************************************************************* **** **** **** Output from PHASE v2.0 **** **** Code by M Stephens, with contributions from N Li **** **** **** ************************************************************* BEGIN COMMAND_LINE /usr/local/genome/lib/phase/PHASE2 -d1 rab38.phase.inp rab38.phase.out END COMMAND_LINE BEGIN OUTFILE_LIST rab38.phase.out_freqs : haplotype frequency estimates rab38.phase.out_pairs : most likely haplotype pairs for each individual rab38.phase.out_recom : estimates of recombination parameters rab38.phase.out_monitor : file for monitoring convergence END OUTFILE_LIST BEGIN INPUT_SUMMARY Number of Individuals: 47 Number of Loci: 81 Positions of loci: 649 1130 1587 1760 1875 1977 2107 2581 2611 2649 3441 4463 5022 5285 13445 13462 14022 14239 14387 14433 14547 14953 15081 15268 15493 15679 15694 15874 24031 24080 24118 24300 24570 24877 25243 25577 25616 26032 26840 28032 28075 28136 28401 28643 34879 36437 36792 36927 37093 37259 46431 46687 47545 48545 48548 48613 55823 56025 56057 56374 56408 56644 57160 57180 57298 57434 58274 58622 60535 60637 60640 60650 61550 61906 61915 62598 63267 63445 63527 63573 63734 END INPUT_SUMMARY List of haplotypes found in best reconstruction, with counts. (See file rab38.phase.out_freqs for haplotype population frequency estimates) BEGIN LIST_SUMMARY 1 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGAAAGAGCGGGCCATAGAAGGATCTGCCDTCTGCAT 2.000000 2 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGAAAGAGGAGGTCATGAAGGGATTTGTCDTCTGCAT 2.000000 3 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGAAAGAGGAGGTCACGAAACCATTCACCITCGGTAC 5.000000 4 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGAAAGAGGAGGTCGTGAAAGGGGTCGCCIGAGATAT 2.000000 5 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGAAAGAGGAGGCCATAGAAGGATCTGCCDTCTGCAT 1.000000 6 ATCCCGCAAGIAAAGAAAGGDTCGATGGCGTCATTACAACDAATAGGAAGAGGAGGTCATGAAAGGGGTCGCCIGAGATAT 1.000000 7 ATCCCGCAAGIAAAGGAAGGDTCGATGGCGTCATTACAACDAATGGAAACAGGAGGTCATGAAGGGATTTGTCDTCTGCAT 5.000000 8 ATCCCGCAAGIAAAGGAAGGDTCGATGGCGTCATTACAACDAATGGAAACAGGAGGTCGTGAAAGGAGTCGCCIGAGATAT 1.000000 9 ATCCCGCAAGIAAAGGAAGGDTCGATGGCGTCATTACAACDAATGGAAACAGGAGGTCGTGAAAGGGGTCGCCIGAGATAT 1.000000 10 ATCCCGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCATGAAAGGATTTGTCDTCGGCGT 1.000000 11 ATCCCGCGGGIGGAGAAAGGDTCGTCAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 12 ATCCCCCGAGDAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTGDTCGGCGT 1.000000 13 ATCCCCCGGGIGGAGAAAGGDTCGACAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 2.000000 14 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCATTACAACIAAGAAAAAGAGGAGGTCATGAAAGGATTTGTCIGAGATAT 1.000000 15 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCATTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCIGAGATAT 1.000000 16 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCATTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 17 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 3.000000 18 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTGDTCGGCGT 5.000000 19 ATCCCCCGGGIGGAGAAAGGDTCGTCAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAGGGATTTGTCDTCTGCAT 1.000000 20 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAAGAGGTGGGGCGGACTATAAGAGGATTTGCCITCGGTAC 2.000000 21 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGAAGAGGCCATAGAAGGATCTGCCDTCTGCAT 1.000000 22 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCATGAAAGGATTTGTCDTCGGCGT 3.000000 23 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCATGAAGGGATTTGTCDTCTGCAT 1.000000 24 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCATGAGAGGATTTGCCITCGGCAT 1.000000 25 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCGTGAAAGGGGTCGCCDTCGGCGT 1.000000 26 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGATCGTGAAAGGGTTCGCCDTCGGCGT 1.000000 27 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGACCATAGAAGGATCTGCCDTCTGCAT 1.000000 28 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGACTATAAGAGGATTTGCCITCGGTAC 1.000000 29 ATCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGGGGACTATAAGAGGATTTGCCITCGGTAC 1.000000 30 ATCCTGCGGGIGGAGAAAGGDTCGACAGCCTCATTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCGT 1.000000 31 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATCGCGAAIAATAGAAAGAGGAGGCCACAGAAGGATCTGCCDTCTGCAT 1.000000 32 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATCGTGAAIAATAGAAAGAGGAGGCCACAGAAGGATCTGCCDTCTGCAT 1.000000 33 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 34 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCGT 2.000000 35 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATTACAACIAAGAGGTGGAGGAGGTCACGAAAGGATTCACCITAGATAT 1.000000 36 ATCCTGCGGGIGGAGAAAGGDTCGACAGCGTCATTACAACIAGGAGGTGGAGGAGGTCACGAAAGGATTCACCITAGATAT 1.000000 37 