
seed used = 140004373

K12                                  ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGC CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGT ATC AAG CTC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCT GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 
S2457T                               ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGT CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGC ATC AAG CAC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCC GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 
Shig4337                             ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGT CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGC ATC AAG CAC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCC GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 
CFT073                               ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGC CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGC ATC AAG CAC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCC GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 
O157                                 ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGC CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGT ATC AAG CTC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCC GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 
EDL933                               ATG TCA ACG ATT ATT ATG GAT TTA TGT AGT TAC ACC CGA CTA GGT TTA ACC GGG TAT CTG TTG AGT AGA GGG GTT AAA AAA AGA GAA ATC AAC GAC ATT GAA ACC GTT GAT GAC CTT GCC ATA GCT TGT GAT TCA CAG CGC CCT TCA GTG GTG TTT ATT AAT GAG GAC TGT TTC ATC CAC GAT GCT TCT AAC AGT CAG CGT ATC AAG CTC ATC ATT AAT CAA CAT CCC AAT ACG TTA TTT ATC GTT TTT ATG GCA ATT GCC AAT GTT CAT TTT GAT GAA TAT CTA TTG GTC AGA AAA AAT TTA TTG ATC AGT TCT AAA TCG ATT AAA CCG GAA TCT CTC GAC GAT ATC CTT GGC GAT ATT CTG AAA AAA GAG ACA ACG ATA ACC TCG TTT TTA AAT ATG CCG ACG TTA TCA TTG AGC CGA ACC GAA TCG AGT ATG TTG CGA ATG TGG ATG GCA GGT CAG GGA ACC ATT CAA ATC TCC GAC CAA ATG AAT ATC AAA GCC AAG ACC GTT TCA TCG CAT AAA GGT AAT ATT AAA CGT AAG ATC AAA ACG CAT AAT AAA CAG GTT ATC TAC CAT GTC GTC CGA CTG ACG GAT AAT GTG ACT AAT GGT ATT TTT GTC AAC ATG CGC 


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1951.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 207
# site patterns = 58
    9    5    6   11    8    6    3    5    2    7    4    2    4    2    2
    3    5    3    6   12    5   11    3    5    2    3    2    2    4    1
    1    3    6   11    2    1    1    3    1    3    1    3    5    1    2
    4    4    2    1    1    1    1    1    1    1    1    1    1

