Supplemental results for CODEML (seqf: Rubredoxins_Aln_Tree.nex_3.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((((O05894MY: 0.230401, (RUBR2PS8: 0.236966, RUBR1PS9: 0.241391): 0.123450): 0.394691, (RUBRACI5: 0.032628, O05893M3: 0.405434): 0.076474): 0.072125, (((((NORVECO1: 0.430256, (RUBLRHIg: 0.077322, (RUBLBRAJ: 0.127280, (HUPJRHOC: 0.160943, (RUBRAZO6: 0.128339, (RUBRCUP7: 0.089929, P955009P: 0.100195): 0.094350): 0.224478): 0.091069): 0.101661): 0.458878): 0.135207, (RUBRMET2: 0.189041, (P94698D1: 0.490951, (RUBRSYN4: 0.303454, O26576M1: 0.828981): 0.191480): 0.088654): 0.176727): 0.000000, (RUBR1ME1: 0.301356, RUBR2ME7: 0.212007): 0.071902): 0.254213, RUBRTHE8: 0.058643): 0.088845, ((RUBRMEG1: 0.233687, O28920AR: 0.087717): 0.084756, ((RUBRPEP7: 0.703106, (O29906AR: 0.513543, ((O50375ME: 0.272852, RUBHMET1: 0.196749): 0.204600, (O29905A1: 0.326832, (O26912M1: 0.669454, O27972A1: 0.000000): 0.190148): 0.560000): 0.320912): 0.634818): 0.000000, (((RUBRCLO3: 0.120800, RUBRCLO4: 0.115307): 0.113961, (RUBR2CL5: 0.151965, (RUBRPYR6: 0.259655, P96745C8: 0.005391): 0.079863): 0.055829): 0.070572, ((RUBRBUT5: 0.148791, RUBRHEL6: 0.129038): 0.035894, (RUBRCHL1: 0.254479, ((RUBRDES2: 0.143520, (RUBRDES3: 0.150322, Q46496DE: 0.091581): 0.033965): 0.048772, (RUBRTRE1: 0.608485, (O26259ME: 0.200057, RUBR1DE4: 0.236149): 0.031696): 0.022142): 0.019435): 0.000000): 0.043537): 0.059919): 0.000000): 0.081735): 0.215244): 0.277610, RUBR2PS2: 0.133086);

((((24, (25, 26)), (16, 17)), (((((29, (30, (31, (32, (33, (34, 35)))))), (20, (21, (27, 39)))), (18, 22)), 12), ((14, 15), ((36, (43, ((37, 38), (40, (42, 41))))), (((10, 11), (7, (8, 9))), ((5, 6), (1, ((2, (3, 4)), (28, (13, 19)))))))))), 23);

  44..45   45..46   46..47   47..24   47..48   48..25   48..26   46..49   49..16   49..17   45..50   50..51   51..52   52..53   53..54   54..29   54..55   55..30   55..56   56..31   56..57   57..32   57..58   58..33   58..59   59..34   59..35   53..60   60..20   60..61   61..21   61..62   62..27   62..39   52..63   63..18   63..22   51..12   50..64   64..65   65..14   65..15   64..66   66..67   67..36   67..68   68..43   68..69   69..70   70..37   70..38   69..71   71..40   71..72   72..42   72..41   66..73   73..74   74..75   75..10   75..11   74..76   76..7    76..77   77..8    77..9    73..78   78..79   79..5    79..6    78..80   80..1    80..81   81..82   82..2    82..83   83..3    83..4    81..84   84..28   84..85   85..13   85..19   44..23 

