Supplemental results for CODEML (seqf: trpa_MOD2_MAFFT7.nex_125.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((((((((((TRPA_VIBCH: 0.106720, TRPA_VIBPA_8_267: 0.158227): 0.096676, H1AFK5_SHEFR: 0.234069): 0.082193, TRPA_HAEIN_8_268: 0.372179): 0.095624, (TRPA_SALTY_8_267: 0.069035, (TRPA_ECOLI_8_267: 0.045018, TRPA_KLEAE_8_267: 0.084751): 0.043425): 0.119456): 0.148698, ((TRPA_BUCSC_14_267: 0.200967, TRPA_BUCBP_9_268: 0.257046): 0.180230, (TRPA_BUCAP_8_267: 0.193427, TRPA_BUCDN_8_267: 0.214926): 0.081889): 0.165023): 0.183336, (TRPA_HELPY_7_261: 0.048196, TRPA_HELPJ_7_261: 0.000736): 0.403754): 0.260972, (TRPA_METTM_7_262: 0.092037, TRPA_METTH_13_268: 0.070992): 0.303428): 0.349633, (TRPA_CAUCR_10_268: 0.365327, (TRPA_RHOSH_8_261: 0.313941, (TRPA_PSEPU_8_265: 0.096983, (TRPA_PSESY_8_265: 0.098738, TRPA_PSEAE_8_265: 0.109135): 0.067296): 0.156387): 0.070376): 0.175827): 0.108678, (TRPA_THETH_7_267: 0.498618, (TRPA_STRCO_10_268: 0.342760, (TRPA_MYCTU_16_265: 0.052243, TRPA_MYCIT_15_265: 0.087763): 0.389222): 0.149182): 0.200768): 0.471080, TRP_YEAST_9_272: 0.039404);

((((((((((1, 2), 3), 7), (4, (5, 6))), ((8, 9), (10, 11))), (12, 13)), (14, 15)), (21, (20, (17, (18, 19))))), (25, (22, (23, 24)))), 16);

  26..27   27..28   28..29   29..30   30..31   31..32   32..33   33..34   34..35   35..1    35..2    34..3    33..7    32..36   36..4    36..37   37..5    37..6    31..38   38..39   39..8    39..9    38..40   40..10   40..11   30..41   41..12   41..13   29..42   42..14   42..15   28..43   43..21   43..44   44..20   44..45   45..17   45..46   46..18   46..19   27..47   47..25   47..48   48..22   48..49   49..23   49..24   26..16 

tree with node labels for Rod Page's TreeView
((((((((((1_TRPA_VIBCH, 2_TRPA_VIBPA_8_267) 35 , 3_H1AFK5_SHEFR) 34 , 7_TRPA_HAEIN_8_268) 33 , (4_TRPA_SALTY_8_267, (5_TRPA_ECOLI_8_267, 6_TRPA_KLEAE_8_267) 37 ) 36 ) 32 , ((8_TRPA_BUCSC_14_267, 9_TRPA_BUCBP_9_268) 39 , (10_TRPA_BUCAP_8_267, 11_TRPA_BUCDN_8_267) 40 ) 38 ) 31 , (12_TRPA_HELPY_7_261, 13_TRPA_HELPJ_7_261) 41 ) 30 , (14_TRPA_METTM_7_262, 15_TRPA_METTH_13_268) 42 ) 29 , (21_TRPA_CAUCR_10_268, (20_TRPA_RHOSH_8_261, (17_TRPA_PSEPU_8_265, (18_TRPA_PSESY_8_265, 19_TRPA_PSEAE_8_265) 46 ) 45 ) 44 ) 43 ) 28 , (25_TRPA_THETH_7_267, (22_TRPA_STRCO_10_268, (23_TRPA_MYCTU_16_265, 24_TRPA_MYCIT_15_265) 49 ) 48 ) 47 ) 27 , 16_TRP_YEAST_9_272) 26 ;

