
seed used = 140014857

K12                                  ATG AAA GAT GAA CGT CGC CCT ATT TGC GAA GTG GTT GCA GAG AGT ATC GAA CGG TTA ATT ATC GAC GGC GTA CTG AAG GTC GGT CAG CCG CTT CCC TCG GAA CGT CGA CTG TGT GAA AAG CTC GGC TTC TCA CGC TCC GCA CTG CGT GAA GGG CTG ACC GTG CTG CGC GGG CGC GGG ATT ATT GAA ACG GCG CAG GGT CGC GAT TCT CGT GTC GCA CGG CTT AAT CGG GTG CAG GAC ACC AGC CCG CTG ATC CAT CTG TTC AGT ACG CAG CCG CGA ACG CTG TAC GAT CTG CTC GAC GTT CGC GCA TTA CTG GAG GGC GAA TCG GCA AGG CTG GCG GCA ACG CTG GGA ACG CAG GCT GAT TTT GTT GTG ATA ACC CGC TGT TAT GAA AAA ATG CTC GCC GCC AGT GAG AAC AAC AAA GAG ATT TCG CTG ATC GAA CAT GCG CAG TTG GAT CAC GCT TTC CAT CTC GCC ATT TGT CAG GCT TCT CAC AAT CAG GTG CTG GTG TTT ACG CTG CAA TCA TTG ACC GAT CTG ATG TTT AAT TCA GTG TTT GCC AGC GTA AAT AAT CTC TAC CAT CGA CCA CAG CAA AAA AAG CAG ATC GAT CGC CAG CAT GCG CGG ATC TAC AAC GCG GTG TTG CAG CGG CTG CCG CAC GTC GCC CAG CGC GCA GCA CGC GAT CAT GTG CGG ACC GTG AAA AAG AAT CTC CAC GAT ATC GAG CTG GAA GGC CAC CAT TTG ATT CGC TCG GCG GTG CCG CTG GAG ATG AAC CTG AGT 
S2457T                               ATG AAA GAT GAA CGT CGC CCT ATT TGC GAA GTG GTT GCA GAG AGT ATC GAA CGG TTA ATT ATC GAC GGC GTA CTG AAG GTC GGT CAG CCG CTT CCC TCG GAA CGT CGA CTG TGT GAA AAG CTC GGC TTC TCA CGC TCC GCA CTG CGT GAA GGG CTG ACC GTG CTG CGC GGG CGC GGG ATT ATT GAA ACG GCG CAG GGT CGC GAT TCT CAT GTC GCA CGG CTT AAT CGG GAG CAG GAC ACC AGC CCG CTG ATC CAT CTG TTC AGT ACG CAG CCG CGA ACG CTG TAC GAT CTG CTC GAC GTT CGC GCA TTA CTG GAG GGC GAA TCG GCA AGG CTG GCG GCA ACG CTG GGA ACG CAG GCT GAT TTT GTT GTG ATA ACC CGC TGT TAT GAA AAA ATG CTC GCC GCC AGT GAG AAC CAC AAA GAG ATT TCG CTG ATC GAA CAT GCG CAG TTG GAT CAC GCT TTC CAT CTC GCC ATT TGT CAG GCT TCT CAC AAT CAG GTG CTG GTG TTT ACG CTG CAA TCA TTG ACC GAT CTG ATG TTT