tree with node labels for Rod Page's TreeView
((((24_O05894MY, (25_RUBR2PS8, 26_RUBR1PS9) 48 ) 47 , (16_RUBRACI5, 17_O05893M3) 49 ) 46 , (((((29_NORVECO1, (30_RUBLRHIg, (31_RUBLBRAJ, (32_HUPJRHOC, (33_RUBRAZO6, (34_RUBRCUP7, 35_P955009P) 59 ) 58 ) 57 ) 56 ) 55 ) 54 , (20_RUBRMET2, (21_P94698D1, (27_RUBRSYN4, 39_O26576M1) 62 ) 61 ) 60 ) 53 , (18_RUBR1ME1, 22_RUBR2ME7) 63 ) 52 , 12_RUBRTHE8) 51 , ((14_RUBRMEG1, 15_O28920AR) 65 , ((36_RUBRPEP7, (43_O29906AR, ((37_O50375ME, 38_RUBHMET1) 70 , (40_O29905A1, (42_O26912M1, 41_O27972A1) 72 ) 71 ) 69 ) 68 ) 67 , (((10_RUBRCLO3, 11_RUBRCLO4) 75 , (7_RUBR2CL5, (8_RUBRPYR6, 9_P96745C8) 77 ) 76 ) 74 , ((5_RUBRBUT5, 6_RUBRHEL6) 79 , (1_RUBRCHL1, ((2_RUBRDES2, (3_RUBRDES3, 4_Q46496DE) 83 ) 82 , (28_RUBRTRE1, (13_O26259ME, 19_RUBR1DE4) 85 ) 84 ) 81 ) 80 ) 78 ) 73 ) 66 ) 64 ) 50 ) 45 , 23_RUBR2PS2) 44 ;

Nodes 44 to 85 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 44, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.019) N(0.002) D(0.000) C(0.000) Q(0.003) E(0.001) G(0.000) H(0.000) I(0.000) L(0.000) K(0.975) M(0.000) F(0.000) P(0.000) S(0.000) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 45, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.009) N(0.001) D(0.000) C(0.000) Q(0.001) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.989) 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   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.014) N(0.003) D(0.000) C(0.000) Q(0.002) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.978) M(0.000) F(0.000) P(0.000) S(0.001) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 47, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.279) R(0.234) N(0.040) D(0.001) C(0.000) Q(0.015) E(0.004) G(0.016) H(0.003) I(0.000) L(0.000) K(0.128) M(0.001) F(0.000) P(0.003) S(0.186) T(0.088) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 48, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.159) R(0.308) N(0.036) D(0.000) C(0.000) Q(0.012) E(0.002) G(0.018) H(0.005) I(0.000) L(0.000) K(0.073) M(0.001) F(0.000) P(0.004) S(0.308) T(0.073) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 49, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.008) N(0.002) D(0.000) C(0.000) Q(0.002) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.986) M(0.000) F(0.000) P(0.000) S(0.000) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 50, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.003) 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(0.997) 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 51, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.012) 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(0.988) 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 52, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.740) N(0.000) D(0.000) C(0.000) Q(0.001) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.259) 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 53, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.740) N(0.000) D(0.000) C(0.000) Q(0.001) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.259) 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 54, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.853) N(0.000) D(0.000) C(0.000) Q(0.003) E(0.000) G(0.000) H(0.001) I(0.000) L(0.000) K(0.142) 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 55, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.994) 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(0.006) 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 56, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.989) N(0.000) D(0.000) C(0.000) Q(0.001) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.007) M(0.000) F(0.000) P(0.000) S(0.000) T(0.001) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 57, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.004) R(0.800) N(0.002) D(0.000) C(0.000) Q(0.004) E(0.000) G(0.001) H(0.002) I(0.082) L(0.006) K(0.043) M(0.017) F(0.000) P(0.000) S(0.006) T(0.017) W(0.000) Y(0.000) V(0.017) 

Prob distribution at node 58, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.010) R(0.717) N(0.002) D(0.000) C(0.000) Q(0.007) E(0.001) G(0.002) H(0.002) I(0.035) L(0.005) K(0.118) M(0.019) F(0.000) P(0.000) S(0.006) T(0.016) W(0.000) Y(0.000) V(0.062) 

Prob distribution at node 59, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.001) R(0.772) N(0.001) D(0.000) C(0.000) Q(0.003) E(0.000) G(0.000) H(0.000) I(0.001) L(0.000) K(0.216) M(0.002) F(0.000) P(0.000) S(0.001) T(0.002) W(0.000) Y(0.000) V(0.001) 

Prob distribution at node 60, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.001) R(0.758) N(0.020) D(0.000) C(0.000) Q(0.009) E(0.001) G(0.002) H(0.009) I(0.000) L(0.000) K(0.189) M(0.001) F(0.000) P(0.000) S(0.006) T(0.004) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 61, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.013) R(0.428) N(0.144) D(0.012) C(0.000) Q(0.028) E(0.010) G(0.010) H(0.035) I(0.002) L(0.005) K(0.200) M(0.019) F(0.000) P(0.001) S(0.048) T(0.044) W(0.000) Y(0.000) V(0.001) 

