Supplemental results for CODEML (seqf: Glucokinases_Aln_Tree.nex_15.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((GLK_ECO: 0.000000, (I0ABJ0: 0.043948, (C9XXD4: 0.062773, GLK_YER: 0.190296): 0.042896): 0.026964): 0.000000, 1SZ2_A: 0.000000);

((2, (3, (4, 5))), 1);

   6..7     7..2     7..8     8..3     8..9     9..4     9..5     6..1  

tree with node labels for Rod Page's TreeView
((2_GLK_ECO, (3_I0ABJ0, (4_C9XXD4, 5_GLK_YER) 9 ) 8 ) 7 , 1_1SZ2_A) 6 ;

Nodes 6 to 9 are ancestral

(1) Marginal reconstruction of ancestral sequences
(eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650).

Prob distribs at nodes, those with p < 0.001 not listed

Prob distribution at node 6, by site

   site  Freq   Data

      1      1   LLLLL: A(0.000) R(0.000) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.000) L(1.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 7, by site

   site  Freq   Data

      1      1   LLLLL: A(0.000) R(0.000) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.000) L(1.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 8, by site

   site  Freq   Data

      1      1   LLLLL: A(0.000) R(0.000) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.000) L(1.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   LLLLL: A(0.000) R(0.000) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.000) L(1.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob of best state at each node, listed by site

   site   Freq   Data: 

   1      1   LLLLL: L(1.000) L(1.000) L(1.000) L(1.000) 

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

Branch 1:    6..7 



Branch 2:    7..2  (GLK_ECO) 



Branch 3:    7..8 



Branch 4:    8..3  (I0ABJ0) 



Branch 5:    8..9 



Branch 6:    9..4  (C9XXD4) 



Branch 7:    9..5  (GLK_YER) 



Branch 8:    6..1  (1SZ2_A) 





List of extant and reconstructed sequences

     9      1

1SZ2_A            L
GLK_ECO           L
I0ABJ0            L
C9XXD4            L
GLK_YER           L
node #6           L
node #7           L
node #8           L
node #9           L


Overall accuracy of the 4 ancestral sequences:
  1.00000  1.00000  1.00000  0.99998
for a site.

  1.00000  1.00000  1.00000  0.99998
for the sequence.


Counts of changes at sites

   1  (0)


(2) Joint reconstruction of ancestral sequences
(eqn. 2 in Yang et al. 1995 Genetics 141:1641-1650), using the algorithm of Pupko et al. (2000 Mol Biol Evol 17:890-896),
modified to generate sub-optimal reconstructions.

Reconstruction (prob.), listed by pattern (use the observed data to find the right site).

Pattern Freq   Data:

   1       1  LLLLL: LLLL (1.000) LLLM (0.000) LLML (0.000) LLLF (0.000) ILLL (0.000) VLLL (0.000)  (total  1.000)



List of extant and reconstructed sequences

     9      1

1SZ2_A            L
GLK_ECO           L
I0ABJ0            L
C9XXD4            L
GLK_YER           L
node #6           L
node #7           L
node #8           L
node #9           L