ATTCCGTGGAIGGAGAAAGGDTCGACAGCGTCATCGTGAAIAATAGAAAGAGGAGGCCACAGAAGGATCTGCCDTCTGCAT 3.000000 38 ACCCTGCGGGIGGAGAAAGGDTCGACGGCGTCATTACAACIAGGAGGTGGGGCGGACTATAAGAGGATTTGCCITCGGTAC 1.000000 39 ACCTCGCGAGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTCIGAGATAT 2.000000 40 ACCTCGCGAGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTCDTCGGCGT 5.000000 41 ACCTCGCGAGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAGGGATTTGTCDTCTGCAT 1.000000 42 ACCTCGCGAGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCGTGAAAGGGGTCGCCIGAGATAT 2.000000 43 ACCTCGCGAGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAGAAGAGGAAGTCGTGAAAGGGGTCGCCIGAGATAT 1.000000 44 ACCTCGCGAGDAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTCDTCGGCGT 3.000000 45 ACCTCGCGAGDAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTGDTCGGCGT 2.000000 46 ACCTCGCGAGDAACGAAAGGDTCGTCAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 47 ACCTCGCGGGIAACAACGAAICTAACGATCGCTTCGCATCICAGAAAAAGAGGAAGTCATGAAAGGATTTGTCIGAGATAT 1.000000 48 ACCTCGCGGGIGGAGAAAGGDTCGACAGCGTCACTACAACIAAGAGGTGGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 49 TTCCCGCGAGIGGAAAAAGGDTCGACGGCGTCATTACAACIAATAGAAAGAGGAGGTCGTGAAAGGGGTCGCCIGAGATAT 1.000000 50 TTCCCGCGAGIGGAAACGGAICTAACGGTCGCTTCGCAACIAAGAGAAGGGGCGGGTCGTGAAAGGGTTTGCCIGCGGTAT 2.000000 51 TTCCCGCGAGIGGAGAAAGGDTCGACGGCGTCATTACAACIAATAGAAAGAGGAGGTCATGAAAGGATTTGTCDTCGGCAT 1.000000 52 TTTCCGTGGAIGGAGAAAGGDTCGACAGCGTCATCGCGAAIAATAGAAAGAAGAGGCCATAGAAGGATCTGCCDTCTGCAT 1.000000 53 TTTCCGTGGAIGGAGAAAGGDTCGACAGCGTCATCGTGAAIAATAGAAAGAGGAGGCCATAGAAGGATCTGCCDTCTGCAT 3.000000 54 TTTCCGTGGAIGGAGAAAGGDTCGACAGCGTTATCGCGAAIAATAGAAAGAAGAGGCCATAGAAGGATCTGCCDTCTGCAT 5.000000 END LIST_SUMMARY Summary of best reconstruction (numbers refer to the list of haplotypes given above) BEGIN BESTPAIRS_SUMMARY DY01: (2,42) DY02: (31,35) DY03: (20,37) DY04: (2,41) DY05: (5,47) DY06: (1,51) DY07: (27,32) DY08: (14,29) DY09: (4,7) DY10: (3,54) DY11: (3,15) DY12: (53,53) DY13: (9,26) DY14: (8,49) DY15: (3,36) DY16: (20,39) DY17: (6,50) DY18: (28,37) DY19: (16,21) DY20: (37,39) DY21: (1,54) DY22: (3,25) DY23: (3,50) DY24: (4,53) E101: (33,34) E102: (13,17) E103: (18,22) E104: (24,45) E105: (7,22) E106: (13,17) E107: (17,40) E108: (38,46) E109: (7,40) E110: (7,18) E111: (11,44) E112: (44,42) E113: (45,54) E114: (12,48) E115: (10,18) E116: (30,54) E117: (7,22) E118: (18,44) E119: (18,43) E120: (19,23) E121: (52,54) E122: (40,40) E123: (34,40) END BESTPAIRS_SUMMARY Haplotype estimates for each individual, with uncertain phases enclosed in () and uncertain genotypes enclosed in []: BEGIN BESTPAIRS1 0 DY01 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A [A] A A G A G G A A G T C G T G A A A G G G G T C G C C I G A G A T A T 0 DY02 A T C C T G C G G G I G G A G A A A G G D T C G A C A G C G T C A T C G C G A A I A A T A G A A A G A G G A G G C C A C A G A A G G A T C T G C C D T C T G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C A G C G T C A T T A C A A C I A A G A G G T G G A G G A G G T C A C G A A A G G A T T C A C C I T A G A T A T 0 DY03 A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A A G A G G T G G G G C G G A C T A T A A G A G G A T T T G C C I T C G G T A C A T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A C A G A A G G A T C T G C C D T C T G C A T 0 DY04 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A G G G A T T T G T C D T C T G C A T 0 DY05 A T C C C G C A (A) G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G C C A T A G A A G G A T C T G C C D T C T G C A T A C C T C G C G (G) G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C I G A G A T A T 0 DY06 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G C G G G C C A T A G A A G G A T C T G C C D T C T G C A T [T] T C C C G C G A G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A A T A G A A A G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T 0 DY07 A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A C C A (T) A G A A G G A T C T G C C D T C T G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A (C) A G A A G G A T C T G C C D T C T G C A T 0 DY08 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A T T A C A A C I A A G A A A A A G A G G A G G T C A T G A A A G G A T T T G T C I G A G A T A T A [T] C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G G G G A C T A T A A G A G G A T T T G C C I T C G G T A C 0 DY09 A T C C C G C A A G I A A A G (A) A A G G D T C G A T G G C G T C A T T A C A A C D A A T (A) G A A A (G) A G G A G G T C G T G A A A G G G G T C G C C I G A G A T A T A T C C C G C A A G I A A A G (G) A A G G D T C G A T G G C G T C A T T A C A A C D A A T (G) G A A A (C) A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T 0 DY10 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A C G A A A C C A T T C A C C I T C G G T A C T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T