AAT TCA GTG TTT GCC AGC GTA AAT GAT CTC TAC CAT CGA CCA CAG CAA AAA AAG CAG ATC GAT CGC CAG CAT GCG CGG ATC TAC AAC GCG GTG TTG CAG CGG CTG CCG CAC GTC GCT CAG CGC GCA GCG CGC GAT CAT GTA CGG ACC GTG AAA AAG AAT CTC CAC GAT ATC GAG CTG GAA GGC CAC CAT TTG ATT CGC TCG GCG GTG CCG CTG GAG ATG AAC AAG GTG 
Shig4337                             ATG AAA GAT GAA CGT CGC CCT ATT TGC GAA GTG GTT GCA GAG AGT ATC GAA CGG TTA ATT ATC GAC GGC GTA CTG AAG GTC GGT CAG CCG CTT CCC TCG GAA CGT CGA CTG TGT GAA AAG CTC GGC TTC TCA AGC TCC GCA CTG CGT GAA GGG CTG ACC GTG CTG CGC GGG CGC GGG ATT ATT GAA ACG GCG CAG GGT CGC GAT TCT CAT GTC GCA CGG CTT AAT CGG GAG CAG GAC ACC AGC CCG CTG ATC CAT CTG TTC AGT ACG CAG CCG CGA ACG CTG TAC GAT CTG CTC GAC GTT CGC GCA TTA CTG GAG GGC GAA TCG GCA AGG CTG GCG GCA ACG CTG GGA ACG CAG GCT GAT TTT GTT GTG ATA ACC CGC TGT TAT GAA AAA ATG CTC GCC GCC AGT GAG AAC CAC AAA GAG ATT TCG CTG ATC GAA CAT GCG CAG TTG GAT CAC GCT TTC CAT CTC GCC ATT TGT CAG GCT TCT CAC AAT CAG GTG CTG GTG TTT ACG CTG CAA TCA TTG ACC GAT CTG ATG TTT AAT TCA GTG TTT GCC AGC GTA AAT AAT CTC TAC CAT CGA CCA CAG CAA AAA AAG CAG ATC GAT CGC CAG CAT GCG CGG ATC TAC AAC GCG GTG TTG CAG CGG CTG CCG CAC GTC GCT CAG CGC GCA GCG CGC GAT CAT GTA CGG ACC GTG AAA AAG AAT CTC CAC GAT ATC GAG CTG GAA GGC CAC CAT TTG ATT CGC TCG GCG GTG CCG CTG GAG ATG AAC AAG GTG 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2980.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 254
# site patterns = 66
    4    5    9   11    3   10    1    7    1    9    3    7    6    3    7
    6    2    3    4    2   19    4    3    2   13    5    2    1    4    3
    3    6    3    3    1    1    3    5    6    6    2    1    5    1    2
    7    3    1    1    3    4    1    1    4    3    1    4    5    2    1
    1    1    1    1    1    1

