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Supplemental results for BASEML
seqf: et_trio2.phy
treef: trio2.phy_phyml_tree.txt
TREE # 1
Ancestral reconstruction by BASEML.
(((((((((((((((((H010: 0.038473, H033: 0.038473): 0.063358, (H027: 0.066349, (H017: 0.066348, H014: 0.066348): 0.000001): 0.035483): 0.000000, H011: 0.101831): 0.000000, H003: 0.101831): 0.028393, H018: 0.130224): 0.000000, (((H022: 0.032888, (H013: 0.015402, H019: 0.015402): 0.017485): 0.018969, H034: 0.051857): 0.050124, H029: 0.101981): 0.028243): 0.012091, H020: 0.142315): 0.000000, H001: 0.142315): 0.000000, H015: 0.142316): 0.036222, H028: 0.178537): 0.041581, H030: 0.220119): 0.025287, ((H006: 0.240097, ((((((H031: 0.080251, H005: 0.080251): 0.000000, (H032: 0.033304, H016: 0.033304): 0.046948): 0.000000, H008: 0.080251): 0.000000, H024: 0.080251): 0.028235, H004: 0.108486): 0.046856, H025: 0.155343): 0.084754): 0.000000, OUTG: 0.240097): 0.005308): 0.030304, H035: 0.275709): 0.000000, H007: 0.275709): 0.040862, (H026: 0.162133, H023: 0.162133): 0.154438): 0.049611, H012: 0.366183): 0.000000, (H021: 0.116893, H002: 0.116893): 0.249290, H009: 0.366183);
(((((((((((((((((13, 19), (6, (16, 34))), 32), 22), 35), (((33, (24, 1)), 5), 21)), 4), 12), 10), 14), 28), ((11, ((((((29, 31), (25, 8)), 20), 15), 3), 26)), 36)), 23), 18), (2, 7)), 30), (27, 9), 17);
37..38 38..39 39..40 40..41 41..42 42..43 43..44 44..45 45..46 46..47 47..48 48..49 49..50 50..51 51..52 52..53 53..13 53..19 52..54 54..6 54..55 55..16 55..34 51..32 50..22 49..35 48..56 56..57 57..58 58..33 58..59 59..24 59..1 57..5 56..21 47..4 46..12 45..10 44..14 43..28 42..60 60..61 61..11 61..62 62..63 63..64 64..65 65..66 66..67 67..29 67..31 66..68 68..25 68..8 65..20 64..15 63..3 62..26 60..36 41..23 40..18 39..69 69..2 69..7 38..30 37..70 70..27 70..9 37..17
tree with node labels for Rod Page's TreeView
(((((((((((((((((13_H010: 0.038473, 19_H033: 0.038473) 53 : 0.063358, (6_H027: 0.066349, (16_H017: 0.066348, 34_H014: 0.066348) 55 : 0.000001) 54 : 0.035483) 52 : 0.000000, 32_H011: 0.101831) 51 : 0.000000, 22_H003: 0.101831) 50 : 0.028393, 35_H018: 0.130224) 49 : 0.000000, (((33_H022: 0.032888, (24_H013: 0.015402, 1_H019: 0.015402) 59 : 0.017485) 58 : 0.018969, 5_H034: 0.051857) 57 : 0.050124, 21_H029: 0.101981) 56 : 0.028243) 48 : 0.012091, 4_H020: 0.142315) 47 : 0.000000, 12_H001: 0.142315) 46 : 0.000000, 10_H015: 0.142316) 45 : 0.036222, 14_H028: 0.178537) 44 : 0.041581, 28_H030: 0.220119) 43 : 0.025287, ((11_H006: 0.240097, ((((((29_H031: 0.080251, 31_H005: 0.080251) 67 : 0.000000, (25_H032: 0.033304, 8_H016: 0.033304) 68 : 0.046948) 66 : 0.000000, 20_H008: 0.080251) 65 : 0.000000, 15_H024: 0.080251) 64 : 0.028235, 3_H004: 0.108486) 63 : 0.046856, 26_H025: 0.155343) 62 : 0.084754) 61 : 0.000000, 36_OUTG: 0.240097) 60 : 0.005308) 42 : 0.030304, 23_H035: 0.275709) 41 : 0.000000, 18_H007: 0.275709) 40 : 0.040862, (2_H026: 0.162133, 7_H023: 0.162133) 69 : 0.154438) 39 : 0.049611, 30_H012: 0.366183) 38 : 0.000000, (27_H021: 0.116893, 9_H002: 0.116893) 70 : 0.249290, 17_H009: 0.366183) 37 ;
Nodes 37 to 70 are ancestral
Unreliable at sites with alignment gaps
(1) Marginal reconstruction of ancestral sequences (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650).