1       
K12                   ATG TCA ACG ATT GAT TTA TGT AGT TAC ACC CGA CTA GGT GGG TAT CTG TTG AGA GTT AAA GAA ATC AAC GAC CTT GCC ATA GCT CAG CGC CCT GTG TTT AAT GAG TTC CAC TCT CGT AAG CTC CAA CAT CCC GCA GTC TCG CCG CTC GGC ACA AGC TGG GGA TCT CGT ACT CGC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... .A. ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  6  6  6  6  6  6 | Ser TCT  4  3  3  3  3  3 | Tyr TAT  2  2  2  2  2  2 | Cys TGT  3  3  3  3  3  3
    TTC  1  1  1  1  1  1 |     TCC  0  1  1  1  1  1 |     TAC  2  2  2  2  2  2 |     TGC  0  0  0  0  0  0
Leu TTA  6  6  6  6  6  6 |     TCA  5  5  5  5  5  5 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  5  5  5  5  5  5 |     TCG  4  4  4  4  4  4 |     TAG  0  0  0  0  0  0 | Trp TGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Leu CTT  2  2  2  2  2  2 | Pro CCT  1  1  1  1  1  1 | His CAT  5  5  5  5  5  5 | Arg CGT  2  2  2  1  2  2
    CTC  2  1  1  1  2  2 |     CCC  1  1  1  1  1  1 |     CAC  1  2  2  2  1  1 |     CGC  2  2  2  3  2  2
    CTA  2  2  2  2  2  2 |     CCA  0  0  0  0  0  0 | Gln CAA  3  3  3  3  3  3 |     CGA  4  4  4  4  4  4
    CTG  3  3  3  3  3  3 |     CCG  2  2  2  2  2  2 |     CAG  4  4  4  4  4  4 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT 11 11 11 11 11 11 | Thr ACT  1  1  1  1  1  1 | Asn AAT 11 11 11 11 11 11 | Ser AGT  5  5  5  5  5  5
    ATC 11 11 11 11 11 11 |     ACC  7  7  7  7  7  7 |     AAC  3  3  3  3  3  3 |     AGC  1  1  1  1  1  1
    ATA  2  2  2  2  2  2 |     ACA  1  1  1  1  1  1 | Lys AAA 12 12 12 12 12 12 | Arg AGA  3  3  3  3  3  3
Met ATG  9  9  9  9  9  9 |     ACG  6  6  6  6  6  6 |     AAG  3  3  3  3  3  3 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  6  6  6  6  6  6 | Ala GCT  2  2  2  2  2  2 | Asp GAT  8  8  8  8  8  8 | Gly GGT  4  4  4  4  4  4
    GTC  4  4  4  4  4  4 |     GCC  3  3  3  3  3  3 |     GAC  5  5  5  5  5  5 |     GGC  1  1  1  1  1  1
    GTA  0  0  0  0  0  0 |     GCA  2  2  2  2  2  2 | Glu GAA  5  5  5  5  5  5 |     GGA  1  1  1  1  1  1
    GTG  3  3  3  3  3  3 |     GCG  0  0  0  0  0  0 |     GAG  2  2  2  2  2  2 |     GGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.35266    C:0.18841    A:0.31884    G:0.14010
position  3:    T:0.35266    C:0.21256    A:0.22222    G:0.21256

#2: S2457T         
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.34783    C:0.18841    A:0.32367    G:0.14010
position  3:    T:0.34783    C:0.21739    A:0.22222    G:0.21256

#3: Shig4337       
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.34783    C:0.18841    A:0.32367    G:0.14010
position  3:    T:0.34783    C:0.21739    A:0.22222    G:0.21256

#4: CFT073         
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.34783    C:0.18841    A:0.32367    G:0.14010
position  3:    T:0.34300    C:0.22222    A:0.22222    G:0.21256

#5: O157           
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.35266    C:0.18841    A:0.31884    G:0.14010
position  3:    T:0.34783    C:0.21739    A:0.22222    G:0.21256

#6: EDL933         
position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.35266    C:0.18841    A:0.31884    G:0.14010
position  3:    T:0.34783    C:0.21739    A:0.22222    G:0.21256

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT      19 | Tyr Y TAT      12 | Cys C TGT      18
      TTC       6 |       TCC       5 |       TAC      12 |       TGC       0
Leu L TTA      36 |       TCA      30 | *** * TAA       0 | *** * TGA       0
      TTG      30 |       TCG      24 |       TAG       0 | Trp W TGG       6
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT       6 | His H CAT      30 | Arg R CGT      11
      CTC       9 |       CCC       6 |       CAC       9 |       CGC      13
      CTA      12 |       CCA       0 | Gln Q CAA      18 |       CGA      24
      CTG      18 |       CCG      12 |       CAG      24 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      66 | Thr T ACT       6 | Asn N AAT      66 | Ser S AGT      30
      ATC      66 |       ACC      42 |       AAC      18 |       AGC       6
      ATA      12 |       ACA       6 | Lys K AAA      72 | Arg R AGA      18
Met M ATG      54 |       ACG      36 |       AAG      18 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      36 | Ala A GCT      12 | Asp D GAT      48 | Gly G GGT      24
      GTC      24 |       GCC      18 |       GAC      30 |       GGC       6
      GTA       0 |       GCA      12 | Glu E GAA      30 |       GGA       6
      GTG      18 |       GCG       0 |       GAG      12 |       GGG      12
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.18841    C:0.16425    A:0.41546    G:0.23188
position  2:    T:0.35024    C:0.18841    A:0.32126    G:0.14010
position  3:    T:0.34783    C:0.21739    A:0.22222    G:0.21256

