Supplemental results for CODEML (seqf: CytochromeP450_Aln_Tree.nex_1.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((CP2A6_H: 0.000000, ((Q8SQ68: 0.038538, CP2A5_M: 0.065489): 0.021289, Q307K8: 0.024340): 0.081534): 0.000000, 1Z10_A: 0.002092);

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

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

tree with node labels for Rod Page's TreeView
((2_CP2A6_H, ((4_Q8SQ68, 5_CP2A5_M) 9 , 3_Q307K8) 8 ) 7 , 1_1Z10_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   KKGQS: 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(0.000) K(1.000) 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   KKGQS: 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(0.000) K(1.000) 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   KKGQS: A(0.024) R(0.034) N(0.015) D(0.000) C(0.000) Q(0.233) E(0.007) G(0.281) H(0.001) I(0.000) L(0.000) K(0.167) M(0.000) F(0.000) P(0.000) S(0.234) T(0.002) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   KKGQS: A(0.027) R(0.027) N(0.014) D(0.000) C(0.000) Q(0.328) E(0.005) G(0.144) H(0.001) I(0.000) L(0.000) K(0.097) M(0.000) F(0.000) P(0.001) S(0.353) 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   KKGQS: K(1.000) K(1.000) G(0.281) S(0.353) 

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

Branch 1:    6..7 



Branch 2:    7..2  (CP2A6_H) 



Branch 3:    7..8 

	   1 K 1.000 -> G 0.281


Branch 4:    8..9 

	   1 G 0.281 -> S 0.353


Branch 5:    9..4  (Q8SQ68) 

	   1 S 0.353 -> Q


Branch 6:    9..5  (CP2A5_M) 



Branch 7:    8..3  (Q307K8) 



Branch 8:    6..1  (1Z10_A) 





List of extant and reconstructed sequences

     9      1

1Z10_A            K
CP2A6_H           K
Q307K8            G
Q8SQ68            Q
CP2A5_M           S
node #6           K
node #7           K
node #8           G
node #9           S


Overall accuracy of the 4 ancestral sequences:
  1.00000  1.00000  0.28124  0.35284
for a site.

  1.00000  1.00000  0.28124  0.35284
for the sequence.


Counts of changes at sites

   1  SQ KG GS (3)


(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  KKGQS: KKSS (0.233) KKQQ (0.233) KKGG (0.144) KKGS (0.104) QQQQ (0.000) SSSS (0.000)  (total  0.714)



List of extant and reconstructed sequences

     9      1

1Z10_A            K
CP2A6_H           K
Q307K8            G
Q8SQ68            Q
CP2A5_M           S
node #6           K
node #7           K
node #8           S
node #9           S


