Supplemental results for CODEML (seqf: PancreaticRibonucleases_Aln_Tree.nex_39.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   RRWSS: A(0.000) R(0.966) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.002) H(0.000) I(0.000) L(0.000) K(0.002) M(0.000) F(0.000) P(0.000) S(0.009) T(0.000) W(0.020) Y(0.000) V(0.000) 

Prob distribution at node 7, by site

   site  Freq   Data

      1      1   RRWSS: A(0.000) R(0.931) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.004) H(0.000) I(0.000) L(0.000) K(0.001) M(0.000) F(0.000) P(0.000) S(0.020) T(0.000) W(0.042) Y(0.000) V(0.000) 

Prob distribution at node 8, by site

   site  Freq   Data

      1      1   RRWSS: A(0.000) R(0.913) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.002) H(0.000) I(0.000) L(0.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.003) T(0.000) W(0.082) Y(0.000) V(0.000) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   RRWSS: A(0.002) R(0.013) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.002) H(0.000) I(0.000) L(0.000) K(0.000) M(0.000) F(0.000) P(0.001) S(0.981) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob of best state at each node, listed by site

   site   Freq   Data: 

   1      1   RRWSS: R(0.966) R(0.931) R(0.913) S(0.981) 

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

Branch 1:    6..7 



Branch 2:    7..8 



Branch 3:    8..2  (RNAS1_1) 



Branch 4:    8..3  (RNAS1_2) 

	   1 R 0.913 -> W


Branch 5:    7..9 

	   1 R 0.931 -> S 0.981


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            R
RNAS1_1           R
RNAS1_2           W
RNAS1_M           S
RNS1B_R           S
node #6           R
node #7           R
node #8           R
node #9           S


Overall accuracy of the 4 ancestral sequences:
  0.96577  0.93133  0.91307  0.98139
for a site.

  0.96577  0.93133  0.91307  0.98139
for the sequence.


Counts of changes at sites

   1  RW RS (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  RRWSS: RRRS (0.885) RRWS (0.027) RWWS (0.022) WWWS (0.019) RRRR (0.012) SSWS (0.004) SSRS (0.003) SSSS (0.001) KRRS (0.001)  (total  0.975)



List of extant and reconstructed sequences

     9      1

1SRN_A            R
RNAS1_1           R
RNAS1_2           W
RNAS1_M           S
RNS1B_R           S
node #6           R
node #7           R
node #8           R
node #9           S