T A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 DY11 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A C G A A A C C A T T C A C C I T C G G T A C A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A T T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C I G A G A T A T 0 DY12 T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A T A G A A G G A T C T G C C D T C T G C A T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 DY13 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C G T G A A A G G G G T C G C C I G A G A T A T A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C G T G A A A G G G T T C G C C D T C G G C G T 0 DY14 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C G T G A A A G G A G T C G C C I G A G A T A T [T] T C C C G C G A G I G G A A A A A G G D T C G A C G G C G T C A T T A C A A C I A A T A G A A A G A G G A G G T C G T G A A A G G G G T C G C C I G A G A T A T 0 DY15 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A (A) T A G A A A G A G G A G G T C A C G A A A C C A T T C A C C I T C G G T A C A T C C T G C G G G I G G A G A A A G G D T C G A C A G C G T C A T T A C A A C I A (G) G A G G T G G A G G A G G T C A C G A A A G G A T T C A C C I T A G A T A T 0 DY16 A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A A G A G G T G G G G C G G A C T A T A A G A G G A T T T G C C I T C G G T A C A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C I G A G A T A T 0 DY17 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G (G) A A G A G G A G G T C A T G A A A G G [G] G T C G C C I G A G A T A T T T C C C G C G A G I G G A A A C G G A I C T A A C G G T C G C T T C G C A A C I A A G A G (A) A G G G G C G G G T C G T G A A A G G G T T T G C C I G C G G T A T 0 DY18 A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A C T A T A A G A G G A T T T G C C I T C G G T A C A T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A C A G A A G G A T C T G C C D T C T G C A T 0 DY19 A T C C (C) (C) C G G G I G G A G A A A G G D T C G (T) C (A) G C G T C A T T A C A A C I A (A) G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A T C C (T) (G) C G G G I G G A G A A A G G D T C G (A) C (G) G C G T C A T T A C A A C I A (G) G A G G T G G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 DY20 A T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A C A G A A G G A T C T G C C D T C T G C A T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C I G A G A T A T 0 DY21 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G C G G G C C A T A G A A G G A T C T G C C D T C T G C A T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T T A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 DY22 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A C G A A A C C A T T C A C C I T C G G T A C A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C G T G A A A G G G G T C G C C D T C G G C G T 0 DY23 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C A C G A A A C C A T T C A C C I T C G G T A C T T C C C G C G A G I G G A A A C G G A I C T A A C G G T C G C T T C G C A A C I A A G A G A A G G G G C G G G T C G T G A A A G G G T T T G C C I G C G G T A T 0 DY24 A T C C C G C A A G I A A A G A A A G G D T C G A T G G C G T C A T T A C A A C D A A T A G A A A G A G G A G G T C G T G A A A G G G G T C G C C I G A G A T A T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G T G A A I A A T A G A A A G A G G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 E101 A T C C T G C G G G I G G A G A A A G G D T C G A C A G C [G] T C A T T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C A G C [G] T C A T T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C G T 0 E102 A T C C C C C G G G I G G A G A A A G G D T C G A C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T 0 E103 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T [G] D T C G G C G T A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A A A G G A T T T G T C D T C G G C G T 0 E104 A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A (G) A G G A T T T G (C) (C) (I) T C G G C (A) T A C C T C G C G A G D A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A (A) A G G A T T T G (T) (G) (D) T C G G C (G) T 0 E105 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A A A G G A T T T G T C D T C G G C G T 0 E106 A T C C C C C G G G I G G A G A A A G G D T C G A C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T 0 E107 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G T 0 E108 A C C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A C T A T A A G A G G A T T T G C C I T C G G T A C A C C T C G C G A G D A A C G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T 0 E109 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G T 0 E110 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T [G] D T C