1       
K12                   ATG AAA GAT GAA CGT CGC CCT ATT TGC GTG GTT GCA GAG AGT ATC CGG TTA GAC GGC GTA CTG AAG GTC GGT CAG CCG CTT CCC TCG CGA TGT CTC TTC TCA CGC TCC GGG ACC ACG GCG TCT CGT AAT GTG AGC CAT TAC AGG GGA GCT TTT ATA TAT GCC AAC AAC TTG CAC CAA AAT CCA GCC GCA GTG CTG AGT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .A. ... .A. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... G.. ... ..T ..G ..A AA. GTG 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... .A. ... .A. ... ... ... ... ... ... ... ... ... ... ... C.. ... ... ... ... ... ..T ..G ..A AA. GTG 

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  4  4  4 | Ser TCT  2  2  2 | Tyr TAT  1  1  1 | Cys TGT  3  3  3
    TTC  3  3  3 |     TCC  1  1  1 |     TAC  3  3  3 |     TGC  1  1  1
Leu TTA  2  2  2 |     TCA  3  3  3 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  4  4  4 |     TCG  4  4  4 |     TAG  0  0  0 | Trp TGG  0  0  0
--------------------------------------------------------------------------
Leu CTT  2  2  2 | Pro CCT  1  1  1 | His CAT  7  8  8 | Arg CGT  4  3  3
    CTC  6  6  6 |     CCC  1  1  1 |     CAC  5  6  6 |     CGC 11 11 10
    CTA  0  0  0 |     CCA  1  1  1 | Gln CAA  2  2  2 |     CGA  3  3  3
    CTG 20 19 19 |     CCG  5  5  5 |     CAG 13 13 13 |     CGG  6  6  6
--------------------------------------------------------------------------
Ile ATT  7  7  7 | Thr ACT  0  0  0 | Asn AAT  6  5  6 | Ser AGT  4  3  3
    ATC  7  7  7 |     ACC  5  5  5 |     AAC  4  3  3 |     AGC  2  2  3
    ATA  1  1  1 |     ACA  0  0  0 | Lys AAA  5  5  5 | Arg AGA  0  0  0
Met ATG  4  4  4 |     ACG  6  6  6 |     AAG  4  5  5 |     AGG  1  1  1
--------------------------------------------------------------------------
Val GTT  3  3  3 | Ala GCT  3  4  4 | Asp GAT  9 10  9 | Gly GGT  2  2  2
    GTC  3  3  3 |     GCC  5  4  4 |     GAC  3  3  3 |     GGC  4  4  4
    GTA  2  3  3 |     GCA  8  7  7 | Glu GAA 11 11 11 |     GGA  1  1  1
    GTG 11 10 10 |     GCG  6  7  7 |     GAG  6  7  7 |     GGG  3  3  3
--------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: K12            
position  1:    T:0.12205    C:0.34252    A:0.22047    G:0.31496
position  2:    T:0.31102    C:0.20079    A:0.31102    G:0.17717
position  3:    T:0.22835    C:0.25197    A:0.15354    G:0.36614

#2: S2457T         
position  1:    T:0.12205    C:0.34252    A:0.21260    G:0.32283
position  2:    T:0.30709    C:0.20079    A:0.32283    G:0.16929
position  3:    T:0.22835    C:0.24803    A:0.15354    G:0.37008

#3: Shig4337       
position  1:    T:0.12205    C:0.33858    A:0.22047    G:0.31890
position  2:    T:0.30709    C:0.20079    A:0.32283    G:0.16929
position  3:    T:0.22835    C:0.24803    A:0.15354    G:0.37008

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      12 | Ser S TCT       6 | Tyr Y TAT       3 | Cys C TGT       9
      TTC       9 |       TCC       3 |       TAC       9 |       TGC       3
Leu L TTA       6 |       TCA       9 | *** * TAA       0 | *** * TGA       0
      TTG      12 |       TCG      12 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       3 | His H CAT      23 | Arg R CGT      10
      CTC      18 |       CCC       3 |       CAC      17 |       CGC      32
      CTA       0 |       CCA       3 | Gln Q CAA       6 |       CGA       9
      CTG      58 |       CCG      15 |       CAG      39 |       CGG      18
------------------------------------------------------------------------------
Ile I ATT      21 | Thr T ACT       0 | Asn N AAT      17 | Ser S AGT      10
      ATC      21 |       ACC      15 |       AAC      10 |       AGC       7
      ATA       3 |       ACA       0 | Lys K AAA      15 | Arg R AGA       0
Met M ATG      12 |       ACG      18 |       AAG      14 |       AGG       3
------------------------------------------------------------------------------
Val V GTT       9 | Ala A GCT      11 | Asp D GAT      28 | Gly G GGT       6
      GTC       9 |       GCC      13 |       GAC       9 |       GGC      12
      GTA       8 |       GCA      22 | Glu E GAA      33 |       GGA       3
      GTG      31 |       GCG      20 |       GAG      20 |       GGG       9
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12205    C:0.34121    A:0.21785    G:0.31890
position  2:    T:0.30840    C:0.20079    A:0.31890    G:0.17192
position  3:    T:0.22835    C:0.24934    A:0.15354    G:0.36877

