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = (C) = (D) = = = = (G) (A) = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY05 = = (C) (G) = = = (C) = = D G A = = G 3 = = = C = = T = = A 3 = I I C = G = (T) T = G = = (T) (C) = = = (T) = = I A G = = T 4 = = = T = = C = = T 2 = D D T = A = (C) C = C 0 DY06 ? = = = = = = = = G I ? ? ? ? ? ? A ? ? = T ? = = = = = = = I = = G T C = = = ? = = = = = = = = A D ? ? ? ? ? ? G ? ? = C ? = = = = = = = D = = A C T = = = 0 DY07 (A) = (T) (C) = = (D) (T) (T) = = (A) (G) = = (T) = = = = = (T) (T) (T) = ? (A) (3) (A) = = = = = = = = = = (T) = (C) (G) = = (I) (C) (C) = = (G) (A) = = (G) = = = = = (C) (C) (C) = ? (T) (2) (G) = = = = = = = = = = 0 DY08 (A) = = ? = = = ? = = = (A) (G) = = (T) = = = = ? T ? ? = A T 2 = = I = = G = C = = = (T) = = ? = = = ? = = = (G) (A) = = (G) = = = = ? C ? ? = C A 3 = = D = = A = T = = = 0 DY09 ? = = = = = (I) = = = = (A) (G) = = (T) = = = ? = = = = = A T 2 = = I = = G T C = = = ? = = = = = (D) = = = = (G) (A) = = (G) = = = ? = = = = = C A 3 = = D = = A C T = = = 0 DY10 (A) = = (C) = = (D) = = (A) (D) ? ? ? ? ? ? = = = = = = C T A T 2 = = = T = = = C C I C (T) = = (G) = = (I) = = (G) (I) ? ? ? ? ? ? = = = = = = T C C A 3 = = = C = = = T T D G 0 DY11 (A) = (T) (C) = = (D) = = = = = = = = = = G C G = C = = = = = = G = D = = A C T = = = (T) = (C) (G) = = (I) = = = = = = = = = = A T A = T = = = = = = A = I = = G T C = = = 0 DY12 (A) = = (G) = = (I) (C) = = (D) = = = = = = G = G ? = = T C C A 3 = I = C = = = = T = G (T) = = (C) = = (D) (T) = = (I) = = = = = = A = A ? = = C T A T 2 = D = T = = = = C = C 0 DY13 (A) = (T) = (C) (T) (D) = = = = A G = = T = A T A = T = = = = = = A = I = = G T C = = = (T) = (C) = (T) (A) (I) = = = = G A = = G = G C G = C = = = = = = G = D = = A C T = = = 0 DY14 A = = C = = = = = = D = = = = T 4 G C G T C (T) C = = T 2 G D D T = A C = C = C T = = G = = = = = = I = = = = G 3 A T A C T (C) T = = A 3 A I I C = G T = T = G 0 DY15 = = = (C) = = D = = = = = = = = = (3) = = = = = = = = = = = A = = = = = = = ? = ? = = = (G) = = I = = = = = = = = = (1) = = = = = = = = = = = G = = = = = = = ? = ? 0 DY16 ? = = = (T) (A) = (C) = G = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = ? = = = (C) (T) = (T) = A = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = 0 DY17 = = = = = (A) = = = = D G A = = = 4 G C G T C C C = = T 2 = D D T = A C = C = C = = = = = (T) = = = = I A G = = = 3 A T A C T T T = = A 3 = I I C = G T = T = G 0 DY18 (A) = = = = = = ? = = = = = = = = = G C G = C = = = = = = G = D = = A C T = = = (T) = = = = = = ? = = = = = = = = = A T A = T = = = = = = A = I = = G T C = = = 0 DY19 = = = = = = = = = = = = = = (G) = = = = = = ? (C) = = = = = = = D = = A ? T = D G = = = = = = = = = = = = = = (A) = = = = = = ? (T) = = = = = = = I = = G ? C = I C 0 DY20 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY21 = (C) = (C) = = = (C) = = D = = = = = = G = G = = ? = T = = (2) = = D T = A ? = C I C = (G) = (G) = = = (T) = = I = = = = = = A = A = = ? = C = = (4) = = I C = G ? = T D G 0 DY22 A = = C = = = ? = = = A G = = = = = C = = C = ? T A T 2 G = D = = A C T C = = T = = G = = = ? = = = G A = = = = = T = = T = ? C C A 3 A = I = = G T C T = = 0 DY23 ? = (T) = = (A) (D) = = (G) = ? ? ? ? ? ? = = = = = = = = ? = = = = (I) = = (G) = (C) = = = ? = (C) = = (T) (I) = = (A) = ? ? ? ? ? ? = = = = = = = = ? = = = = (D) = = (A) = (T) = = = 0 DY24 = = (C) = = = (I) = = = = G A = = = 4 = = = ? = = = C C = = = D = = = = = = = D = = = (T) = = = (D) = = = = A G = = = 3 = = = ? = = = T A = = = I = = = = = = = I = 0 E101 = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = 0 E103 = = = = (T) = = = = = D G A = = T 4 G = G T = = = C C = = = D = = C = = = = = = = = = = (C) = = = = = I A G = = G 3 A = A C = = = T A = = = I = = G = = = = = = 0 E104 A = T C C = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T = C G T = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 = = = = = = I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E106 (A) = (T) (C) (C) = = = = = (D) = = (G) = = 3 A T A C T T T = = A 3 ? I I C = G T = T = G (T) = (C) (G) (T) = = = = = (I) = = (A) = = 4 G C G T C C C = = T 2 ? D D T = A C = C = C 0 E107 = = = = = = I = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = D = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = (C) (T) = (T) = I = = = = = = A A = = ? ? ? ? = = = = = = = ? = = = = = = = = = = = (G) (C) = (C) = D = = = = = = G G = = ? ? ? ? = = = = = = = ? = = = = = = = = = = 0 E109 = C T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 (A) (G) = (C) (C) = = = = = = = = = G = 4 G = G = = ? ? = = = = = = = = C = = = = = = (T) (C) = (G) (T) = = = = = = = = = A = 3 A = A = = ? ? = = = = = = = = G = = = = = = 0 E111 = C T = = T = ? = = = (G) = = = = = (G) = = = ? = = ? ? = ? ? = = = = = = = = = = = G C = = A = ? = = = (A) = = = = = (A) = = = ? = = ? ? = ? ? = = = = = = = = = = 0 E112 = = = = = = (I) = = = I A G A A = 3 A = A C = = = T A = = = = = = = = = = = = = = = = = = = (D) = = = D G A G G = 4 G = G T = = = C C = = = = = = = = = = = = = 0 E113 = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = I = = G = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = D = = C = = = = = = 0 E114 = (C) (T) = (T) = (D) ? = = = = = = = = = = = = = = = = = = = = = (I) = = (G) = = = = = = = (G) (C) = (C) = (I) ? = = = = = = = = = = = = = = = = = = = = = (D) = = (C) = = = = = = 0 E115 = (C) (T) = = (T) = = = = = = = G = G 3 A = A = = = = = = = = = = = = G = = = = = = = (G) (C) = = (A) = = = = = = = A = T 4 G = G = = = = = = = = = = = = C = = = = = = 0 E116 = C T = = T = = = = = = = G G = = = T = ? ? = ? T A T 2 G = D T G A C = C = C = G C = = A = = = = = = = A A = = = C = ? ? = ? C C A 3 A = I C C G T = T = G 0 E117 ? (C) = = = = = = = = = = = G G G = = = = = = = = (T) = = = = = = = = = = ? = = = ? (G) = = = = = = = = = = = A A T = = = = = = = = (C) = = = = = = = = = = ? = = = 0 E118 (A) = (T) = (T) = I = = = = = = A A T = = = = = = = = = = = = = = = = = = = = = = = (T) = (C) = (C) = D = = = = = = G G G = = = = = = = = = = = = = = = = = = = = = = = 0 E119 = (C) (T) = = (T) = = T = = = = = = = = = = = = = = = T A = = ? I = = G = = = = = = = (G) (C) = = (A) = = C = = = = = = = = = = = = = = = C C = = ? D = = C = = = = = = 0 E120 = = = = (T) (A) = = = = = = = A A T = = = = = = = = = = = = = = = = = = = = = = = = = = = (C) (T) = = = = = = = G G G = = = = = = = = = = = = = = = = = = = = = = = 0 E121 (A) = (T) (C) (C) = = = C = = = = A A = = = C = = C C C = = T 2 G D D T = A C = C = C (T) = (C) (G) (T) = = = T = = = = G G = = = T = = T T T = = A 3 A I I C = G T = T = G 0 E122 = = = = = = (I) = C = = = = = = = = = ? ? = = = = C C = = = D = = C = = = = = = = = = = = = (D) = T = = = = = = = = = ? ? = = = = T A = = = I = = G = = = = = = 0 E123 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS ? = 0.97 0.99 = = 0.94 = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = 0.74 = 0.76 0.76 0.75 = 0.97 = 0.92 0.86 0.86 = = 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 = 0.74 = = 1.00 1.00 ? ? ? ? ? ? 1.00 = 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 = 0.84 = 0.79 = = = = 0.83 0.83 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.66 0.72 = = = 0.90 = = 0.90 0.98 0.98 = = 1.00 1.00 = = = 1.00 = = 1.00 = = 1.00 1.00 = 1.00 1.00 1.00 = 1.00 = 0.84 1.00 = 1.00 ? = = = = = = = = 1.00 1.00 ? ? ? ? ? ? 