Supplemental results for CODEML (seqf: DNAK_2_MAFFT22.nex_120.nex  treef: OptimizedTreeFile.tre)


TREE #  1

Ancestral reconstruction by AAML.

((((((((((((DNAK_ECOLI_3_603: 0.019146, DNAK_SALTY_3_603: 0.011557): 0.032710, (DNAK_BUCAI_4_604: 0.108574, DNAK_BUCBP_4_604: 0.159096): 0.141522): 0.080580, DNAK_VIBCH_4_603: 0.173535): 0.030969, DNAK_HAEIN_3_602: 0.131058): 0.158707, DNAK_COXBU_4_609: 0.179250): 0.049346, (DNAK_HELPY_3_599: 0.213737, DNAK_CAMJE_4_600: 0.174628): 0.126141): 0.046836, (DNAK_RICPR_4_598: 0.187143, (DNAK_RHIME_4_601: 0.135239, DNAK_CAUCR_4_598: 0.178597): 0.030222): 0.066511): 0.059380, (DNAK_CLOPE_4_575: 0.270913, (DNAK_LISMO_4_574: 0.097151, ((DNAK_BACSU_3_573: 0.080789, DNAK_BACST_3_572: 0.127290): 0.076057, (DNAK_LACLC_4_574: 0.033703, (DNAK_STRPY_4_574: 0.030810, (DNAK_STRMU_4_575: 0.092811, DNAK_STRPN_4_574: 0.027659): 0.014183): 0.131772): 0.069400): 0.044577): 0.197090): 0.078094): 0.021929, (DNAK_BORBU_4_599: 0.171505, DNAK_TREPA_4_598: 0.161853): 0.083591): 0.040363, (((DNAK_CHLTR_9_602: 0.024103, DNAK_CHLMU_9_602: 0.029120): 0.064644, DNAK_CHLPN_10_603: 0.085306): 0.315807, (DNAK_AQUAE_8_606: 0.311914, (((DNAK_MYCGE_8_593: 0.042970, DNAK_MYCPN_8_586: 0.004701): 0.568803, DNAK_THETH_4_597: 0.318281): 0.066934, ((DNAK_THEMA_8_586: 0.340615, DNAK_THEAC_4_581: 0.305467): 0.097339, (DNAK_CYACA_4_599: 0.213675, (DNAK_GUITH_4_599: 0.143609, (DNAK_PORPU_4_597: 0.155472, DNAK_PAVLU_4_601: 0.242150): 0.034761): 0.092592): 0.140457): 0.058528): 0.065209): 0.081806): 0.042069): 0.128067, (DNAK_MYCTU_3_582: 0.027745, DNAK_MYCLE_3_583: 0.020015): 0.186077): 0.430705, HSP71_HUMAN: 0.110260);

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

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

tree with node labels for Rod Page's TreeView
((((((((((((1_DNAK_ECOLI_3_603, 2_DNAK_SALTY_3_603) 50 , (4_DNAK_BUCAI_4_604, 5_DNAK_BUCBP_4_604) 51 ) 49 , 6_DNAK_VIBCH_4_603) 48 , 3_DNAK_HAEIN_3_602) 47 , 7_DNAK_COXBU_4_609) 46 , (8_DNAK_HELPY_3_599, 9_DNAK_CAMJE_4_600) 52 ) 45 , (12_DNAK_RICPR_4_598, (10_DNAK_RHIME_4_601, 11_DNAK_CAUCR_4_598) 54 ) 53 ) 44 , (24_DNAK_CLOPE_4_575, (21_DNAK_LISMO_4_574, ((19_DNAK_BACSU_3_573, 20_DNAK_BACST_3_572) 58 , (15_DNAK_LACLC_4_574, (18_DNAK_STRPY_4_574, (16_DNAK_STRMU_4_575, 17_DNAK_STRPN_4_574) 61 ) 60 ) 59 ) 57 ) 56 ) 55 ) 43 , (13_DNAK_BORBU_4_599, 14_DNAK_TREPA_4_598) 62 ) 42 , (((25_DNAK_CHLTR_9_602, 26_DNAK_CHLMU_9_602) 65 , 27_DNAK_CHLPN_10_603) 64 , (28_DNAK_AQUAE_8_606, (((36_DNAK_MYCGE_8_593, 37_DNAK_MYCPN_8_586) 69 , 35_DNAK_THETH_4_597) 68 , ((33_DNAK_THEMA_8_586, 34_DNAK_THEAC_4_581) 71 , (32_DNAK_CYACA_4_599, (30_DNAK_GUITH_4_599, (29_DNAK_PORPU_4_597, 31_DNAK_PAVLU_4_601) 74 ) 73 ) 72 ) 70 ) 67 ) 66 ) 63 ) 41 , (22_DNAK_MYCTU_3_582, 23_DNAK_MYCLE_3_583) 75 ) 40 , 38_HSP71_HUMAN) 39 ;