Codon frequencies under model, for use in evolver:
  0.00880208  0.00961146  0.00591864  0.01421485
  0.00573071  0.00625768  0.00385341  0.00925478
  0.00910172  0.00993866  0.00000000  0.00000000
  0.00490669  0.00535788  0.00000000  0.00792402
  0.02460796  0.02687076  0.01654673  0.03974044
  0.01602135  0.01749458  0.01077298  0.02587357
  0.02544568  0.02778551  0.01711003  0.04109331
  0.01371763  0.01497902  0.00922392  0.02215318
  0.01571124  0.01715595  0.01056445  0.02537274
  0.01022902  0.01116962  0.00687813  0.01651928
  0.01624609  0.01773998  0.01092409  0.02623650
  0.00875818  0.00956353  0.00588912  0.01414396
  0.02299898  0.02511383  0.01546483  0.03714203
  0.01497380  0.01635070  0.01006859  0.02418183
  0.02378192  0.02596877  0.01599129  0.03840644
  0.01282071  0.01399962  0.00862082  0.02070471



Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.8274 (0.0151 0.0183)
Shig4337             0.8254 (0.0151 0.0183)-1.0000 (0.0035 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 10
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1090.263679     +0.000000
   4..1     4..5     5..2     5..3  
  0.06338  0.00000  0.00342  0.00406  2.96752  0.98249  0.00000  0.43985 86.81278
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.07086

(1: 0.063381, (2: 0.003416, 3: 0.004058): 0.000000);

(K12: 0.063381, (S2457T: 0.003416, Shig4337: 0.004058): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.96752


dN/dS for site classes (K=3)

p:   0.98249  0.00000  0.01751
w:   0.43985  1.00000 86.81278

dN & dS for each branch

 branch           t        S        N    dN/dS       dN       dS   S*dS   N*dN

   4..1       0.063    217.4    544.6   1.9519   0.0245   0.0126    2.7   13.4
   4..5       0.000    217.4    544.6   1.9519   0.0000   0.0000    0.0    0.0
   5..2       0.003    217.4    544.6   1.9519   0.0013   0.0007    0.1    0.7
   5..3       0.004    217.4    544.6   1.9519   0.0016   0.0008    0.2    0.9


Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

   253 L      0.991**       86.026
   254 S      1.000**       86.801


Bayes Empirical Bayes (BEB) analysis
Positively selected sites (*: P>95%; **: P>99%)

            Pr(w>1)     post mean +- SE for w

    45 R      0.540         4.576 +- 3.885
    70 R      0.534         4.532 +- 3.880
    77 V      0.526         4.467 +- 3.874
   138 N      0.537         4.549 +- 3.882
   187 N      0.542         4.590 +- 3.886
   253 L      0.882         7.113 +- 3.132
   254 S      0.961*        7.649 +- 2.634



The grid (see ternary graph for p0-p1)

w0:   0.050  0.150  0.250  0.350  0.450  0.550  0.650  0.750  0.850  0.950
w2:   1.500  2.500  3.500  4.500  5.500  6.500  7.500  8.500  9.500 10.500


Posterior on the grid

w0:   0.171  0.151  0.133  0.116  0.100  0.087  0.075  0.064  0.055  0.048
w2:   0.016  0.029  0.042  0.059  0.078  0.100  0.124  0.152  0.183  0.218

Posterior for p0-p1 (see the ternary graph)

 0.013
 0.009 0.018 0.015
 0.002 0.006 0.012 0.022 0.016
 0.001 0.002 0.003 0.008 0.015 0.026 0.018
 0.001 0.001 0.001 0.002 0.004 0.010 0.018 0.030 0.020
 0.000 0.001 0.001 0.001 0.002 0.003 0.005 0.013 0.023 0.035 0.021
 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.004 0.006 0.016 0.029 0.040 0.021
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.002 0.002 0.005 0.008 0.021 0.036 0.045 0.021
 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.006 0.010 0.027 0.044 0.048 0.020
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.008 0.014 0.034 0.054 0.051 0.018

sum of density on p0-p1 =   1.000000
