Supplemental results for BASEML

seqf:  trio2.phy
treef: trio2.phy_phyml_tree.txt


TREE #  1

Ancestral reconstruction by BASEML.

(((((((((((((((((H010: 0.035163, H033: 0.035163): 0.051559, (H027: 0.057874, (H017: 0.057874, H014: 0.057874): 0.000000): 0.028848): 0.000000, H011: 0.086722): 0.000000, H003: 0.086722): 0.025300, H018: 0.112022): 0.000000, (((H022: 0.035387, (H013: 0.016460, H019: 0.016460): 0.018928): 0.021351, H034: 0.056739): 0.022749, H029: 0.079488): 0.032534): 0.014469, H020: 0.126491): 0.000000, H001: 0.126491): 0.000000, H015: 0.126491): 0.015976, H028: 0.142467): 0.048638, H030: 0.191105): 0.020845, ((H006: 0.211909, ((((((H031: 0.068986, H005: 0.068986): 0.000000, (H032: 0.029484, H016: 0.029484): 0.039502): 0.000000, H008: 0.068986): 0.000000, H024: 0.068986): 0.029849, H004: 0.098835): 0.041617, H025: 0.140453): 0.071456): 0.000000, OUTG: 0.211909): 0.000041): 0.027363, H035: 0.239313): 0.000000, H007: 0.239313): 0.037161, (H026: 0.078062, H023: 0.078062): 0.198413): 0.052620, H012: 0.329094): 0.000000, (H021: 0.132628, H002: 0.132628): 0.196467, H009: 0.329095);

(((((((((((((((((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: 0.035163, 19_H033: 0.035163) 53 : 0.051559, (6_H027: 0.057874, (16_H017: 0.057874, 34_H014: 0.057874) 55 : 0.000000) 54 : 0.028848) 52 : 0.000000, 32_H011: 0.086722) 51 : 0.000000, 22_H003: 0.086722) 50 : 0.025300, 35_H018: 0.112022) 49 : 0.000000, (((33_H022: 0.035387, (24_H013: 0.016460, 1_H019: 0.016460) 59 : 0.018928) 58 : 0.021351, 5_H034: 0.056739) 57 : 0.022749, 21_H029: 0.079488) 56 : 0.032534) 48 : 0.014469, 4_H020: 0.126491) 47 : 0.000000, 12_H001: 0.126491) 46 : 0.000000, 10_H015: 0.126491) 45 : 0.015976, 14_H028: 0.142467) 44 : 0.048638, 28_H030: 0.191105) 43 : 0.020845, ((11_H006: 0.211909, ((((((29_H031: 0.068986, 31_H005: 0.068986) 67 : 0.000000, (25_H032: 0.029484, 8_H016: 0.029484) 68 : 0.039502) 66 : 0.000000, 20_H008: 0.068986) 65 : 0.000000, 15_H024: 0.068986) 64 : 0.029849, 3_H004: 0.098835) 63 : 0.041617, 26_H025: 0.140453) 62 : 0.071456) 61 : 0.000000, 36_OUTG: 0.211909) 60 : 0.000041) 42 : 0.027363, 23_H035: 0.239313) 41 : 0.000000, 18_H007: 0.239313) 40 : 0.037161, (2_H026: 0.078062, 7_H023: 0.078062) 69 : 0.198413) 39 : 0.052620, 30_H012: 0.329094) 38 : 0.000000, (27_H021: 0.132628, 9_H002: 0.132628) 70 : 0.196467, 17_H009: 0.329095) 37 ;

