Supplemental results for CODEML (seqf: PancreaticRibonucleases_Aln_Tree.nex_59.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

(((RNAS1_1: 0.162443, RNAS1_2: 0.087616): 0.102522, (RNAS1_M: 0.095750, RNS1B_R: 0.206332): 0.117698): 0.106399, 1SRN_A: 0.088987);

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

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

tree with node labels for Rod Page's TreeView
(((2_RNAS1_1, 3_RNAS1_2) 8 , (4_RNAS1_M, 5_RNS1B_R) 9 ) 7 , 1_1SRN_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   SFLSS: A(0.002) 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(0.008) K(0.000) M(0.000) F(0.009) P(0.001) S(0.978) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 7, by site

   site  Freq   Data

      1      1   SFLSS: A(0.001) 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(0.018) K(0.000) M(0.000) F(0.020) P(0.001) S(0.957) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 8, by site

   site  Freq   Data

      1      1   SFLSS: 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(0.001) L(0.533) K(0.000) M(0.000) F(0.413) P(0.001) S(0.051) T(0.000) W(0.000) Y(0.000) V(0.001) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   SFLSS: 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(0.000) M(0.000) F(0.001) P(0.000) S(0.998) 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   SFLSS: S(0.978) S(0.957) L(0.533) S(0.998) 

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

Branch 1:    6..7 



Branch 2:    7..8 

	   1 S 0.957 -> L 0.533


Branch 3:    8..2  (RNAS1_1) 

	   1 L 0.533 -> F


Branch 4:    8..3  (RNAS1_2) 



Branch 5:    7..9 



Branch 6:    9..4  (RNAS1_M) 



Branch 7:    9..5  (RNS1B_R) 



Branch 8:    6..1  (1SRN_A) 





List of extant and reconstructed sequences

     9      1

1SRN_A            S
RNAS1_1           F
RNAS1_2           L
RNAS1_M           S
RNS1B_R           S
node #6           S
node #7           S
node #8           L
node #9           S


Overall accuracy of the 4 ancestral sequences:
  0.97786  0.95743  0.53263  0.99833
for a site.

  0.97786  0.95743  0.53263  0.99833
for the sequence.


Counts of changes at sites

   1  LF SL (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  SFLSS: SSLS (0.510) SSFS (0.391) SSSS (0.051) SFFS (0.010) FFFS (0.008) LLLS (0.007) PPLS (0.000)  (total  0.978)



List of extant and reconstructed sequences

     9      1

1SRN_A            S
RNAS1_1           F
RNAS1_2           L
RNAS1_M           S
RNS1B_R           S
node #6           S
node #7           S
node #8           L
node #9           S