Prob distribution at node 62, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.010) R(0.080) N(0.544) D(0.107) C(0.000) Q(0.021) E(0.022) G(0.015) H(0.037) I(0.001) L(0.001) K(0.095) M(0.002) F(0.000) P(0.001) S(0.040) T(0.025) W(0.000) Y(0.000) V(0.000) 

Prob distribution at node 63, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.730) N(0.000) D(0.000) C(0.000) Q(0.001) E(0.000) G(0.000) H(0.000) I(0.000) L(0.000) K(0.268) 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 64, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 65, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) 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(0.999) 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 66, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 67, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 68, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.009) R(0.411) N(0.011) D(0.000) C(0.000) Q(0.035) E(0.004) G(0.003) H(0.009) I(0.012) L(0.015) K(0.415) M(0.034) F(0.000) P(0.001) S(0.008) T(0.030) W(0.000) Y(0.000) V(0.003) 

Prob distribution at node 69, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.008) R(0.029) N(0.005) D(0.000) C(0.000) Q(0.006) E(0.001) G(0.001) H(0.002) I(0.155) L(0.062) K(0.035) M(0.608) F(0.000) P(0.000) S(0.006) T(0.059) W(0.000) Y(0.000) V(0.024) 

Prob distribution at node 70, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) N(0.000) D(0.000) C(0.000) Q(0.000) E(0.000) G(0.000) H(0.000) I(0.015) L(0.011) K(0.001) M(0.963) F(0.000) P(0.000) S(0.000) T(0.006) W(0.000) Y(0.000) V(0.002) 

Prob distribution at node 71, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(0.965) L(0.005) K(0.000) M(0.014) F(0.000) P(0.000) S(0.000) T(0.004) W(0.000) Y(0.000) V(0.011) 

Prob distribution at node 72, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 73, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 74, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 75, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) 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(0.999) 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 76, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 77, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 78, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 79, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 80, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 81, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(1.000) 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 82, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) N(0.001) 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(0.997) 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 83, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: 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(0.999) 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 84, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) 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(0.999) 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 85, by site

   site  Freq   Data

      1      1   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: A(0.000) R(0.001) 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(0.999) 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   KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: K(0.975) K(0.989) K(0.978) A(0.279) S(0.308) K(0.986) K(0.997) K(0.988) R(0.740) R(0.740) R(0.853) R(0.994) R(0.989) R(0.800) R(0.717) R(0.772) R(0.758) R(0.428) N(0.544) R(0.730) K(1.000) K(0.999) K(1.000) K(1.000) K(0.415) M(0.608) M(0.963) I(0.965) I(1.000) K(1.000) K(1.000) K(0.999) K(1.000) K(1.000) K(1.000) K(1.000) K(1.000) K(1.000) K(0.997) K(0.999) K(0.999) K(0.999) 

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

Branch 1:   44..45



Branch 2:   45..46



Branch 3:   46..47

	   1 K 0.978 -> A 0.279


Branch 4:   47..24 (O05894MY) 



Branch 5:   47..48

	   1 A 0.279 -> S 0.308


Branch 6:   48..25 (RUBR2PS8) 



Branch 7:   48..26 (RUBR1PS9) 

	   1 S 0.308 -> R


Branch 8:   46..49



Branch 9:   49..16 (RUBRACI5) 



Branch 10:   49..17 (O05893M3) 

	   1 K 0.986 -> L


Branch 11:   45..50



Branch 12:   50..51



Branch 13:   51..52

	   1 K 0.988 -> R 0.740


Branch 14:   52..53



Branch 15:   53..54



Branch 16:   54..29 (NORVECO1) 



Branch 17:   54..55



Branch 18:   55..30 (RUBLRHIg) 



Branch 19:   55..56



Branch 20:   56..31 (RUBLBRAJ) 



Branch 21:   56..57



Branch 22:   57..32 (HUPJRHOC) 

	   1 R 0.800 -> I


Branch 23:   57..58



Branch 24:   58..33 (RUBRAZO6) 

	   1 R 0.717 -> V


Branch 25:   58..59



Branch 26:   59..34 (RUBRCUP7) 



