Supplemental results for CODEML (seqf: CytochromeP450_Aln_Tree.nex_304.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   RRRRR: A(0.000) R(1.000) 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   RRRRR: A(0.000) R(1.000) 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   RRRRR: A(0.000) R(1.000) 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 9, by site

   site  Freq   Data

      1      1   RRRRR: A(0.000) R(1.000) 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 of best state at each node, listed by site

   site   Freq   Data: 

   1      1   RRRRR: R(1.000) R(1.000) R(1.000) R(1.000) 

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 



Branch 4:    8..9 



Branch 5:    9..4  (Q8SQ68) 



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            R
CP2A6_H           R
Q307K8            R
Q8SQ68            R
CP2A5_M           R
node #6           R
node #7           R
node #8           R
node #9           R


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

  1.00000  1.00000  1.00000  1.00000
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  RRRRR: RRRR (1.000) RRRK (0.000) RRKR (0.000) RRRH (0.000) KRRR (0.000) GRRR (0.000)  (total  1.000)



List of extant and reconstructed sequences

     9      1

1Z10_A            R
CP2A6_H           R
Q307K8            R
Q8SQ68            R
CP2A5_M           R
node #6           R
node #7           R
node #8           R
node #9           R