G G C G T 0 E111 A (T) C (C) C G C G (G) G (I) (G) G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T A (C) C (T) C G C G (A) G (D) (A) [A] C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G T 0 E112 A C C T C G C G A G (D) A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T [C] D T C G G C G T A C C T C G C G A G (I) A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C G T G A A A G G G G T C G C C I G A G A T A T 0 E113 A C C T C G C G A G D A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T G D T C G G C G T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T T A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 E114 A T C C C C C G A G D A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T G D T C G G C G T A C C T C G C G G G I G G A G A A A G G D T C G A C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C A T 0 E115 A T C C C G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A A A G G A T T T G T C D T C G G C G T A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T G D T C G G C G T 0 E116 A T C C T G C G G G I G G A G A A A G G D T C G A C A G C (C) T C A T T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C G T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C (G) T T A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 E117 A T C C C G C A A G I A A A G G A A G G D T C G A T G G C G T C A T T A C A A C D A A T G G A A A C A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A A A G G A T T T G T C D T C G G C G T 0 E118 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T (G) D T C G G C G T A C C T C G C G A G D A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T (C) D T C G G C G T 0 E119 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T G D T C G G C G T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A G A A G A G G A A G T C G T G A A A G G G G T C G C C I G A G A T A T 0 E120 A T C C C C C G G G I G G A G A A A G G D T C G T C A G C G T C A C T A C A A C I A A G A G G T G G A G G A G G T C A T G A A G G G A T T T G T C D T C T G C A T A T C C T G C G G G I G G A G A A A G G D T C G A C G G C G T C A T T A C A A C I A G G A G G T G G G G C G G A T C A T G A A G G G A T T T G T C D T C T G C A T 0 E121 T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T C A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T T T T C C G T G G A I G G A G A A A G G D T C G A C A G C G T T A T C G C G A A I A A T A G A A A G A A G A G G C C A T A G A A G G A T C T G C C D T C T G C A T 0 E122 A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G T 0 E123 A T C C T G C G G G I G G A G A A A G G D T C G A C A G C G T C A T T A C A A C I A A G A G G T G G A G G A G G T C A T G A A A G G A T T T G T C D T C G G C G T A C C T C G C G A G I A A C A A C G A A I C T A A C G A T C G C T T C G C A T C I C A G A A A A A G A G G A A G T C A T G A A A G G A T T T G T C D T C G G C G 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 DY01 = ? = C = = = A = = ? = ? ? G = ? ? ? ? ? T C G = T = G C G T = A = T A = = ? = D ? = T = G ? ? ? ? = = ? = G = = = A = = ? = G = = A T ? ? ? ? = D T C ? G C = = = ? = T = = = G = = ? = ? ? A = ? ? ? ? ? C T A = C = A T C G = T = C G = = ? = I ? = G = A ? ? ? ? = = ? = A = = = G = = ? = A = = G G ? ? ? ? = I G A ? A T = = 0 DY02 ? = = = = = = = = = ? = ? = = = = ? ? ? ? = = = = = = = = = = = = = C G = G ? A = = = T = ? ? ? ? ? = = ? = = = C = = = A ? = = = = ? = C T G = = ? = C T G C = = ? = = = = = = = = = ? = ? = = = = ? ? ? ? = = = = = = = = = = = = = T A = A ? C = = = G = ? ? ? ? ? = = ? = = = T = = = G ? = = = = ? = T C A = = ? = A G A T = = 0 DY03 = = C = T = C = = G = = = = = = = = = = = = = = = = G = = = = = = = T A C A = C = = = G = ? G T G = G = C G = A = T = T = A G = = = = = T = = = = ? = = G = T = C = = T = C = T = = A = = = = = = = = = = = = = = = = A = = = = = = = C G T G = A = = = T = ? A A A = A = G A = G = C = C = G A = = = = = C = = = = ? = = T = C = T 0 DY04 = ? = C = = = A = = = = = A G = A A ? ? D T C G = T = G ? G ? ? ? = T A = = A = D ? = T ? G = = = = = = = = G = = = = = = ? = = = = = = ? ? ? ? ? = = = = ? ? = = = ? = T = = = G = = = = = C A = C G ? ? I C T A = C = A ? C ? ? ? = C G = = T = I ? = G ? A = = = = = = = = A = = = = = = ? = = = = = = ? ? ? ? ? = = = = ? ? = = 0 DY05 = T = C = = = A (A) = = = = A G = A A ? ? D T C G = T = G C G T = A = T A = = A = D ? = T = G = = = = = = = = G = C = = = A G = = = = = = C = = C = D T C T G C = = = C = T = = = G (G) = = = = C A = C G ? ? I C T A = C = A T C G = T = C G = = T = I ? = G = A = = = = = = = = A = T = = = G A = = = = = = T = = T = I G A G A T = = 0 DY06 ? = = = = = = A = = = ? ? ? = = = = = = = = = = = T = = = = = = = = = = = = = = D ? ? = = = = = = = = = C G = = C = = ? ? G = = = = = = C = = C = = = = T = = = = ? = = = = = = G = = = ? ? ? = = = = = = = = = = = C = = = = = = = = = = = = = = I ? ? = = = = = = = = = G A = = T = = ? ? A = = = = = = T = = T = = = = G = = = = 0 DY07 = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = T A C A = C = = G G = ? G T G = G = C G = A = = = (T) = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = C G T G = A = = A T = ? A A A = A = G A = G = = = (C) = ? = = = = = = = = = = = = = = = = = = = 0 DY08 ? ? = = C C = = = = = = ? ? = = ? = = = ? = = = T = A = = = = = ? = = = = = = = = = A = = A A A A = A = = A = G T C = = G ? A = = = ? ? = = ? ? ? ? G A ? ? ? ? T ? ? = = T G = = = = = = ? ? = = ? = = = ? = = = A = G = = = = = ? = = = = = = = = = G = = G G T G = G = = G = A C T = = A ? G = = = ? ? = = ? ? ? ? T C ? ? ? ? C 0 DY09 = = = = = = = = = = = = = = = (A) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (A) = = = = (G) = = = = = = = = G = = = = A = = G G = C = C = I G A ? A T = = = = = = = = = = = = = = = = = (G) = = = = = = = = = = = = = = = = = = = = = = = = = = = = (G) = = = = (C) = = = = = = = = A = = = = G = = A T = T = T = D T C ? G C = = 0 DY10 A = C = = = C A A G = A A = = = = = = = = = = = = T G = = = = C = = T A = A = C D = = = = = = = = = = G = = = = T = = C G A = = C C = = T C A = = I = = G = T = C T = T = = = T G G A = G G = = = = = = = = = = = = C A = = = = T = = C G = G = A I = = = = = = = = = = A = = = = C = = T A G = = G G = = C T G = = D = = T = C = T 0 DY11 = = = = = G = A A = = A A = = = = = = = = = = = A T G = = = = = = = = = = = = = D ? = T = = A A A = = = = = = = = = = C = = = = C C = = = C A C = = T C = G = = C = = = = = C = G G = = G G = = = = = = = = = = = T C A = = = = = = = = = = = = = I ? = G = = G T G = = = = = = = = = = T = = = = G G = = = T G T = = G A = A = = T 0 DY12 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY13 ? = = = C = = A A = = A A = = G = = = = = = = = = T = = = = = = ? ? = = = = = = D ? A T ? = A A A C A = ? ? ? ? = = = = = = = = = = = G = ? ? = ? ? ? ? = A T A = ? = = = T = = G G = = G G = = A = = = = = = = = = C = = = = = = ? ? = = = = = = I ? G G ? = G T G G G = ? ? ? ? = = = = = = = = = = = T = ? ? = ? ? ? ? = G C G = 0 DY14 ? = = = = = = A = = = A A = G G = = = = ? = = = = T = = = = = = = = ? ? ? = = = D = ? = G = = = = C = = = = = = = = = = = ? = = = = A ? = = = = = ? = = = = = = = ? = = = = = = G = = = G G = A A = = = = ? = = = = C = = = = = = = = ? ? ? = = = I = ? = A = = = = G = = = = = = = = = = = ? = = = = G ? = = = = = ? = = = = = = = 0 DY15 = = = = C = = A A = = A A = = = = = = = = = = = = T G = = = = = = = = = = = = = D ? (A) T = = A A A = = = = = = = = = = = = = = = C C = = = = = = = ? = C = G = = C = = = = T = = G G = = G G = = = = = = = = = = = = C A = = = = = = = = = = = = = I ? (G) G = = G T G = = = = = = = = = = = = = = = G G = = = = = = = ? = A = A = = T 0 DY16 = T = C T = = = G = = G G A G = A A G G D ? C G = = = G C G T = A = T A = = A = = A = = = G G T G = G = C G G A C T = = A = G = = = = = = = = C = = T C = G = = C = C = T C = = = A = = A A C A = C G A A I ? T A = = = A T C G = T = C G = = T = = C = = = A A A A = A = G A A G T C = = G = A = = = = = = = = T = = G A = A = = T 0 DY17 A = = = = = = A = = = A A = G = A A = G D T C G = T = = C G T = A = T A = = = = ? = = T = = (G) = A = A = G A = = = = A = = ? = = = = ? ? = ? ? = = = = A = A = = = T = = = = = = G = = = G G = A = C G = A I C T A = C = = T C G = T = C G = = = = ? = = G = = (A) = G = G = C G = = = = G = = ? = = = = ? ? = ? ? = = = = C = G = = = 0 DY18 = = C = T = C = = G = = = = = = ? = = = = = = = = = G = = = = = = = T A C A = C = = G G = = G T G = G = C G = A = T = T = A G = = = = = T = = = = I = = G = T = C = = T = C = T = = A = = = = = = ? = = = = = = = = = A = = = = = = = C G T G = A = = A T = = A A A = A = G A = G = C = C = G A = = = = = C = = = = D = = T = C = T 0 DY19 = = = = (C) (C) = = = = = = = = = = = = = = = = = = (T) = (A) = = = = = = = = = = = = = = = (A) = = = = = = = = G = = = = T = = = G A = = = = = = T = = T = = = = G = = = = = = = = (T) (G) = = = = = = = = = = = = = = = = = = (A) = (G) = = = = = = = = = = = = = = = (G) = = = = = = = = A = = = = C = = = A G = = = = = = C = = C = = = = T = = = = 0 DY20 = T T C = = T = G A = G G A G = A A G G D T C G = = A G C G T = A = = = T G A A = A = T = G = = = = = = = = G = C = = C A G = = = = = = C = = C = D T C T G C = = = C C T = = C = A G = A A C A = C G A A I C T A = = G A T C G = T = = = C A T C = C = G = A = = = = = = = = A = T = = T G A = = = = = = T = = T = I G A G A T = = 0 DY21 A = C = = = C A A G = A A = = = = = = = = = = = = T G = = = = C = = T A = A = C D ? = = = = = = = = = G C G = = = = = = = = = = = = = = = = = = = = = = = = = = = T = T = = = T G G A = G G = = = = = = = = = = = = C A = = = = T = = C G = G = A I ? = = = = = = = = = A G A = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 DY22 = = = = C = = A A = = A A = = = = = = = = = = = = T = = = = = = = = = = = = = = D ? A T = = A A A = A = G A = G = = A C = = = = C C A T = = A = = I = = = = T A C = = = = T = = G G = = G G = = = = = = = = = = = = C = = = = = = = = = = = = = = I ? G G = = G T G = G = C G = A = = G T = = = = G G G G = = G = = D = = = = C G T 0 DY23 A = = = = = = A = = = A A = G = A A = G D T C G = T = = C G T = A = T A = = = = D = = T = = = = A = A = G A = = = = A C = = = = C C A = = C A = = = T = = = = = C T = = = = = = G = = = G G = A = C G = A I C T A = C = = T C G = T = C G = = = = I = = G = = = = G = G = C G = = = = G T = = = = G G G = = T G = = = G = = = = = T 0 DY24 A = C = = = C A A G = A A = ? ? = = = = = = = = = T G = = = = = = = T A C A = C D ? = = = = = = = = = = = = = = T = G = G A = = = = G G T C = = ? I G A G A T = = T = T = = = T G G A = G G = ? ? = = = = = = = = = C A = = = = = = = C G T G = A I ? = = = = = = = = = = = = = = C = A = A G = = = = A T C T = = ? D T C T G C = = 0 E101 = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? ? ? ? = = = ? ? ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = 0 E102 = ? = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E103 ? = = = C C = = = = ? = = = = = = = = = = = = = T = A = = = = = = C = = = = = = = = A = = = = = = = A = G A = G = = = = = = = = = = = = = = = = ? = = = = = = = = ? = = = T G = = = = ? = = = = = = = = = = = = = A = G = = = = = = T = = = = = = = = G = = = = = = = G = C G = A = = = = = = = = = = = = = = = = ? = = = = = = = = 0 E104 = ? = C T = = = G = I G G A G = A A G G D T C G = = = G C G T = A = T A = = A = = A G = = G G T G = G = C G G A = = = = = = (G) = = = = = = = = (C) (C) (I) = = = = = (A) = = ? = T C = = = A = D A A C A = C G A A I C T A = = = A T C G = T = C G = = T = = C A = = A A A A = A = G A A G = = = = = = (A) = = = = = = = = (T) (G) (D) = = = = = (G) = 0 E105 = = = = C = = A A = = A A = = G = = = = = = = = = T = = = = = = = = = = = = = = D ? A T G = A A A C A = G A = G = = = = = = = G = = = = = = = = = = = = T = = A = = = = = T = = G G = = G G = = A = = = = = = = = = C = = = = = = = = = = = = = = I ? G G A = G T G G G = C G = A = = = = = = = A = = = = = = = = = = = = G = = G = 0 E106 = ? = = ? = = = = = = = = = = = = = = = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = ? = = = = = = = = = = = = = = = = = = = T = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0 E107 = T = C = C = = G = = G G A G = A A G G D T C G T = A G C G T = A C T A = = A = = A = = = G G T G = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = A = = C = T = G = = A = = A A C A = C G A A I C T A A = G A T C G = T T C G = = T = = C = = = A A A A = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = G = 0 E108 = = = C T = = ? ? ? I G G A = = = = = = = = = = A = G = = = = = = T = = = = = = = = G = = = = = = = ? ? C G = A C T = = A = G = = = = = = = = C ? I = = = = T = C = = = T C = = ? ? ? D A A C = = = = = = = = = = T = A = = = = = = C = = = = = = = = A = = = = = = = ? ? G A = G T C = = G = A = = = = = = = = T ? D = = = = C = T 0 E109 = T = C = = = ? ? ? = = = A G G A A ? ? ? T C G = T = G C G T = A = T A = = A = D ? = T G G ? = = C = = = ? ? = = = = = = ? = G = = = = ? = = = = = = = T = = A = = C = T = = = ? ? ? = = = C A A C G ? ? ? C T A = C = A T C G = T = C G = = T = I ? = G A A ? = = G = = = ? ? = = = = = = ? = A = = = = ? = = = = = = = G = = G = 0 E110 ? = = = = G = A A = ? A A = = G = = = = ? = = = A T G = = = = = = T = = = = = = D ? = T G = A A A C = = ? = = = = = = = = = = G = = = = = = = = ? = = = T = = A = ? = = = = C = G G = ? G G = = A = = = = ? = = = T C A = = = = = = C = = = = = = I ? = G A = G T G G = = ? = = = = = = = = = = A = = = = = = = = ? = = = G = = G = 0 E111 = (T) = (C) = = = = (G) = (I) (G) ? ? G = A A G G D T C G T = A G C G T = A C ? ? ? = A = = A = = = G ? T G = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = A = = (C) = (T) = = = = (A) = (D) (A) ? ? A = C G A A I C T A A = G A T C G = T T ? ? ? = T = = C = = = A ? A A = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = G = 0 E112 = ? = = = = = = = = (D) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = A = = = = = = = A T = T = T ? D T C = G C G = = ? = = = = = = = = (I) = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = G = = = = = = = G G = C = C ? I G A = A T A = 0 E113 A C C T = = C = A G D A A ? A = C G A A I C T ? = = G A T C G C T = = = = A T C = C = G = A = = = = = G = = A = T = = = G A = = = = = = T = = T G = = = G = = G = T T T C = = T = G A I G G ? G = A A G G D T C ? = = A G C G T T A = = = = G A A = A = T = G = = = = = A = = G = C = = = A G = = = = = = C = = C C = = = T = = A = 0 E114 = ? = C = C = = A = D A A C A = C G A A I C T A = = G A T C G = ? T C G = = T = = C = = = A A A A = = = = = A = = = = = = = = = = = = = = ? ? = G = = = = ? ? G = = ? = T = G = = G = I G G A G = A A G G D T C G = = A G C G T = ? C T A = = A = = A = = = G G T G = = = = = G = = = = = = = = = = = = = = ? ? = C = = = = ? ? A = 0 E115 = = = = = G = = = = = = = = = = = = = = = = = = A = G = = = = = = T = = = = = = = = G = = = = = = = ? ? ? G = A = = = = = = = = = = = = = = = = C = = = = = = = = = = = = = C = = = = = = = = = = = = = = = = = = T = A = = = = = = C = = = = = = = = A = = = = = = = ? ? ? A = G = = = = = = = = = = = = = = = = G = = = = = = = = 0 E116 ? = C = T = C = = G = = = = = = = = = = ? = = = = = = = = (C) = C ? ? T ? ? A = C = = = G = ? G T G = = G = = = = T = = = G A = = = = = = T = = T = = = = G = = G = ? = T = C = T = = A = = = = = = = = = = ? = = = = = = = = (G) = T ? ? C ? ? G = A = = = T = ? A A A = = A = = = = C = = = A G = = = = = = C = = C = = = = T = = A = 0 E117 = = = = C = = A A = = A A = = G = = = = = = = = = T = = = = = = = = = = = = ? = D ? ? T G = A A A C ? = G A = G = = = = = = = G = ? ? ? ? ? ? ? = = = ? T = = A = = = = = T = = G G = = G G = = A = = = = = = = = = C = = = = = = = = = = = = ? = I ? ? G A = G T G G ? = C G = A = = = = = = = A = ? ? ? ? ? ? ? = = = ? G = = G = 0 E118 = T = C = C = = G = I G G A G = A A G G D T C G T = A G C G T = A C T A = = A = = A = = = G G T G = = = = = G = = = = = = = = = = = = = ? ? ? ? (G) = = = = = = = = = C = T = G = = A = D A A C A = C G A A I C T A A = G A T C G = T T C G = = T = = C = = = A A A A = = = = = A = = = = = = = = = = = = = ? ? ? ? (C) = = = = = = = = 0 E119 ? T = C = C = = G = = G G A G = ? A G G D T C G T = A ? C G T = A C T A = = A = = A = = = G = T G = = = = = G = = = A = = = = = = = ? T = T = T G D T C = G C G = ? C = T = G = = A = = A A C A = ? G A A I C T A A = G ? T C G = T T C G = = T = = C = = = A = A A = = = = = A = = = G = = = = = = = ? G = C = C C I G A = A T A = 0 E120 = ? = = C C = = = = = = = = = = = = = = = = = = T = A = = = = = = C = = = ? = = = = A = ? = = = = = ? ? G A = G ? ? ? = = = = = = ? = = = = = = = = = = = = = = = = ? = = T G = = = = = = = = = = = = = = = = = = A = G = = = = = = T = = = ? = = = = G = ? = = = = = ? ? C G = A ? ? ? = = = = = = ? = = = = = = = = = = = = = = = 0 E121 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = C ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = T ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = 0 E122 = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? = = ? ? = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? = = ? ? = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = 0 E123 = ? = C T = = = G = = G G A G = A A G G ? T C G = = A G C G T = A = T A = = A = = A = = = G G T G = = = = = G = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = T C = = = A = = A A C A = C G A A ? C T A = = G A T C G = T = C G = = T = = C = = = A A A A = = = = = A = = = = = = = = = = = = = = = = = = = = = = = = = = END BESTPAIRS2 Phase probabilities at each site with phase known positions indicated by = and missing data positions indicated by ? BEGIN PHASEPROBS = ? = 1.00 = = = 1.00 = = ? = ? ? 1.00 = ? ? ? ? ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = ? = 1.00 ? = 1.00 = 1.00 ? ? ? ? = = ? = 1.00 = = = 1.00 = = ? = 1.00 = = 1.00 1.00 ? ? ? ? = 1.00 1.00 1.00 ? 1.00 1.00 = = ? = = = = = = = = = ? = ? = = = = ? ? ? ? = = = = = = = = = = = = = 1.00 1.00 = 1.00 ? 1.00 = = = 1.00 = ? ? ? ? ? = = ? = = = 1.00 = = = 1.00 ? = = = = ? = 1.00 1.00 1.00 = = ? = 1.00 1.00 1.00 1.00 = = = = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 = ? 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 = = = = ? = = 1.00 = 1.00 = 1.00 = ? = 1.00 = = = 1.00 = = = = = 1.00 1.00 = 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 ? 1.00 ? ? ? = 1.00 1.00 = = 1.00 = 1.00 ? = 1.00 ? 1.00 = = = = = = = = 1.00 = = = = = = ? = = = = = = ? ? ? ? ? = = = = ? ? = = = 1.00 = 1.00 = = = 1.00 0.50 = = = = 1.00 1.00 = 1.00 1.00 ? ? 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = 1.00 ? = 1.00 = 1.00 = = = = = = = = 1.00 = 0.94 = = = 0.94 0.94 = = = = = = 0.94 = = 0.94 = 0.94 0.94 0.94 0.94 0.94 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 = = = 0.77 = ? = = = = = = = = = = = = = = = = = = = ? ? = = 0.99 0.99 = = = = = = ? ? = = ? = = = ? = = = 0.99 = 0.99 = = = = = ? = = = = = = = = = 0.99 = = 0.99 0.99 0.99 0.99 = 0.99 = = 1.00 = 1.00 1.00 1.00 = = 1.00 ? 1.00 = = = ? ? = = ? ? ? ? 1.00 1.00 ? ? ? ? 1.00 = = = = = = = = = = = = = = = 0.69 = = = = = = = = = = = = = = = = = = = = = = = = = = = = 0.69 = = = = 0.69 = = = = = = = = 1.00 = = = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 = 1.00 1.00 1.00 ? 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 = = = = = = = = = = 1.00 = = = = 1.00 = = 1.00 1.00 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 = = 1.00 = = 1.00 = 1.00 = 1.00 = = = = = 1.00 = 1.00 1.00 = = 1.00 1.00 = = = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = 1.00 ? = 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = 0.96 = = = = 0.96 0.96 = = = 0.96 0.96 0.96 = = 0.96 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 = = = = ? = = = = 1.00 = = = = = = = = ? ? ? = = = 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 1.00 = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = 1.00 1.00 = = = = = = = ? = 1.00 = 1.00 = = 1.00 = 1.00 = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 ? 