Nodes 39 to 75 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 39, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(0.995) K(0.000) M(0.001) F(0.001) P(0.000) S(0.000) T(0.000) W(0.000) Y(0.000) V(0.001) 

Prob distribution at node 40, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 43, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 48, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 49, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 50, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 51, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 52, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 53, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 54, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 55, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 56, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 57, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 58, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 59, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 60, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 61, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 62, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 63, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 64, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 65, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 66, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 67, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 68, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 69, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 70, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 71, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 72, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 74, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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 75, by site

   site  Freq   Data

      1      1   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: 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(1.000) 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   LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: L(0.995) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) L(1.000) 

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

Branch 1:   39..40



Branch 2:   40..41



Branch 3:   41..42



Branch 4:   42..43



Branch 5:   43..44



Branch 6:   44..45



Branch 7:   45..46



Branch 8:   46..47



Branch 9:   47..48



Branch 10:   48..49



Branch 11:   49..50



Branch 12:   50..1  (DNAK_ECOLI_3_603) 



Branch 13:   50..2  (DNAK_SALTY_3_603) 



Branch 14:   49..51



Branch 15:   51..4  (DNAK_BUCAI_4_604) 



Branch 16:   51..5  (DNAK_BUCBP_4_604) 



Branch 17:   48..6  (DNAK_VIBCH_4_603) 



Branch 18:   47..3  (DNAK_HAEIN_3_602) 



Branch 19:   46..7  (DNAK_COXBU_4_609) 



Branch 20:   45..52



Branch 21:   52..8  (DNAK_HELPY_3_599) 



Branch 22:   52..9  (DNAK_CAMJE_4_600) 



Branch 23:   44..53



Branch 24:   53..12 (DNAK_RICPR_4_598) 



Branch 25:   53..54



Branch 26:   54..10 (DNAK_RHIME_4_601) 



Branch 27:   54..11 (DNAK_CAUCR_4_598) 



Branch 28:   43..55



Branch 29:   55..24 (DNAK_CLOPE_4_575) 



Branch 30:   55..56



Branch 31:   56..21 (DNAK_LISMO_4_574) 



Branch 32:   56..57



Branch 33:   57..58



Branch 34:   58..19 (DNAK_BACSU_3_573) 



Branch 35:   58..20 (DNAK_BACST_3_572) 



Branch 36:   57..59



Branch 37:   59..15 (DNAK_LACLC_4_574) 



Branch 38:   59..60



Branch 39:   60..18 (DNAK_STRPY_4_574) 



Branch 40:   60..61



Branch 41:   61..16 (DNAK_STRMU_4_575) 



Branch 42:   61..17 (DNAK_STRPN_4_574) 



Branch 43:   42..62



Branch 44:   62..13 (DNAK_BORBU_4_599) 



Branch 45:   62..14 (DNAK_TREPA_4_598) 



Branch 46:   41..63



Branch 47:   63..64



Branch 48:   64..65



Branch 49:   65..25 (DNAK_CHLTR_9_602) 



Branch 50:   65..26 (DNAK_CHLMU_9_602) 



Branch 51:   64..27 (DNAK_CHLPN_10_603) 



Branch 52:   63..66



Branch 53:   66..28 (DNAK_AQUAE_8_606) 



Branch 54:   66..67



Branch 55:   67..68



Branch 56:   68..69



Branch 57:   69..36 (DNAK_MYCGE_8_593) 



Branch 58:   69..37 (DNAK_MYCPN_8_586) 



Branch 59:   68..35 (DNAK_THETH_4_597) 



Branch 60:   67..70



Branch 61:   70..71



Branch 62:   71..33 (DNAK_THEMA_8_586) 



Branch 63:   71..34 (DNAK_THEAC_4_581) 



Branch 64:   70..72



Branch 65:   72..32 (DNAK_CYACA_4_599) 



Branch 66:   72..73



Branch 67:   73..30 (DNAK_GUITH_4_599) 



Branch 68:   73..74



Branch 69:   74..29 (DNAK_PORPU_4_597) 



Branch 70:   74..31 (DNAK_PAVLU_4_601) 



Branch 71:   40..75



Branch 72:   75..22 (DNAK_MYCTU_3_582) 



Branch 73:   75..23 (DNAK_MYCLE_3_583) 



Branch 74:   39..38 (HSP71_HUMAN) 