Prob of best character at each node, listed by site
Site Freq Data:
1 1 GGGCGCCGCCCCCCGCCCGGGCCGGGGCGCGCGGCC: C(0.987) C(0.987) C(0.991) C(0.999) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(0.937) C(0.997) C(0.997) G(0.852) G(0.997) G(1.000) G(1.000) C(0.995) C(0.995) G(0.921) G(0.995) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.856) C(0.789)
2 1 CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC: C(0.998) C(0.998) C(0.999) C(0.998) C(0.998) C(0.989) C(0.923) G(0.557) G(0.623) G(0.623) G(0.623) C(0.993) C(0.993) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(1.000) C(1.000) C(1.000) C(0.989) C(0.989) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.996) C(0.996)
3 1 GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG: C(0.889) C(0.889) C(0.730) G(0.966) G(0.966) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.991) C(0.991) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.957) C(0.991)
4 1 GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG: C(0.983) C(0.983) C(0.963) C(0.871) C(0.871) G(0.991) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(0.998) G(0.998) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.996) G(0.996) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.975) C(0.991) C(0.996)
5 1 CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG: G(0.975) G(0.975) G(0.996) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.994) G(0.884) C(0.972) C(1.000) G(0.999) G(0.999) G(0.801) C(0.948) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.996) C(0.947)
6 1 GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC: G(0.662) G(0.662) C(0.906) C(0.994) C(0.994) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.997) C(0.997) C(1.000) C(0.994) C(0.958) G(0.988) C(0.999) C(0.999) C(0.954) C(0.802) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.982) G(0.981)
7 1 CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG: G(0.998) G(0.998) G(0.999) G(1.000) G(1.000) G(0.999) G(0.901) C(0.874) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.999) G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.958) G(0.996) G(0.997)
8 1 CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG: G(0.951) G(0.951) G(0.993) G(1.000) G(1.000) G(1.000) G(0.980) G(0.822) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.995) G(0.779)
9 1 CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG: G(0.998) G(0.998) G(0.999) G(0.999) G(0.999) G(0.991) C(0.697) C(0.955) C(0.998) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.996) G(0.996) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.996) G(0.997)
10 1 CCCGGGCCCCCCGCCCCCGCCCGGCCCCCCGCGCCC: C(0.998) C(0.998) C(0.999) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.999) C(0.999) G(0.978) C(0.997) C(0.997) C(0.945) G(0.958) G(0.974) G(0.959) C(1.000) C(1.000) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.996) C(0.996)
11 1 ?GGCG?C?GC?CCGGCCCCGCGGGC?G?G??CG???: G(0.743) G(0.743) G(0.753) G(0.760) G(0.760) G(0.764) G(0.696) G(0.587) C(0.995) C(0.995) C(0.995) C(0.995) C(0.995) C(0.999) C(0.999) C(0.999) C(1.000) C(0.997) C(0.997) C(0.939) G(0.982) G(0.999) G(0.999) G(0.772) G(0.772) G(0.911) G(0.994) G(0.999) G(0.999) G(0.999) G(0.999) C(0.587) G(0.690) G(0.985)
Summary of changes along branches.
Check root for directions of change.