Codon frequencies under model, for use in evolver:
  0.02371538  0.01482211  0.01515149  0.01449273
  0.01275724  0.00797327  0.00815046  0.00779609
  0.02175273  0.01359546  0.00000000  0.00000000
  0.00948615  0.00592885  0.00000000  0.00579709
  0.02067495  0.01292184  0.01320899  0.01263469
  0.01112170  0.00695106  0.00710553  0.00679659
  0.01896392  0.01185245  0.01211584  0.01158906
  0.00826998  0.00516874  0.00528360  0.00505388
  0.05229546  0.03268466  0.03341099  0.03195834
  0.02813135  0.01758209  0.01797281  0.01719138
  0.04796756  0.02997972  0.03064594  0.02931351
  0.02091818  0.01307386  0.01336439  0.01278333
  0.02918816  0.01824260  0.01864799  0.01783721
  0.01570122  0.00981326  0.01003133  0.00959519
  0.02677259  0.01673287  0.01710471  0.01636103
  0.01167526  0.00729704  0.00745920  0.00713488



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               0.0943 (0.0021 0.0220)
Shig4337             0.0943 (0.0021 0.0220)-1.0000 (0.0000 0.0000)
CFT073               0.1421 (0.0021 0.0146) 0.0000 (0.0000 0.0073) 0.0000 (0.0000 0.0073)
O157                 0.0000 (0.0000 0.0072) 0.1421 (0.0021 0.0146) 0.1421 (0.0021 0.0146) 0.2857 (0.0021 0.0073)
EDL933               0.0000 (0.0000 0.0072) 0.1421 (0.0021 0.0146) 0.1421 (0.0021 0.0146) 0.2857 (0.0021 0.0073)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 6
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):   -862.697478     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.02163  0.00604  0.00000  0.00000  0.00000  0.00000  0.01372  0.00000  0.00000  3.65458  0.99484  0.00000  0.00000 82.23370
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.04141

((1: 0.021626, (2: 0.000004, 3: 0.000004): 0.006045): 0.000000, (4: 0.000004, (5: 0.000004, 6: 0.000004): 0.013719): 0.000000);

((K12: 0.021626, (S2457T: 0.000004, Shig4337: 0.000004): 0.006045): 0.000000, (CFT073: 0.000004, (O157: 0.000004, EDL933: 0.000004): 0.013719): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  3.65458


dN/dS for site classes (K=3)

p:   0.99484  0.00000  0.00516
w:   0.00000  1.00000 82.23370

dN & dS for each branch

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

   7..8       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
   8..1       0.022    169.7    451.3   0.4241   0.0053   0.0124    2.1    2.4
   8..9       0.006    169.7    451.3   0.4241   0.0015   0.0035    0.6    0.7
   9..2       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
   9..3       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
   7..10      0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
  10..4       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
  10..11      0.014    169.7    451.3   0.4241   0.0033   0.0079    1.3    1.5
  11..5       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0
  11..6       0.000    169.7    451.3   0.4241   0.0000   0.0000    0.0    0.0


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

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

    70 L      1.000**       82.234


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

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

    70 L      0.827         5.100 +- 3.206



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:   0.561  0.238  0.105  0.048  0.023  0.012  0.006  0.003  0.002  0.001
w2:   0.142  0.114  0.106  0.102  0.099  0.095  0.092  0.088  0.084  0.079

Posterior for p0-p1 (see the ternary graph)

 0.001
 0.000 0.000 0.001
 0.000 0.000 0.000 0.001 0.002
 0.000 0.000 0.000 0.000 0.000 0.001 0.004
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.008
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.005 0.017
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.010 0.036
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.007 0.023 0.079
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.003 0.006 0.014 0.049 0.172
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.007 0.013 0.030 0.108 0.374

sum of density on p0-p1 =   1.000000