Nodes 37 to 70 are ancestral

(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(0.989) C(0.989) C(0.993) 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(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(0.948) C(0.998) C(0.998) G(0.948) G(0.997) G(1.000) G(1.000) C(0.999) C(0.999) G(0.924) G(0.995) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.824) C(0.824) 
   2      1   CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC: C(0.998) C(0.998) C(0.999) C(0.999) C(0.999) C(0.992) C(0.932) G(0.758) G(0.787) G(0.787) G(0.787) 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(0.992) C(0.992) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.996) 
   3      1   GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG: C(0.908) C(0.908) C(0.703) G(0.975) G(0.975) 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(0.992) C(0.992) 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) C(0.990) C(0.989) 
   4      1   GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG: C(0.989) C(0.989) C(0.967) C(0.892) C(0.892) G(0.997) G(0.999) G(1.000) 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(0.997) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.977) C(0.998) C(0.996) 
   5      1   CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG: G(0.974) G(0.974) 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(0.943) C(0.969) C(1.000) G(1.000) G(1.000) G(0.826) C(0.942) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.999) C(0.916) 
   6      1   GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC: G(0.757) G(0.757) C(0.896) C(0.995) C(0.995) 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(0.998) C(0.998) C(1.000) C(0.997) C(0.956) G(0.987) C(1.000) C(1.000) C(0.968) C(0.844) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.996) G(0.978) 
   7      1   CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG: G(0.999) G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(0.932) C(0.956) 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(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.964) G(0.999) G(0.997) 
   8      1   CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG: G(0.949) G(0.949) G(0.993) G(1.000) G(1.000) G(1.000) G(0.978) G(0.696) 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(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(0.999) G(0.809) 
   9      1   CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG: G(0.999) G(0.999) G(0.999) G(1.000) G(1.000) G(0.997) C(0.670) C(0.982) 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(0.997) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) 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(0.998) C(0.998) C(0.902) G(0.903) G(0.942) G(0.927) 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(0.999) C(0.996) 

Summary of changes along branches.
Check root for directions of change.

Branch 1:   37..38



Branch 2:   38..39

	   6 G 0.757 -> C 0.896


Branch 3:   39..40

	   3 C 0.703 -> G 0.975


Branch 4:   40..41



Branch 5:   41..42

	   4 C 0.892 -> G 0.997


Branch 6:   42..43

	   9 G 0.997 -> C 0.670


Branch 7:   43..44

	   2 C 0.932 -> G 0.758
	   7 G 0.932 -> C 0.956


Branch 8:   44..45

	   8 G 0.696 -> C 0.998


Branch 9:   45..46



Branch 10:   46..47



Branch 11:   47..48

	   2 G 0.787 -> C 0.994


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 0.948 -> G


Branch 19:   52..54

	   3 G 1.000 -> C 0.992


Branch 20:   54..6  (H027) 

	   6 C 0.998 -> G
	  10 C 0.998 -> G


Branch 21:   54..55



Branch 22:   55..16 (H017) 



Branch 23:   55..34 (H014) 

	   1 C 0.998 -> G


Branch 24:   51..32 (H011) 



Branch 25:   50..22 (H003) 

	   5 G 1.000 -> C


Branch 26:   49..35 (H018) 



Branch 27:   48..56

	   1 C 0.999 -> G 0.948


Branch 28:   56..57

	  10 C 0.902 -> G 0.903


Branch 29:   57..58

	   5 G 0.943 -> C 0.969


Branch 30:   58..33 (H022) 



Branch 31:   58..59

	   6 C 0.956 -> G 0.987


Branch 32:   59..24 (H013) 



Branch 33:   59..1  (H019) 

	  10 G 0.927 -> C


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) 



Branch 41:   42..60



Branch 42:   60..61



Branch 43:   61..11 (H006) 

	   2 C 0.992 -> G


Branch 44:   61..62

	   1 C 0.999 -> G 0.924


Branch 45:   62..63

	   5 G 0.826 -> C 0.942


Branch 46:   63..64

	   6 C 0.844 -> 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


Branch 52:   66..68

	   4 G 1.000 -> C 0.977


Branch 53:   68..25 (H032) 

	   7 G 0.964 -> C


Branch 54:   68..8  (H016) 



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) 



Branch 59:   60..36 (OUTG) 



Branch 60:   41..23 (H035) 

	  10 C 0.998 -> G


Branch 61:   40..18 (H007) 



Branch 62:   39..69



Branch 63:   69..2  (H026) 

	   1 C 0.824 -> G


Branch 64:   69..7  (H023) 