Branch 1: 37..38
Branch 2: 38..39
6 G 0.662 -> C 0.906
Branch 3: 39..40
3 C 0.730 -> G 0.966
Branch 4: 40..41
Branch 5: 41..42
4 C 0.871 -> G 0.991
Branch 6: 42..43
9 G 0.991 -> C 0.697
Branch 7: 43..44
2 C 0.923 -> G 0.557
7 G 0.901 -> C 0.874
Branch 8: 44..45
8 G 0.822 -> C 0.999
11 G 0.587 -> C 0.995
Branch 9: 45..46
Branch 10: 46..47
Branch 11: 47..48
2 G 0.623 -> C 0.993
Branch 12: 48..49
Branch 13: 49..50
4 G 0.998 -> C 0.999
Branch 14: 50..51
Branch 15: 51..52
Branch 16: 52..53
10 C 0.999 -> G 0.978
Branch 17: 53..13 (H010)
Branch 18: 53..19 (H033)
1 C 0.937 -> G
Branch 19: 52..54
3 G 1.000 -> C 0.991
Branch 20: 54..6 (H027)
6 C 0.997 -> G
10 C 0.997 -> G
11 C 0.997 -> ?
Branch 21: 54..55
Branch 22: 55..16 (H017)
Branch 23: 55..34 (H014)
1 C 0.997 -> G
11 C 0.997 -> ?
Branch 24: 51..32 (H011)
Branch 25: 50..22 (H003)
5 G 1.000 -> C
11 C 0.999 -> G
Branch 26: 49..35 (H018)
11 C 0.995 -> ?
Branch 27: 48..56
1 C 0.998 -> G 0.852
Branch 28: 56..57
10 C 0.945 -> G 0.958
11 C 0.939 -> G 0.982
Branch 29: 57..58
5 G 0.884 -> C 0.972
Branch 30: 58..33 (H022)
Branch 31: 58..59
6 C 0.958 -> G 0.988
Branch 32: 59..24 (H013)
Branch 33: 59..1 (H019)
10 G 0.959 -> C
11 G 0.999 -> ?
Branch 34: 57..5 (H034)
Branch 35: 56..21 (H029)
Branch 36: 47..4 (H020)
10 C 1.000 -> G
Branch 37: 46..12 (H001)
Branch 38: 45..10 (H015)
9 C 0.998 -> G
Branch 39: 44..14 (H028)
Branch 40: 43..28 (H030)
11 G 0.696 -> ?
Branch 41: 42..60
Branch 42: 60..61
Branch 43: 61..11 (H006)
2 C 0.989 -> G
11 G 0.772 -> ?
Branch 44: 61..62
1 C 0.995 -> G 0.921
Branch 45: 62..63
5 G 0.801 -> C 0.948
Branch 46: 63..64
6 C 0.802 -> G 1.000
Branch 47: 64..65
Branch 48: 65..66
Branch 49: 66..67
Branch 50: 67..29 (H031)
8 G 1.000 -> C
Branch 51: 67..31 (H005)
10 C 1.000 -> G
11 G 0.999 -> ?
Branch 52: 66..68
4 G 1.000 -> C 0.975
11 G 0.999 -> C 0.587
Branch 53: 68..25 (H032)
7 G 0.958 -> C
Branch 54: 68..8 (H016)
11 C 0.587 -> ?
Branch 55: 65..20 (H008)
Branch 56: 64..15 (H024)
9 G 1.000 -> C
Branch 57: 63..3 (H004)
Branch 58: 62..26 (H025)
11 G 0.911 -> ?
Branch 59: 60..36 (OUTG)
11 G 0.772 -> ?
Branch 60: 41..23 (H035)
10 C 0.998 -> G
Branch 61: 40..18 (H007)
11 G 0.760 -> C
Branch 62: 39..69
Branch 63: 69..2 (H026)
1 C 0.856 -> G
Branch 64: 69..7 (H023)
11 G 0.690 -> C
Branch 65: 38..30 (H012)
11 G 0.743 -> ?
Branch 66: 37..70
5 G 0.975 -> C 0.947
Branch 67: 70..27 (H021)
1 C 0.789 -> G
8 G 0.779 -> C
Branch 68: 70..9 (H002)
Branch 69: 37..17 (H009)
8 G 0.951 -> C
11 G 0.743 -> C
List of extant and reconstructed sequences
H019 GCGGCGCCCC ?