Branch 27:   59..35 (P955009P) 

	   1 R 0.772 -> K


Branch 28:   53..60



Branch 29:   60..20 (RUBRMET2) 



Branch 30:   60..61



Branch 31:   61..21 (P94698D1) 

	   1 R 0.428 -> M


Branch 32:   61..62

	   1 R 0.428 -> N 0.544


Branch 33:   62..27 (RUBRSYN4) 



Branch 34:   62..39 (O26576M1) 

	   1 N 0.544 -> D


Branch 35:   52..63



Branch 36:   63..18 (RUBR1ME1) 

	   1 R 0.730 -> K


Branch 37:   63..22 (RUBR2ME7) 



Branch 38:   51..12 (RUBRTHE8) 



Branch 39:   50..64



Branch 40:   64..65



Branch 41:   65..14 (RUBRMEG1) 



Branch 42:   65..15 (O28920AR) 



Branch 43:   64..66



Branch 44:   66..67



Branch 45:   67..36 (RUBRPEP7) 



Branch 46:   67..68



Branch 47:   68..43 (O29906AR) 

	   1 K 0.415 -> R


Branch 48:   68..69

	   1 K 0.415 -> M 0.608


Branch 49:   69..70



Branch 50:   70..37 (O50375ME) 



Branch 51:   70..38 (RUBHMET1) 



Branch 52:   69..71

	   1 M 0.608 -> I 0.965


Branch 53:   71..40 (O29905A1) 



Branch 54:   71..72



Branch 55:   72..42 (O26912M1) 

	   1 I 1.000 -> Y


Branch 56:   72..41 (O27972A1) 



Branch 57:   66..73



Branch 58:   73..74



Branch 59:   74..75



Branch 60:   75..10 (RUBRCLO3) 



Branch 61:   75..11 (RUBRCLO4) 



Branch 62:   74..76



Branch 63:   76..7  (RUBR2CL5) 



Branch 64:   76..77



Branch 65:   77..8  (RUBRPYR6) 



Branch 66:   77..9  (P96745C8) 



Branch 67:   73..78



Branch 68:   78..79



Branch 69:   79..5  (RUBRBUT5) 



Branch 70:   79..6  (RUBRHEL6) 



Branch 71:   78..80



Branch 72:   80..1  (RUBRCHL1) 



Branch 73:   80..81



Branch 74:   81..82



Branch 75:   82..2  (RUBRDES2) 

	   1 K 0.997 -> I


Branch 76:   82..83



Branch 77:   83..3  (RUBRDES3) 



Branch 78:   83..4  (Q46496DE) 



Branch 79:   81..84



Branch 80:   84..28 (RUBRTRE1) 

	   1 K 0.999 -> T


Branch 81:   84..85



Branch 82:   85..13 (O26259ME) 



Branch 83:   85..19 (RUBR1DE4) 



Branch 84:   44..23 (RUBR2PS2) 





List of extant and reconstructed sequences

    85      1

RUBRCHL1          K
RUBRDES2          I
RUBRDES3          K
Q46496DE          K
RUBRBUT5          K
RUBRHEL6          K
RUBR2CL5          K
RUBRPYR6          K
P96745C8          K
RUBRCLO3          K
RUBRCLO4          K
RUBRTHE8          K
O26259ME          K
RUBRMEG1          K
O28920AR          K
RUBRACI5          K
O05893M3          L
RUBR1ME1          K
RUBR1DE4          K
RUBRMET2          R
P94698D1          M
RUBR2ME7          R
RUBR2PS2          K
O05894MY          A
RUBR2PS8          S
RUBR1PS9          R
RUBRSYN4          N
RUBRTRE1          T
NORVECO1          R
RUBLRHIg          R
RUBLBRAJ          R
HUPJRHOC          I
RUBRAZO6          V
RUBRCUP7          R
P955009P          K
RUBRPEP7          K
O50375ME          M
RUBHMET1          M
O26576M1          D
O29905A1          I
O27972A1          I
O26912M1          Y
O29906AR          R
node #44          K
node #45          K
node #46          K
node #47          A
node #48          S
node #49          K
node #50          K
node #51          K
node #52          R
node #53          R
node #54          R
node #55          R
node #56          R
node #57          R
node #58          R
node #59          R
node #60          R
node #61          R
node #62          N
node #63          R
node #64          K
node #65          K
node #66          K
node #67          K
node #68          K
node #69          M
node #70          M
node #71          I
node #72          I
node #73          K
node #74          K
node #75          K
node #76          K
node #77          K
node #78          K
node #79          K
node #80          K
node #81          K
node #82          K
node #83          K
node #84          K
node #85          K


