Supplemental results for CODEML (seqf: PancreaticRibonucleases_Aln_Tree.nex_23.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   SSPPP: A(0.012) R(0.001) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.001) H(0.000) I(0.000) L(0.002) K(0.000) M(0.000) F(0.000) P(0.392) S(0.586) T(0.004) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 7, by site

   site  Freq   Data

      1      1   SSPPP: 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(0.000) K(0.000) M(0.000) F(0.000) P(0.881) S(0.117) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 8, by site

   site  Freq   Data

      1      1   SSPPP: 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(0.000) K(0.000) M(0.000) F(0.000) P(0.882) S(0.116) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 9, by site

   site  Freq   Data

      1      1   SSPPP: 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(0.000) P(0.998) S(0.002) 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   SSPPP: S(0.586) P(0.881) P(0.882) P(0.998) 

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

Branch 1:    6..7 

	   1 S 0.586 -> P 0.881


Branch 2:    7..8 



Branch 3:    8..2  (RNAS1_1) 

	   1 P 0.882 -> S


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           S
RNAS1_2           P
RNAS1_M           P
RNS1B_R           P
node #6           S
node #7           P
node #8           P
node #9           P


Overall accuracy of the 4 ancestral sequences:
  0.58576  0.88149  0.88238  0.99763
for a site.

  0.58576  0.88149  0.88238  0.99763
for the sequence.


Counts of changes at sites

   1  PS SP (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  SSPPP: SPPP (0.465) PPPP (0.389) SSSP (0.108) APPP (0.011) SSPP (0.006) TPPP (0.004) SPSP (0.003) PPSP (0.002) LPPP (0.002) GPPP (0.001) RPPP (0.001)  (total  0.993)



List of extant and reconstructed sequences

     9      1

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


