Supplemental results for CODEML (seqf: Homogentisate_Aln_Tree.nex_255.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((HGD_HUM: 0.002246, (B8YB76_B: 0.029948, (HGD_MOU: 0.015790, Q6AYR0: 0.027504): 0.035239): 0.022660): 0.000000, 1EY2_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_HGD_HUM, (3_B8YB76_B, (4_HGD_MOU, 5_Q6AYR0) 9 ) 8 ) 7 , 1_1EY2_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   AAACS: A(1.000) 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(0.000) 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   AAACS: A(1.000) 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(0.000) 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   AAACS: A(0.995) 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(0.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.005) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   AAACS: A(0.160) R(0.000) N(0.000) D(0.000) C(0.126) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.710) T(0.002) W(0.000) Y(0.000) V(0.000) 

Prob of best state at each node, listed by site

   site   Freq   Data: 

   1      1   AAACS: A(1.000) A(1.000) A(0.995) S(0.710) 

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

Branch 1:    6..7 



Branch 2:    7..2  (HGD_HUM) 



Branch 3:    7..8 



Branch 4:    8..3  (B8YB76_B) 



Branch 5:    8..9 

	   1 A 0.995 -> S 0.710


Branch 6:    9..4  (HGD_MOU) 

	   1 S 0.710 -> C


Branch 7:    9..5  (Q6AYR0) 



Branch 8:    6..1  (1EY2_A) 





List of extant and reconstructed sequences

     9      1

1EY2_A            A
HGD_HUM           A
B8YB76_B          A
HGD_MOU           C
Q6AYR0            S
node #6           A
node #7           A
node #8           A
node #9           S


Overall accuracy of the 4 ancestral sequences:
  1.00000  1.00000  0.99515  0.71014
for a site.

  1.00000  1.00000  0.99515  0.71014
for the sequence.


Counts of changes at sites

   1  SC AS (2)


(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  AAACS: AAAS (0.705) AAAA (0.160) AAAC (0.126) AASS (0.005) SSSS (0.000) TTTS (0.000)  (total  0.996)



List of extant and reconstructed sequences

     9      1

1EY2_A            A
HGD_HUM           A
B8YB76_B          A
HGD_MOU           C
Q6AYR0            S
node #6           A
node #7           A
node #8           A
node #9           S


