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)