Overall accuracy of the 42 ancestral sequences:
  0.97481  0.98860  0.97827  0.27943  0.30826  0.98634  0.99717  0.98754  0.73977  0.73977  0.85312  0.99371  0.98941  0.79991  0.71669  0.77164  0.75754  0.42826  0.54359  0.73002  0.99982  0.99930  0.99982  0.99982  0.41475  0.60761  0.96330  0.96484  1.00000  0.99991  0.99977  0.99936  0.99970  0.99995  1.00000  0.99973  1.00000  0.99990  0.99738  0.99939  0.99888  0.99893
for a site.

  0.97481  0.98860  0.97827  0.27943  0.30826  0.98634  0.99717  0.98754  0.73977  0.73977  0.85312  0.99371  0.98941  0.79991  0.71669  0.77164  0.75754  0.42826  0.54359  0.73002  0.99982  0.99930  0.99982  0.99982  0.41475  0.60761  0.96330  0.96484  1.00000  0.99991  0.99977  0.99936  0.99970  0.99995  1.00000  0.99973  1.00000  0.99990  0.99738  0.99939  0.99888  0.99893
for the sequence.


Counts of changes at sites

   1  KI KL RK RM SR KT RI RV RK ND IY KR KA AS KR RN KM MI (18)


(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  KIKKKKKKKKKKKKKKLKKRMRKASRNTRRRIVRKKMMDIIYR: KKKRRKKKRRRRRRRRRRNRKKKKKMMIIKKKKKKKKKKKKK (0.006) KKKRRKKKRRRRRRRRRRNRKKKKRMMIIKKKKKKKKKKKKK (0.005) KKKSSKKKRRRRRRRRRRNRKKKKKMMIIKKKKKKKKKKKKK (0.004) KKKSSKKKRRRRRRRRRRNRKKKKRMMIIKKKKKKKKKKKKK (0.004) RKKRRKKKRRRRRRRRRRNRKKKKKMMIIKKKKKKKKKKKKK (0.000) RKKRRKKKRRRRRRRRRRNRKKKKRMMIIKKKKKKKKKKKKK (0.000)  (total  0.020)



List of extant and reconstructed sequences

    85      1

RUBRCHL1          K
RUBRDES2          I
RUBRDES3          K
Q46496DE          K
RUBRBUT5          K
RUBRHEL6          K
RUBR2CL5          K
RUBRPYR6          K
P96745C8          K
RUBRCLO3          K
RUBRCLO4          K
RUBRTHE8          K
O26259ME          K
RUBRMEG1          K
O28920AR          K
RUBRACI5          K
O05893M3          L
RUBR1ME1          K
RUBR1DE4          K
RUBRMET2          R
P94698D1          M
RUBR2ME7          R
RUBR2PS2          K
O05894MY          A
RUBR2PS8          S
RUBR1PS9          R
RUBRSYN4          N
RUBRTRE1          T
NORVECO1          R
RUBLRHIg          R
RUBLBRAJ          R
HUPJRHOC          I
RUBRAZO6          V
RUBRCUP7          R
P955009P          K
RUBRPEP7          K
O50375ME          M
RUBHMET1          M
O26576M1          D
O29905A1          I
O27972A1          I
O26912M1          Y
O29906AR          R
node #44          K
node #45          K
node #46          K
node #47          R
node #48          R
node #49          K
node #50          K
node #51          K
node #52          R
node #53          R
node #54          R
node #55          R
node #56          R
node #57          R
node #58          R
node #59          R
node #60          R
node #61          R
node #62          N
node #63          R
node #64          K
node #65          K
node #66          K
node #67          K
node #68          K
node #69          M
node #70          M
node #71          I
node #72          I
node #73          K
node #74          K
node #75          K
node #76          K
node #77          K
node #78          K
node #79          K
node #80          K
node #81          K
node #82          K
node #83          K
node #84          K
node #85          K