List of extant and reconstructed sequences

    75      1

DNAK_ECOLI_3_603   L
DNAK_SALTY_3_603   L
DNAK_HAEIN_3_602   L
DNAK_BUCAI_4_604   L
DNAK_BUCBP_4_604   L
DNAK_VIBCH_4_603   L
DNAK_COXBU_4_609   L
DNAK_HELPY_3_599   L
DNAK_CAMJE_4_600   L
DNAK_RHIME_4_601   L
DNAK_CAUCR_4_598   L
DNAK_RICPR_4_598   L
DNAK_BORBU_4_599   L
DNAK_TREPA_4_598   L
DNAK_LACLC_4_574   L
DNAK_STRMU_4_575   L
DNAK_STRPN_4_574   L
DNAK_STRPY_4_574   L
DNAK_BACSU_3_573   L
DNAK_BACST_3_572   L
DNAK_LISMO_4_574   L
DNAK_MYCTU_3_582   L
DNAK_MYCLE_3_583   L
DNAK_CLOPE_4_575   L
DNAK_CHLTR_9_602   L
DNAK_CHLMU_9_602   L
DNAK_CHLPN_10_603   L
DNAK_AQUAE_8_606   L
DNAK_PORPU_4_597   L
DNAK_GUITH_4_599   L
DNAK_PAVLU_4_601   L
DNAK_CYACA_4_599   L
DNAK_THEMA_8_586   L
DNAK_THEAC_4_581   L
DNAK_THETH_4_597   L
DNAK_MYCGE_8_593   L
DNAK_MYCPN_8_586   L
HSP71_HUMAN       L
node #39          L
node #40          L
node #41          L
node #42          L
node #43          L
node #44          L
node #45          L
node #46          L
node #47          L
node #48          L
node #49          L
node #50          L
node #51          L
node #52          L
node #53          L
node #54          L
node #55          L
node #56          L
node #57          L
node #58          L
node #59          L
node #60          L
node #61          L
node #62          L
node #63          L
node #64          L
node #65          L
node #66          L
node #67          L
node #68          L
node #69          L
node #70          L
node #71          L
node #72          L
node #73          L
node #74          L
node #75          L


Overall accuracy of the 37 ancestral sequences:
  0.99550  0.99968  0.99999  1.00000  1.00000  0.99999  0.99999  0.99996  0.99998  0.99998  0.99999  1.00000  0.99993  0.99987  0.99999  0.99998  0.99989  0.99997  0.99999  0.99998  0.99999  1.00000  1.00000  0.99993  0.99997  0.99995  1.00000  0.99995  0.99998  0.99970  1.00000  0.99997  0.99973  0.99992  0.99998  0.99996  1.00000
for a site.

  0.99550  0.99968  0.99999  1.00000  1.00000  0.99999  0.99999  0.99996  0.99998  0.99998  0.99999  1.00000  0.99993  0.99987  0.99999  0.99998  0.99989  0.99997  0.99999  0.99998  0.99999  1.00000  1.00000  0.99993  0.99997  0.99995  1.00000  0.99995  0.99998  0.99970  1.00000  0.99997  0.99973  0.99992  0.99998  0.99996  1.00000
for the sequence.


Counts of changes at sites

   1  (0)


(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  LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL: LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.994) MLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.001) FLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.001) VLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.001) ILLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.000) PLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL (0.000)  (total  0.998)



List of extant and reconstructed sequences

    75      1

DNAK_ECOLI_3_603   L
DNAK_SALTY_3_603   L
DNAK_HAEIN_3_602   L
DNAK_BUCAI_4_604   L
DNAK_BUCBP_4_604   L
DNAK_VIBCH_4_603   L
DNAK_COXBU_4_609   L
DNAK_HELPY_3_599   L
DNAK_CAMJE_4_600   L
DNAK_RHIME_4_601   L
DNAK_CAUCR_4_598   L
DNAK_RICPR_4_598   L
DNAK_BORBU_4_599   L
DNAK_TREPA_4_598   L
DNAK_LACLC_4_574   L
DNAK_STRMU_4_575   L
DNAK_STRPN_4_574   L
DNAK_STRPY_4_574   L
DNAK_BACSU_3_573   L
DNAK_BACST_3_572   L
DNAK_LISMO_4_574   L
DNAK_MYCTU_3_582   L
DNAK_MYCLE_3_583   L
DNAK_CLOPE_4_575   L
DNAK_CHLTR_9_602   L
DNAK_CHLMU_9_602   L
DNAK_CHLPN_10_603   L
DNAK_AQUAE_8_606   L
DNAK_PORPU_4_597   L
DNAK_GUITH_4_599   L
DNAK_PAVLU_4_601   L
DNAK_CYACA_4_599   L
DNAK_THEMA_8_586   L
DNAK_THEAC_4_581   L
DNAK_THETH_4_597   L
DNAK_MYCGE_8_593   L
DNAK_MYCPN_8_586   L
HSP71_HUMAN       L
node #39          L
node #40          L
node #41          L
node #42          L
node #43          L
node #44          L
node #45          L
node #46          L
node #47          L
node #48          L
node #49          L
node #50          L
node #51          L
node #52          L
node #53          L
node #54          L
node #55          L
node #56          L
node #57          L
node #58          L
node #59          L
node #60          L
node #61          L
node #62          L
node #63          L
node #64          L
node #65          L
node #66          L
node #67          L
node #68          L
node #69          L
node #70          L
node #71          L
node #72          L
node #73          L
node #74          L
node #75          L