Nodes 26 to 49 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 26, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.001) R(0.000) N(0.947) D(0.034) C(0.000) Q(0.000) E(0.001) G(0.001) H(0.001) I(0.000) L(0.000) K(0.001) M(0.000) F(0.000) P(0.000) S(0.008) T(0.004) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 27, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.012) R(0.000) N(0.559) D(0.334) C(0.000) Q(0.001) E(0.006) G(0.002) H(0.003) I(0.000) L(0.000) K(0.002) M(0.000) F(0.000) P(0.000) S(0.040) T(0.041) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 28, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.003) R(0.000) N(0.284) D(0.679) C(0.000) Q(0.000) E(0.004) G(0.000) H(0.001) I(0.000) L(0.000) K(0.000) M(0.000) F(0.000) P(0.000) S(0.011) T(0.019) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 29, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.004) R(0.000) N(0.221) D(0.693) C(0.000) Q(0.000) E(0.014) G(0.001) H(0.001) I(0.000) L(0.000) K(0.001) M(0.000) F(0.000) P(0.000) S(0.015) T(0.048) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 30, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.020) D(0.974) C(0.000) Q(0.000) E(0.004) 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 31, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.001) D(0.998) C(0.000) Q(0.000) E(0.001) 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 32, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 33, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 34, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 35, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 36, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 37, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 38, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 39, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(0.999) C(0.000) Q(0.000) E(0.001) 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 40, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 41, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 42, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.001) R(0.000) N(0.002) 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(0.000) S(0.002) T(0.994) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 43, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.017) D(0.981) C(0.000) Q(0.000) E(0.001) 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 44, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.004) D(0.996) C(0.000) Q(0.000) E(0.001) 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 45, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 46, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.000) R(0.000) N(0.000) D(1.000) 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(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 47, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.133) R(0.001) N(0.287) D(0.079) C(0.001) Q(0.002) E(0.006) G(0.003) H(0.010) I(0.000) L(0.001) K(0.003) M(0.001) F(0.000) P(0.002) S(0.181) T(0.283) W(0.000) Y(0.003) V(0.002) 

Prob distribution at node 48, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.239) R(0.003) N(0.182) D(0.052) C(0.003) Q(0.004) E(0.006) G(0.004) H(0.022) I(0.001) L(0.007) K(0.004) M(0.004) F(0.001) P(0.006) S(0.231) T(0.214) W(0.001) Y(0.013) V(0.006) 

Prob distribution at node 49, by site

   site  Freq   Data

      1      1   DDDDDDDDDDDDDTTNDDDDDALYT: A(0.008) R(0.003) N(0.019) D(0.004) C(0.007) Q(0.004) E(0.000) G(0.000) H(0.066) I(0.003) L(0.362) K(0.001) M(0.008) F(0.026) P(0.004) S(0.090) T(0.017) W(0.009) Y(0.364) V(0.004) 

Prob of best state at each node, listed by site

   site   Freq   Data: 

   1      1   DDDDDDDDDDDDDTTNDDDDDALYT: N(0.947) N(0.559) D(0.679) D(0.693) D(0.974) D(0.998) D(1.000) D(1.000) D(1.000) D(1.000) D(1.000) D(1.000) D(1.000) D(0.999) D(1.000) D(1.000) T(0.994) D(0.981) D(0.996) D(1.000) D(1.000) N(0.287) A(0.239) Y(0.364) 

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

Branch 1:   26..27



Branch 2:   27..28

	   1 N 0.559 -> D 0.679


Branch 3:   28..29



Branch 4:   29..30



Branch 5:   30..31



Branch 6:   31..32



Branch 7:   32..33



Branch 8:   33..34



Branch 9:   34..35



Branch 10:   35..1  (TRPA_VIBCH) 



Branch 11:   35..2  (TRPA_VIBPA_8_267) 



Branch 12:   34..3  (H1AFK5_SHEFR) 



Branch 13:   33..7  (TRPA_HAEIN_8_268) 



Branch 14:   32..36



Branch 15:   36..4  (TRPA_SALTY_8_267) 



Branch 16:   36..37



Branch 17:   37..5  (TRPA_ECOLI_8_267) 



Branch 18:   37..6  (TRPA_KLEAE_8_267) 



Branch 19:   31..38



Branch 20:   38..39



Branch 21:   39..8  (TRPA_BUCSC_14_267) 



Branch 22:   39..9  (TRPA_BUCBP_9_268) 



Branch 23:   38..40



Branch 24:   40..10 (TRPA_BUCAP_8_267) 



Branch 25:   40..11 (TRPA_BUCDN_8_267) 



Branch 26:   30..41



Branch 27:   41..12 (TRPA_HELPY_7_261) 



Branch 28:   41..13 (TRPA_HELPJ_7_261) 



Branch 29:   29..42

	   1 D 0.693 -> T 0.994


Branch 30:   42..14 (TRPA_METTM_7_262) 



Branch 31:   42..15 (TRPA_METTH_13_268) 



Branch 32:   28..43



Branch 33:   43..21 (TRPA_CAUCR_10_268) 



Branch 34:   43..44



Branch 35:   44..20 (TRPA_RHOSH_8_261) 



Branch 36:   44..45



Branch 37:   45..17 (TRPA_PSEPU_8_265) 



Branch 38:   45..46



Branch 39:   46..18 (TRPA_PSESY_8_265) 



Branch 40:   46..19 (TRPA_PSEAE_8_265) 



Branch 41:   27..47



Branch 42:   47..25 (TRPA_THETH_7_267) 

	   1 N 0.287 -> T


Branch 43:   47..48

	   1 N 0.287 -> A 0.239


Branch 44:   48..22 (TRPA_STRCO_10_268) 



