Supplemental results for CODEML (seqf: PancreaticRibonucleases_Aln_Tree.nex_37.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   KQQNK: A(0.000) R(0.004) N(0.004) D(0.000) C(0.000) Q(0.018) E(0.001) G(0.000) H(0.000) I(0.000) L(0.000) K(0.973) 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   KQQNK: A(0.000) R(0.005) N(0.008) D(0.000) C(0.000) Q(0.041) E(0.001) G(0.000) H(0.000) I(0.000) L(0.000) K(0.945) 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   KQQNK: A(0.000) R(0.001) N(0.000) D(0.000) C(0.000) Q(0.984) E(0.001) G(0.000) H(0.000) I(0.000) L(0.000) K(0.014) 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   KQQNK: A(0.000) R(0.002) N(0.039) D(0.000) C(0.000) Q(0.010) E(0.001) G(0.000) H(0.000) I(0.000) L(0.000) K(0.948) 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   KQQNK: K(0.973) K(0.945) Q(0.984) K(0.948) 

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

Branch 1:    6..7 



Branch 2:    7..8 

	   1 K 0.945 -> Q 0.984


Branch 3:    8..2  (RNAS1_1) 



Branch 4:    8..3  (RNAS1_2) 



Branch 5:    7..9 



Branch 6:    9..4  (RNAS1_M) 

	   1 K 0.948 -> N


Branch 7:    9..5  (RNS1B_R) 



Branch 8:    6..1  (1SRN_A) 





List of extant and reconstructed sequences

     9      1

1SRN_A            K
RNAS1_1           Q
RNAS1_2           Q
RNAS1_M           N
RNS1B_R           K
node #6           K
node #7           K
node #8           Q
node #9           K


Overall accuracy of the 4 ancestral sequences:
  0.97286  0.94482  0.98420  0.94763
for a site.

  0.97286  0.94482  0.98420  0.94763
for the sequence.


Counts of changes at sites

   1  KN KQ (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  KQQNK: KKQK (0.907) KKQN (0.020) KKKK (0.014) KQQK (0.011) QQQK (0.009) QQQN (0.005) QQQQ (0.004) NNQN (0.003) RRQK (0.001) RKQK (0.001)  (total  0.975)



List of extant and reconstructed sequences

     9      1

1SRN_A            K
RNAS1_1           Q
RNAS1_2           Q
RNAS1_M           N
RNS1B_R           K
node #6           K
node #7           K
node #8           Q
node #9           K