1.00 ? ? = 1.00 ? = = = = = = = 1.00 = = 1.00 1.00 1.00 = = = 0.70 = 0.70 0.70 = = 0.71 0.75 0.69 = = 0.65 0.65 = = 0.65 = = = = = 0.83 0.83 0.83 = ? 0.83 0.83 0.83 = = = = = = = = = = 0.50 = = ? = = = ? = = = 0.89 0.89 = = 0.89 = = = = ? 1.00 ? ? = 1.00 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = = = ? = = = = = 0.52 = = = = 0.73 0.73 = = 0.73 = = = ? = = = = = 1.00 1.00 1.00 = = 1.00 = = 1.00 1.00 1.00 = = = 0.58 = = 0.51 = = 0.59 = = 0.67 0.67 ? ? ? ? ? ? = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = = = 1.00 1.00 1.00 1.00 0.80 = 0.81 0.83 = = 0.83 = = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 0.69 = = 0.57 = = 0.70 0.78 = = 0.80 = = = = = = 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 = 0.51 0.51 0.57 = = = = 0.96 0.96 = = 0.96 = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = 0.95 = = 0.96 = = = = = = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.63 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = 0.87 = = 0.95 = = = = = = = = = 0.84 = = = = = = = = = = = 0.97 = = = = = = = ? = ? ? = = = 0.80 0.80 = 0.78 = 0.94 = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.56 = = = = 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 0.74 = = = = = = ? = = = = = = = = = 1.00 1.00 1.00 = 1.00 = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = 0.52 = = = = = = ? 0.67 = = = = = = = 1.00 = = 1.00 ? 1.00 = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.59 = 0.88 = = = 0.85 = = 1.00 = = = = = = 1.00 = 1.00 = = ? = 1.00 = = 0.55 = = 1.00 1.00 = 1.00 ? = 1.00 1.00 1.00 0.96 = = 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 = = ? = 0.77 = = 0.76 0.82 = = 0.83 = ? ? ? ? ? ? = = = = = = = = ? = = = = 0.74 = = 0.74 = 0.74 = = = = = 0.76 = = = 0.77 = = = = 1.00 1.00 = = = 1.00 = = = ? = = = 1.00 1.00 = = = 1.00 = = = = = = = 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0.71 = = = = = 0.99 0.99 0.99 = = 1.00 1.00 1.00 = 1.00 1.00 = = = 1.00 1.00 = = = 1.00 = = 1.00 = = = = = = 0.96 = 0.96 1.00 0.95 = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.58 = 0.58 0.58 0.54 = = = = = 0.56 = = 0.74 = = 1.00 1.00 1.00 1.00 1.00 1.00 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 0.73 = 0.72 = 0.92 = = = = = = 0.93 0.93 = = ? ? ? ? = = = = = = = ? = = = = = = = = = = = 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.62 0.62 = 0.62 0.62 = = = = = = = = = 1.00 = 1.00 1.00 = 1.00 = = ? ? = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = = 1.00 = ? = = = 0.50 = = = = = 0.50 = = = ? = = ? ? = ? ? = = = = = = = = = = = = = = = = 0.81 = = = 1.00 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 0.88 = 0.88 = 0.84 ? = = = = = = = = = = = = = = = = = = = = = 0.87 = = 0.87 = = = = = = = 0.88 0.88 = = 0.87 = = = = = = = 1.00 = 1.00 1.00 1.00 = 1.00 = = = = = = = = = = = = 1.00 = = = = = = = 0.92 0.92 = = 0.92 = = = = = = = 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 ? 0.80 = = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = 0.50 = = = = = = = = = = ? = = = 0.62 = 0.62 = 0.53 = 0.94 = = = = = = 0.97 0.97 0.97 = = = = = = = = = = = = = = = = = = = = = = = = 0.53 0.53 = = 0.53 = = 1.00 = = = = = = = = = = = = = = = 1.00 1.00 = = ? 1.00 = = 1.00 = = = = = = = = = = 0.73 0.73 = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = 0.57 = 0.57 0.58 0.58 = = = 1.00 = = = = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = = = = = = 0.78 = 1.00 = = = = = = = = = ? ? = = = = 1.00 1.00 = = = 1.00 = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS