************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 avr1b.phase.inp avr1b.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST avr1b.phase.out_freqs : haplotype frequency estimates avr1b.phase.out_pairs : most likely haplotype pairs for each individual avr1b.phase.out_recom : estimates of recombination parameters avr1b.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 58 Positions of loci: 94 338 734 799 1225 1354 1376 1389 1440 1613 2015 2142 2469 2887 3068 3169 4754 5165 5509 5617 5701 5921 6027 6305 6484 6579 6685 6812 6894 7024 7301 7347 7361 7668 7969 8008 8104 8230 8448 8617 8698 8711 8766 9027 9055 9220 9221 9272 9328 9333 9498 9680 9895 10630 10872 11087 11208 11280 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file avr1b.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ACCCCCTCCACATGGTGCACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGGC 1.000000 2 ACCCCCTCCACATGGTGCGTCTTCGGACTCCAGAAGITGCGACGGGGGGGTDIGAAGC 1.000000 3 ACCCCTTCCACATGGTGCACCCGCGGACTCTAGTCGDCACGTTGACAAGAADIATGGC 2.000000 4 ACCCCTTCCACATGGTGGGCCCTCGAACTCCCAAAGITGGATCGGCGGAGTDDAAGGC 1.000000 5 ACCCCTTCCACACCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIATGAT 1.000000 6 ACCCCTCGTACATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGGC 35.000000 7 ACCCCTCGTACATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGGT 1.000000 8 ACCCCTCGTACATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGAC 1.000000 9 ACCCCTCGTACATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGAT 4.000000 10 ACCCTCTCCACATGGTGCGTCTTCGGACTCCAGAAAITGCGACGGGGGGGTDIGAAGC 1.000000 11 ACCCTCTCCACATGGTGCGTCTTCGGACTCCAGAAAITGCGACGGGGGGGTDIGAGGC 3.000000 12 ACCCTCTCCACATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGGC 1.000000 13 ACTCCCCGCACTCCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGAT 1.000000 14 ACTCCCCGCGCTCGCTGGGCCCTTGGACTCCCAAAGITGCGACGGGGGGGTDIATGAT 1.000000 15 ACTCCCCGCGCTCCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGGC 1.000000 16 ACTCCCCGCGCTCCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGAC 1.000000 17 ACTCCCCGCGCTCCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGAT 1.000000 18 ACTCCCCGCGCTCCCTACACCCTCTGGGCGCCGTAGDCACGTTGACGAGATIIATGAT 3.000000 19 ATTCCCCGTAGATGGTGGGCCCTTGAACTCCCAAAGITGGATCGACGGAGTDDAAGGC 2.000000 20 ATTCCCCGTAGATGGTGGGCCCTTGAACTCCCAAAGITGGATCGACGGAGTDDATGAT 1.000000 21 ATTCCCCGTAGATGGTGGGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGGC 5.000000 22 ATTTCCCGCGCATGGCGCACGCGCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGGC 1.000000 23 ATTTCCCGTACATGGTGCGCCCTTGAACTCCCAAAGITGGATCGGCGGAGTDDAAGAC 1.000000 24 ATTTCCCGTGCATGGTGCGCCTTCGGACTCTAGTCGDCACGTTGACAAGAAIIATGGC 2.000000 25 ATTTCCCGTGCATGGTGCGCCTTCGGACTCTAGTCGDCACGTTAACAAGAAIIAAGGC 2.000000 26 ATTTCCCGTGCATGGTGCGCCTTCGGACTCTAGTCGDCACGTTAACAAGAAIIATGGC 2.000000 27 ATTTCCCGTGCATGGTGCGCCTTCGGACTCTAGTCGDCACGTTAACAAGAAIIATGGT 2.000000 28 ATTTCCCGTGCATGGTGCGCCTTCGGACTCTAGTCGDCACGTTAACAAGAAIIATGAT 7.000000 29 GCCCCTTCCACATGGCGCACGCGCTGGGCGCCGTAGDCACGTTGACGAGATIIAAAGC 5.000000 30 GCCCCTTCCACATGGCGCACGCGCTGGGCGCCGTAGDCACGTTGACGAGATIIAAGGC 3.000000 31 GCCCTCTCCACATGGTGCGTCTTCGGACTCCAGAAAITGCGACGGGGGGGTDIGAGGC 1.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (12,29) DY02: (10,19) DY03: (14,22) DY04: (2,11) DY05: (16,18) DY06: (13,21) DY07: (11,30) DY08: (24,28) DY09: (18,29) DY10: (6,26) DY11: (24,27) DY12: (6,21) DY13: (6,31) DY14: (11,30) DY15: (18,21) DY16: (5,29) DY17: (26,29) DY18: (6,30) DY19: (20,21) DY20: (17,29) DY21: (1,19) DY22: (4,21) DY23: (3,23) DY24: (3,6) E101: (6,6) E102: (6,9) E103: (6,9) E104: (6,6) E105: (6,28) E106: (6,9) E107: (6,6) E108: (6,25) E109: (6,6) E110: (6,15) E111: (6,6) E112: (6,7) E113: (6,28) E114: (6,28) E115: (28,28) E116: (6,6) E117: (6,6) E118: (8,9) E119: (6,6) E120: (6,27) E121: (6,28) E122: (6,6) E123: (6,25) 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 C T C T C C A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A A G C 0 DY02 A C C C T C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A A I T G C G A C G G G G G G G T D I G A (A) G C A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G A C G G A G T D D A A (G) G C 0 DY03 A (C) T (C) C C C G C G C (T) (C) G (C) T G G G C C C T T G G A C T C C C A A A G I T G C G A C G G G G G G G T D I A T G A T A (T) T (T) C C C G C G C (A) (T) G (G) C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C 0 DY04 A C C C (C) C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A (G) I T G C G A C G G G G G G G T D I G A (A) G C A C C C (T) C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A (A) I T G C G A C G G G G G G G T D I G A (G) G C 0 DY05 A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A (A) G A C A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A (T) G A T 0 DY06 A C T C C C C G C A C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G A T A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 DY07 A C C C T C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A A I T G C G A C G G G G G G G T D I G A G G C G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C 0 DY08 A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T G A C A A G A A I I A T G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G A T 0 DY09 A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A T G A T G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A A G C 0 DY10 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G G C 0 DY11 A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T G A C A A G A A I I A T G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G G T 0 DY12 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 DY13 (A) C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C (G) C C C T C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A A I T G C G A C G G G G G G G T D I G A G G C 0 DY14 A C C C T C T C C A C A T G G T G C G T C T T C G G A C T C C A G A A A I T G C G A C G G G G G G G T D I G A G G C G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C 0 DY15 A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A T G A T A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 DY16 A C C C C T T C C A C A C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A T G A T G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A A G C 0 DY17 A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G G C G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A A G C 0 DY18 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C 0 DY19 A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G (A) C G G A G T D D A T G A T A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G (G) C G G A G T D D A A G G C 0 DY20 A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G A T G C C C C T T C C A C A T G G C G C A C G C G C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A A G C 0 DY21 A C C C C C T C C A C A T G G T G C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C A T T C C C C G T A G A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G A C G G A G T D D A A G G C 0 DY22 A C C C C T T C C A C A T G G T G G G C C C T (C) G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T C C C C G T A G A T G G T G G G C C C T (T) G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 DY23 A C C C C T T C C A C A T G G T G C A C C C G C G G A C T C T A G T C G D C A C G T T G A C A A G A A D I A T G G C A T T T C C C G T A C A T G G T G C G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A C 0 DY24 A C C C C T T C C A C A T G G T G C A C C C G C G G A C T C T A G T C G D C A C G T T G A C A A G A A D I A T G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E101 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E102 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A T 0 E103 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A T 0 E104 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E105 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G A T 0 E106 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A T 0 E107 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E108 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A A G G C 0 E109 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E110 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C T C C C C G C G C T C C C T A C A C C C T C T G G G C G C C G T A G D C A C G T T G A C G A G A T I I A A G G C 0 E111 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E112 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G T 0 E113 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G (G) (C) A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G (A) (T) 0 E114 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G (G) (C) A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G (A) (T) 0 E115 A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G A T A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G A T 0 E116 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E117 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E118 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G A T 0 E119 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E120 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G (C) A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A [T] G G (T) 0 E121 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A T G A T 0 E122 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C 0 E123 A C C C C T C G T A C A T G G T G G G C C C T T G A A C T C C C A A A G I T G G A T C G G C G G A G T D D A A G G C A T T T C C C G T G C A T G G T G C G C C T T C G G A C T C T A G T C G D C A C G T T A A C A A G A A I I A A G G 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 A = = = T C = = = = = = = = = T = G G = C = T T G A A C T C = = A A = = I T G G A = C = G = = G A G = D D = = G = = G = = = C T = = = = = = = = = C = C A = G = G C T G G G C G = = G T = = D C A C G = T = A = = A G A = I I = = A = = 0 DY02 = C C = T = T C C = C = = = = = = C = T = T = C = G = = = = = A G = = A = = = C G A = = G G = = G = = = I G = (A) = = = T T = C = C G T = G = = = = = = G = C = C = T = A = = = = = C A = = G = = = G A T = = A C = = A = = = D A = (G) = = 0 DY03 = (C) = (C) = = = = = = = (T) (C) = (C) T = G G = C = T T G = A C T C = = A A = = I T G = = A C = G G = G = G = D = = T = A T = (T) = (T) = = = = = = = (A) (T) = (G) C = C A = G = G C T = G G C G = = G T = = D C A = = T T = A C = A = A = I = = A = G C 0 DY04 = = = = (C) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = (A) = = = = = = (T) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = (G) = = 0 DY05 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = (T) = = T 0 DY06 = C = = = = = = C = C T C C C = A C A = = = = C T G G G C G = = G T = = D C A C G = T = A = = A G A = I I = = = A T = T = = = = = = T = G A T G G = G G G = = = = T G A A C T C = = A A = = I T G G A = C = G = = G A G = D D = = = G C 0 DY07 A = = = T C = = = = = = = = = T = = G T C T T = G = A C T C = A = A = A I T G = = A C = G G = G = G = D = G = = = = G = = = C T = = = = = = = = = C = = A C G C G = T = G G C G = C = T = G D C A = = T T = A C = A = A = I = A = = = = 0 DY08 = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = = = = = = = = = = G = = = = = = = = = = = = G C = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = = = = = = = = = = A = = = = = = = = = = = = A T 0 DY09 A = T = = C C G = G = T C C C T A = = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T G A T G = C = = T T C = A = A T G G C G = = = G = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A G C 0 DY10 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D = A = = = = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I = T = = = 0 DY11 = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = G = = = = = = = = = = = = = C = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = A = = = = = = = = = = = = = T 0 DY12 = C C = = T = = = = C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T T = = C = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY13 (A) = = = C T C G T = = = = = = = = G = C = C = T = A = = = = = C A = = G = = = G A T = = = C = = A = = = D A = = = = (G) = = = T C T C C = = = = = = = = C = T = T = C = G = = = = = A G = = A = = = C G A = = = G = = G = = = I G = = = = 0 DY14 A = = = T C = = = = = = = = = T = = G T C T T = ? = A C T ? = A = A = A I T G = = A C = G G = G = G = D = G = = = = G = = = C T = = = = = = = = = C = = A C G C G = ? = G G C ? = C = T = G D C A = = T T = A C = A = A = I = A = = = = 0 DY15 ? ? ? = = = = = C G C T C C C = A C A = = = = C T G G G C G = = G T = = D C A C G = T = A = = A G A = I I = T = A T ? ? ? = = = = = T A G A T G G = G G G = = = = T G A A C T C = = A A = = I T G G A = C = G = = G A G = D D = A = G C 0 DY16 A = = = = = = = = = = = C C C T A = = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T G A T G = = = = = = = = = = = T G G C G = = = G = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A A G C 0 DY17 A T T T = C C G T G = = = = = T = = G = C T T = G = A C T C T A = = C = = = = = = = = A = = A = = = A = = = T G = = G C C C = T T C C A = = = = = C = = A = G C G = T = G G C G C C = = A = = = = = = = = G = = G = = = T = = = A A = = 0 DY18 A = = = = = C G T = = = = = = T = G G = C = T T G A A C T C = = A A = = I T G G A = C = G = = G A G = D D = = = = = G = = = = = T C C = = = = = = C = C A = G = G C T G G G C G = = G T = = D C A C G = T = A = = A G A = I I = = = = = 0 DY19 = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = (A) = = = = = = = = = T = A T = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = (G) = = = = = = = = = A = G C 0 DY20 A = T = = C C G = G = T C C C T A = = = C = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G A T G = C = = T T C = A = A T G G C G = = = G = G = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A G C 0 DY21 = C C = = = T C C = C = = = = = = C A = = = = C T G G G C G = = G T = = D C A C G = T = = = = A G A = ? I = = = = = = T T = = = C G T = G = = = = = = G G = = = = T G A A C T C = = A A = = I T G G A = C = = = = G A G = ? D = = = = = 0 DY22 = C C = = T T C C = C = = = = = = = = = = = = (C) = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T T = = C C G T = G = = = = = = = = = = = = (T) = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY23 = C C C = T T C C = = = = = = = = = A = = = G C = G = = = = T A G T C = D C A C G = T = A = A A G A A = I = T = G = = T T T = C C G T = = = = = = = = = G = = = T T = A = = = = C C A A A = I T G G A = C = G = G G A G T = D = A = A = 0 DY24 = = = = = = T C C = = = = = = = = C A = = = G C = G = = = = T A G T C = D C A C G = T = A = A A G A A = I = T = = = = = = = = = C G T = = = = = = = = G G = = = T T = A = = = = C C A A A = I T G G A = C = G = G G A G T = D = A = = = 0 E101 = = ? ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E102 = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T 0 E103 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T 0 E104 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E105 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D = A = G C = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I = T = A T 0 E106 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G C = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A T 0 E107 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E108 = C C C = T = = = A = = = ? = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D = = = = = = T T T = C = = = G = = = ? = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I = = = = = 0 E109 = = ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E110 ? ? ? = = T = = T A = A T G G = G G G = ? ? ? ? G A A C T C = = A A = = I T G G A = C ? ? ? ? ? ? ? ? D D = = = = = ? ? ? = = C = = C G = T C C C = A C A = ? ? ? ? T G G G C G = = G T = = D C A C G = T ? ? ? ? ? ? ? ? I I = = = = = 0 E111 = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E112 ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = ? ? = = C ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = ? ? ? ? ? ? ? = = = ? ? = = T 0 E113 = C C C = T = = = A = = = = = = = G = = ? ? ? ? = A = = = = C C A A A = I T G G A = C ? ? ? ? ? ? ? ? D D ? ? = (G) (C) = T T T = C = = = G = = = = = = = C = = ? ? ? ? = G = = = = T A G T C = D C A C G = T ? ? ? ? ? ? ? ? I I ? ? = (A) (T) 0 E114 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D ? ? = (G) (C) = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I ? ? = (A) (T) 0 E115 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E116 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E117 = = = = = = = = = = = = = ? ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E118 = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = C = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = T 0 E119 ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = 0 E120 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D ? ? = = (C) = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I ? ? = = (T) 0 E121 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D = A = G C = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I = T = A T 0 E122 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = 0 E123 = C C C = T = = = A = = = = = = = G = = = C = T = A = = = = C C A A A = I T G G A = C G G = G G A G T D D = = = = = = T T T = C = = = G = = = = = = = C = = = T = C = G = = = = T A G T C = D C A C G = T A A = A A G A A I I = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS 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 = 0.55 = = = 0.50 = 0.50 = = = = = = = 0.52 0.52 = 0.71 1.00 = 1.00 1.00 = 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 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 = 0.91 0.91 = = = = 0.80 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.83 = = = = = = = = = = = = = = = = = = = 0.72 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.73 = = 1.00 = 1.00 = = = = = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 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 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 0.99 = = = = = = = ? ? ? ? ? ? = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = 0.93 = = = = = = = = = = = = = 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 = = = = 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 = = 1.00 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 = = = = ? ? ? = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 = = 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 = 0.93 0.93 0.96 = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 = = = 1.00 = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = = = = = = = = 1.00 = = 1.00 = = = 1.00 = = = 1.00 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 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = 0.55 = = = = = = = = = 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 = = = = = = = = = = = = 0.51 = = ? ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.95 0.95 0.95 = 0.95 0.96 0.96 0.96 = = = = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 0.90 = = = = = = = 0.96 0.96 0.96 = = = = = = = = 1.00 1.00 = = = 1.00 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = = = = = ? ? = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.99 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 = 0.93 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 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 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 ? ? ? ? ? ? ? ? 1.00 1.00 ? ? = 0.86 0.87 = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 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 0.89 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? ? ? = = = = = = = 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 ? ? = = 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 = 0.93 0.94 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? = = = = 1.00 1.00 1.00 = 1.00 = = = 1.00 = = = = = = = 1.00 = = = 1.00 = 1.00 = 1.00 = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 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