Branch 65:   38..30 (H012) 



Branch 66:   37..70

	   5 G 0.974 -> C 0.916


Branch 67:   70..27 (H021) 

	   1 C 0.824 -> G
	   8 G 0.809 -> C


Branch 68:   70..9  (H002) 



Branch 69:   37..17 (H009) 

	   8 G 0.949 -> C




List of extant and reconstructed sequences

H019              GCGGCGCCCC 
H026              GCCCGCGGGC 
H004              GCGGCCGGGC 
H020              CGGGGCCCCG 
H034              GCGGGCCCCG 
H027              CCCCGGCCCG 
H023              CCCCGCGGGC 
H016              GCGCCGGGGC 
H002              CCCCCGGGGC 
H015              CGGGGCCCGC 
H006              CGGGGCGGGC 
H001              CGGGGCCCCC 
H010              CCGCGCCCCG 
H028              CGGGGCCGCC 
H024              GCGGCGGGCC 
H017              CCCCGCCCCC 
H009              CCCCGGGCGC 
H007              CCGCGCGGGC 
H033              GCGCGCCCCG 
H008              GCGGCGGGGC 
H029              GCGGGCCCCC 
H003              CCGCCCCCCC 
H035              CCGCGCGGGG 
H013              GCGGCGCCCG 
H032              GCGCCGCGGC 
H025              GCGGGCGGGC 
H021              GCCCCGGCGC 
H030              CCGGGCGGCC 
H031              GCGGCGGCGC 
H012              CCCCGGGGGC 
H005              GCGGCGGGGG 
H011              CCGCGCCCCC 
H022              GCGGCCCCCG 
H014              GCCCGCCCCC 
H018              CCGGGCCCCC 
OUTG              CCGGGCGGGC 
node #37          CCCCGGGGGC 
node #38          CCCCGGGGGC 
node #39          CCCCGCGGGC 
node #40          CCGCGCGGGC 
node #41          CCGCGCGGGC 
node #42          CCGGGCGGGC 
node #43          CCGGGCGGCC 
node #44          CGGGGCCGCC 
node #45          CGGGGCCCCC 
node #46          CGGGGCCCCC 
node #47          CGGGGCCCCC 
node #48          CCGGGCCCCC 
node #49          CCGGGCCCCC 
node #50          CCGCGCCCCC 
node #51          CCGCGCCCCC 
node #52          CCGCGCCCCC 
node #53          CCGCGCCCCG 
node #54          CCCCGCCCCC 
node #55          CCCCGCCCCC 
node #56          GCGGGCCCCC 
node #57          GCGGGCCCCG 
node #58          GCGGCCCCCG 
node #59          GCGGCGCCCG 
node #60          CCGGGCGGGC 
node #61          CCGGGCGGGC 
node #62          GCGGGCGGGC 
node #63          GCGGCCGGGC 
node #64          GCGGCGGGGC 
node #65          GCGGCGGGGC 
node #66          GCGGCGGGGC 
node #67          GCGGCGGGGC 
node #68          GCGCCGGGGC 
node #69          CCCCGCGGGC 
node #70          CCCCCGGGGC 


Overall accuracy of the 34 ancestral sequences:
  0.95602  0.95602  0.95455  0.98584  0.98584  0.99846  0.95098  0.93915  0.97828  0.97828  0.97828  0.99902  0.99902  0.99985  0.99985  0.99985  0.99250  0.99861  0.99861  0.98433  0.98398  0.98669  0.99137  0.99846  0.99846  0.97139  0.97803  0.99999  0.99999  0.99999  0.99999  0.99410  0.97995  0.94975
for a site.

  0.61783  0.61783  0.59678  0.86222  0.86222  0.98464  0.56794  0.49507  0.78363  0.78363  0.78363  0.99023  0.99023  0.99850  0.99850  0.99850  0.92619  0.98612  0.98612  0.84934  0.84626  0.87260  0.91468  0.98469  0.98469  0.73579  0.79053  0.99994  0.99994  0.99994  0.99994  0.94183  0.80398  0.57972
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)