Branch 45:   48..49

	   1 A 0.239 -> Y 0.364


Branch 46:   49..23 (TRPA_MYCTU_16_265) 

	   1 Y 0.364 -> L


Branch 47:   49..24 (TRPA_MYCIT_15_265) 



Branch 48:   26..16 (TRP_YEAST_9_272) 





List of extant and reconstructed sequences

    49      1

TRPA_VIBCH        D
TRPA_VIBPA_8_267   D
H1AFK5_SHEFR      D
TRPA_SALTY_8_267   D
TRPA_ECOLI_8_267   D
TRPA_KLEAE_8_267   D
TRPA_HAEIN_8_268   D
TRPA_BUCSC_14_267   D
TRPA_BUCBP_9_268   D
TRPA_BUCAP_8_267   D
TRPA_BUCDN_8_267   D
TRPA_HELPY_7_261   D
TRPA_HELPJ_7_261   D
TRPA_METTM_7_262   T
TRPA_METTH_13_268   T
TRP_YEAST_9_272   N
TRPA_PSEPU_8_265   D
TRPA_PSESY_8_265   D
TRPA_PSEAE_8_265   D
TRPA_RHOSH_8_261   D
TRPA_CAUCR_10_268   D
TRPA_STRCO_10_268   A
TRPA_MYCTU_16_265   L
TRPA_MYCIT_15_265   Y
TRPA_THETH_7_267   T
node #26          N
node #27          N
node #28          D
node #29          D
node #30          D
node #31          D
node #32          D
node #33          D
node #34          D
node #35          D
node #36          D
node #37          D
node #38          D
node #39          D
node #40          D
node #41          D
node #42          T
node #43          D
node #44          D
node #45          D
node #46          D
node #47          N
node #48          A
node #49          Y


Overall accuracy of the 24 ancestral sequences:
  0.94671  0.55933  0.67873  0.69274  0.97422  0.99819  0.99972  0.99960  0.99973  0.99979  0.99995  0.99998  0.99955  0.99890  0.99954  1.00000  0.99443  0.98148  0.99587  0.99980  0.99990  0.28744  0.23853  0.36414
for a site.

  0.94671  0.55933  0.67873  0.69274  0.97422  0.99819  0.99972  0.99960  0.99973  0.99979  0.99995  0.99998  0.99955  0.99890  0.99954  1.00000  0.99443  0.98148  0.99587  0.99980  0.99990  0.28744  0.23853  0.36414
for the sequence.


Counts of changes at sites

   1  YL NT ND DT NA AY (6)


(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  DDDDDDDDDDDDDTTNDDDDDALYT: NNDDDDDDDDDDDDDDTDDDDNNY (0.037) NDDDDDDDDDDDDDDDTDDDDAAL (0.034) NDDDDDDDDDDDDDDDTDDDDDDY (0.024) NNNNDDDDDDDDDDDDTDDDDNNY (0.023) DDDDDDDDDDDDDDDDTDDDDAAL (0.004) DDDDDDDDDDDDDDDDTDDDDDDY (0.003) DDDDDDDDDDDDDDDDTDDDDTTL (0.002) DDDDDDDDDDDDDDDDTDDDDAAY (0.002) TTDDDDDDDDDDDDDDTDDDDTTL (0.000)  (total  0.128)



List of extant and reconstructed sequences

    49      1

TRPA_VIBCH        D
TRPA_VIBPA_8_267   D
H1AFK5_SHEFR      D
TRPA_SALTY_8_267   D
TRPA_ECOLI_8_267   D
TRPA_KLEAE_8_267   D
TRPA_HAEIN_8_268   D
TRPA_BUCSC_14_267   D
TRPA_BUCBP_9_268   D
TRPA_BUCAP_8_267   D
TRPA_BUCDN_8_267   D
TRPA_HELPY_7_261   D
TRPA_HELPJ_7_261   D
TRPA_METTM_7_262   T
TRPA_METTH_13_268   T
TRP_YEAST_9_272   N
TRPA_PSEPU_8_265   D
TRPA_PSESY_8_265   D
TRPA_PSEAE_8_265   D
TRPA_RHOSH_8_261   D
TRPA_CAUCR_10_268   D
TRPA_STRCO_10_268   A
TRPA_MYCTU_16_265   L
TRPA_MYCIT_15_265   Y
TRPA_THETH_7_267   T
node #26          N
node #27          N
node #28          D
node #29          D
node #30          D
node #31          D
node #32          D
node #33          D
node #34          D
node #35          D
node #36          D
node #37          D
node #38          D
node #39          D
node #40          D
node #41          D
node #42          T
node #43          D
node #44          D
node #45          D
node #46          D
node #47          N
node #48          N
node #49          Y