H026 GCCCGCGGGC G
H004 GCGGCCGGGC G
H020 CGGGGCCCCG C
H034 GCGGGCCCCG G
H027 CCCCGGCCCG ?
H023 CCCCGCGGGC C
H016 GCGCCGGGGC ?
H002 CCCCCGGGGC G
H015 CGGGGCCCGC C
H006 CGGGGCGGGC ?
H001 CGGGGCCCCC C
H010 CCGCGCCCCG C
H028 CGGGGCCGCC G
H024 GCGGCGGGCC G
H017 CCCCGCCCCC C
H009 CCCCGGGCGC C
H007 CCGCGCGGGC C
H033 GCGCGCCCCG C
H008 GCGGCGGGGC G
H029 GCGGGCCCCC C
H003 CCGCCCCCCC G
H035 CCGCGCGGGG G
H013 GCGGCGCCCG G
H032 GCGCCGCGGC C
H025 GCGGGCGGGC ?
H021 GCCCCGGCGC G
H030 CCGGGCGGCC ?
H031 GCGGCGGCGC G
H012 CCCCGGGGGC ?
H005 GCGGCGGGGG ?
H011 CCGCGCCCCC C
H022 GCGGCCCCCG G
H014 GCCCGCCCCC ?
H018 CCGGGCCCCC ?
OUTG CCGGGCGGGC ?
node #37 CCCCGGGGGC G
node #38 CCCCGGGGGC G
node #39 CCCCGCGGGC G
node #40 CCGCGCGGGC G
node #41 CCGCGCGGGC G
node #42 CCGGGCGGGC G
node #43 CCGGGCGGCC G
node #44 CGGGGCCGCC G
node #45 CGGGGCCCCC C
node #46 CGGGGCCCCC C
node #47 CGGGGCCCCC C
node #48 CCGGGCCCCC C
node #49 CCGGGCCCCC C
node #50 CCGCGCCCCC C
node #51 CCGCGCCCCC C
node #52 CCGCGCCCCC C
node #53 CCGCGCCCCG C
node #54 CCCCGCCCCC C
node #55 CCCCGCCCCC C
node #56 GCGGGCCCCC C
node #57 GCGGGCCCCG G
node #58 GCGGCCCCCG G
node #59 GCGGCGCCCG G
node #60 CCGGGCGGGC G
node #61 CCGGGCGGGC G
node #62 GCGGGCGGGC G
node #63 GCGGCCGGGC G
node #64 GCGGCGGGGC G
node #65 GCGGCGGGGC G
node #66 GCGGCGGGGC G
node #67 GCGGCGGGGC G
node #68 GCGCCGGGGC C
node #69 CCCCGCGGGC G
node #70 CCCCCGGGGC G
Overall accuracy of the 34 ancestral sequences:
0.92564 0.92564 0.93903 0.96221 0.96221 0.97558 0.92659 0.89023 0.96490 0.96490 0.96490 0.99854 0.99854 0.99966 0.99966 0.99966 0.99221 0.99808 0.99808 0.97517 0.98317 0.99119 0.99506 0.97690 0.97690 0.96189 0.97620 0.99989 0.99989 0.99989 0.99989 0.95631 0.94999 0.95031
for a site.
0.39024 0.39024 0.46884 0.63139 0.63139 0.73932 0.39368 0.22377 0.61720 0.61720 0.61720 0.98406 0.98406 0.99626 0.99627 0.99626 0.91570 0.97905 0.97905 0.74913 0.82403 0.90618 0.94621 0.75203 0.75203 0.63713 0.75137 0.99876 0.99876 0.99876 0.99876 0.54788 0.53582 0.54717
for the sequence.
Counts of changes at sites
1 CG CG CG CG CG CG (6)
2 CG CG GC (3)
3 CG GC (2)
4 CG GC GC (3)
5 GC GC GC GC (4)
6 CG GC CG CG (4)
7 GC GC (2)
8 GC GC GC GC (4)
9 CG GC GC (3)
10 GC CG CG CG CG CG CG (7)
11 G? C? GC C? G? GC GC CG G? G? G? G? C? C? G? GC CG GC (18)
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