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = = = = = = 1.00 = = 1.00 1.00 = 1.00 = = 1.00 1.00 = = = = = = 1.00 = = = 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = = = ? = = 1.00 = = 0.60 = 1.00 = 1.00 = 1.00 1.00 = = = = 1.00 = = ? = = = = ? ? = ? ? = = = = 1.00 = 1.00 = = = = = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = ? = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 1.00 1.00 = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = 1.00 = 1.00 = 1.00 = 1.00 1.00 = = = = = 1.00 = = = = 1.00 = = 1.00 = 1.00 = 1.00 = = = = 0.89 0.89 = = = = = = = = = = = = = = = = = = 0.89 = 0.89 = = = = = = = = = = = = = = = 0.89 = = = = = = = = 1.00 = = = = 1.00 = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = = = = 1.00 = = = = = 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = = = = = 1.00 = 1.00 = = 1.00 1.00 1.00 = = = = = = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 1.00 = = = = = = = = = = = = 1.00 1.00 = = = = 1.00 = = 1.00 1.00 = 1.00 = 1.00 1.00 ? = = = = = = = = = 1.00 1.00 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = 1.00 1.00 = = 1.00 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 0.91 = = = = 0.91 0.91 0.91 0.91 = = 0.91 = = 0.91 = = = = 0.91 0.91 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 ? = = = = = = = = = = = = = = 0.96 = 0.96 = 0.96 0.96 = = = = 0.96 0.96 0.96 0.96 = = ? 0.96 0.96 0.96 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 1.00 1.00 1.00 1.00 = = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = = = = = = 0.89 = = = = = = = = 0.89 0.89 0.89 = = = = = 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 = = = = = = = 0.91 = = = = = = = = = = = = 0.91 = = 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 = = = = = = = = = = = = = = = = = = = = = = = = 0.96 = = = = 0.96 0.96 = = ? ? ? 0.96 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 1.00 = 1.00 = 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = 1.00 ? = 1.00 1.00 1.00 ? = = 1.00 = = = ? ? = = = = = = ? = 0.96 = = = = ? = = = = = = = 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 = = ? = = = = = = = = = = 0.98 = = = = = = = = ? = = = 0.98 = = 0.98 = = 0.89 = 0.89 = = = = 0.89 = 0.86 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 = = = = = = = = = = = = = = = = = = = = = = = = 0.91 = = ? = = = = = = = = 0.55 = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 = = = = = = = 1.00 1.00 = 1.00 = 1.00 ? 1.00 1.00 1.00 = 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 ? 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ? = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = = = 1.00 1.00 1.00 = 1.00 = 1.00 = 1.00 = = = = = 1.00 = = 1.00 = 1.00 = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 1.00 = = = 1.00 = = 1.00 = = ? = 1.00 = 1.00 = = 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = ? 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = ? ? = 1.00 = = = = ? ? 1.00 = = = = = = 0.97 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 = = = = = = = = 1.00 = = = = = = = ? ? ? 1.00 = 1.00 = = = = = = = = = = = = = = = = 0.91 = = = = = = = = ? = 1.00 = 1.00 = 1.00 = = 1.00 = = = = = = = = = = ? = = = = = = = = 0.66 = 1.00 ? ? 1.00 ? ? 1.00 = 1.00 = = = 1.00 = ? 1.00 1.00 1.00 = = 1.00 = = = = 1.00 = = = 1.00 1.00 = = = = = = 1.00 = = 1.00 = = = = 1.00 = = 1.00 = = = = = 1.00 = = 1.00 1.00 = = 1.00 1.00 = = 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 = ? ? ? ? ? ? ? = = = ? 0.91 = = 0.91 = = 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 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 = ? 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 = 1.00 ? 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 = 1.00 1.00 = = = = = 1.00 = = = 0.97 = = = = = = = ? 0.97 = 0.97 = 0.97 0.97 0.97 0.97 0.97 = 0.97 0.97 0.97 = = ? = = 1.00 1.00 = = = = = = = = = = = = = = = = = = 1.00 = 1.00 = = = = = = 1.00 = = = ? = = = = 1.00 = ? = = = = = ? ? 1.00 1.00 = 1.00 ? ? ? = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 1.00 ? = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = ? = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = ? = = = = = = = = = = ? = = ? ? = ? = = = = = = = = = = = = ? ? ? = = = = = = = = = = ? = 1.00 1.00 = = = 1.00 = = 1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 ? 1.00 1.00 1.00 = = 1.00 1.00 1.00 1.00 1.00 = 1.00 = 1.00 1.00 = = 1.00 = = 1.00 = = = 1.00 1.00 1.00 1.00 = = = = = 1.00 = = = = = = = = = = = = = = = = = = = = = = = = = = END PHASEPROBS