Supplemental results for CODEML (seqf: PancreaticRibonucleases_Aln_Tree.nex_103.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   NEEQQ: A(0.003) R(0.002) N(0.499) D(0.110) C(0.000) Q(0.129) E(0.218) G(0.006) H(0.007) I(0.000) L(0.000) K(0.017) M(0.000) F(0.000) P(0.001) S(0.006) T(0.003) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 7, by site

   site  Freq   Data

      1      1   NEEQQ: A(0.001) R(0.001) N(0.038) D(0.036) C(0.000) Q(0.299) E(0.612) G(0.001) H(0.001) I(0.000) L(0.000) K(0.009) M(0.000) F(0.000) P(0.000) S(0.001) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 8, by site

   site  Freq   Data

      1      1   NEEQQ: A(0.000) R(0.000) N(0.000) D(0.004) C(0.000) Q(0.006) E(0.989) 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   NEEQQ: A(0.000) R(0.000) N(0.000) D(0.000) C(0.000) Q(0.981) E(0.018) 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   NEEQQ: N(0.499) E(0.612) E(0.989) Q(0.981) 

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

Branch 1:    6..7 

	   1 N 0.499 -> E 0.612


Branch 2:    7..8 



Branch 3:    8..2  (RNAS1_1) 



Branch 4:    8..3  (RNAS1_2) 



Branch 5:    7..9 

	   1 E 0.612 -> Q 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            N
RNAS1_1           E
RNAS1_2           E
RNAS1_M           Q
RNS1B_R           Q
node #6           N
node #7           E
node #8           E
node #9           Q


Overall accuracy of the 4 ancestral sequences:
  0.49852  0.61219  0.98878  0.98137
for a site.

  0.49852  0.61219  0.98878  0.98137
for the sequence.


Counts of changes at sites

   1  NE EQ (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  NEEQQ: NEEQ (0.275) EEEQ (0.208) NQEQ (0.147) QQEQ (0.123) DEEQ (0.088) NNEQ (0.036) NDEQ (0.018) DDEQ (0.015) KEEQ (0.007) EEEE (0.006) HQEQ (0.005) KQEQ (0.005) GEEQ (0.005) KKEQ (0.004) DQEQ (0.003) SEEQ (0.003) EQEQ (0.003) QEEQ (0.003) QQQQ (0.003) DEEE (0.003) AEEQ (0.002) SQEQ (0.002) TEEQ (0.001) RQEQ (0.001) TQEQ (0.001)  (total  0.967)



List of extant and reconstructed sequences

     9      1

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


