
seed used = 140021877

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3578.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 425
# site patterns = 65
   24    8   10   27   27   15   16    1    7    8   17    8   16    9    9
    2    7   15   12    9    2   10   14    4    4    5    5    3    4    7
    1   12    5    3    1    9    5   14    2    3    3    7    5    9    1
    1    1    3    2    2    1    1    1    1    3    3    2    5    4    5
    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT 15 15 15 | Ser TCT  5  5  5 | Tyr TAT  4  3  3 | Cys TGT  1  1  1
    TTC  9  9  9 |     TCC  7  7  7 |     TAC  3  4  4 |     TGC  2  2  2
Leu TTA 12 13 13 |     TCA  6  5  5 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG  7  7  7 |     TCG  1  1  1 |     TAG  0  0  0 | Trp TGG 10  9  9
--------------------------------------------------------------------------
Leu CTT  7  7  7 | Pro CCT  8  8  8 | His CAT  2  2  2 | Arg CGT  2  2  2
    CTC  4  5  5 |     CCC  3  3  3 |     CAC  1  1  1 |     CGC  5  5  5
    CTA  1  1  1 |     CCA  3  3  3 | Gln CAA  4  4  4 |     CGA  0  0  0
    CTG 28 27 27 |     CCG 12 12 12 |     CAG  4  4  4 |     CGG  1  2  2
--------------------------------------------------------------------------
Ile ATT 28 27 27 | Thr ACT  0  0  0 | Asn AAT  4  3  3 | Ser AGT  2  2  2
    ATC 17 17 17 |     ACC  9  9  9 |     AAC  5  5  5 |     AGC  4  4  4
    ATA  0  1  1 |     ACA  3  3  3 | Lys AAA  9  9  9 | Arg AGA  1  1  1
Met ATG 25 25 25 |     ACG  5  5  5 |     AAG  1  1  1 |     AGG  0  0  0
--------------------------------------------------------------------------
Val GTT 14 14 14 | Ala GCT  8  8  8 | Asp GAT 10 10 10 | Gly GGT  8 10 10
    GTC 14 14 14 |     GCC 16 16 16 |     GAC  2  2  2 |     GGC 18 16 16
    GTA  5  6  6 |     GCA  9  9  9 | Glu GAA  5  5  5 |     GGA  3  3  3
    GTG 10 10 10 |     GCG 15 15 15 |     GAG  1  1  1 |     GGG  7  7  7
--------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19294    C:0.20000    A:0.26588    G:0.34118
position  2:    T:0.46118    C:0.25882    A:0.12941    G:0.15059
position  3:    T:0.27765    C:0.28000    A:0.14353    G:0.29882

#2: S2457T         
position  1:    T:0.19059    C:0.20235    A:0.26353    G:0.34353
position  2:    T:0.46588    C:0.25647    A:0.12706    G:0.15059
position  3:    T:0.27529    C:0.28000    A:0.14824    G:0.29647

#3: Shig4337       
position  1:    T:0.19059    C:0.20235    A:0.26353    G:0.34353
position  2:    T:0.46588    C:0.25647    A:0.12706    G:0.15059
position  3:    T:0.27529    C:0.28000    A:0.14824    G:0.29647

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      45 | Ser S TCT      15 | Tyr Y TAT      10 | Cys C TGT       3
      TTC      27 |       TCC      21 |       TAC      11 |       TGC       6
Leu L TTA      38 |       TCA      16 | *** * TAA       0 | *** * TGA       0
      TTG      21 |       TCG       3 |       TAG       0 | Trp W TGG      28
------------------------------------------------------------------------------
Leu L CTT      21 | Pro P CCT      24 | His H CAT       6 | Arg R CGT       6
      CTC      14 |       CCC       9 |       CAC       3 |       CGC      15
      CTA       3 |       CCA       9 | Gln Q CAA      12 |       CGA       0
      CTG      82 |       CCG      36 |       CAG      12 |       CGG       5
------------------------------------------------------------------------------
Ile I ATT      82 | Thr T ACT       0 | Asn N AAT      10 | Ser S AGT       6
      ATC      51 |       ACC      27 |       AAC      15 |       AGC      12
      ATA       2 |       ACA       9 | Lys K AAA      27 | Arg R AGA       3
Met M ATG      75 |       ACG      15 |       AAG       3 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      42 | Ala A GCT      24 | Asp D GAT      30 | Gly G GGT      28
      GTC      42 |       GCC      48 |       GAC       6 |       GGC      50
      GTA      17 |       GCA      27 | Glu E GAA      15 |       GGA       9
      GTG      30 |       GCG      45 |       GAG       3 |       GGG      21
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19137    C:0.20157    A:0.26431    G:0.34275
position  2:    T:0.46431    C:0.25725    A:0.12784    G:0.15059
position  3:    T:0.27608    C:0.28000    A:0.14667    G:0.29725

Codon frequencies under model, for use in evolver:
  0.02490726  0.02526106  0.01323198  0.02681776
  0.01379997  0.01399599  0.00733123  0.01485849
  0.00685791  0.00695533  0.00000000  0.00000000
  0.00807803  0.00819278  0.00000000  0.00869765
  0.02623429  0.02660694  0.01393697  0.02824658
  0.01453521  0.01474168  0.00772183  0.01565013
  0.00722329  0.00732590  0.00383737  0.00777735
  0.00850842  0.00862928  0.00452010  0.00916105
  0.03440061  0.03488925  0.01827532  0.03703929
  0.01905979  0.01933053  0.01012552  0.02052177
  0.00947179  0.00960633  0.00503189  0.01019832
  0.01115695  0.01131543  0.00592713  0.01201274
  0.04460850  0.04524214  0.02369827  0.04803018
  0.02471552  0.02506659  0.01313012  0.02661131
  0.01228241  0.01245687  0.00652503  0.01322452
  0.01446762  0.01467313  0.00768592  0.01557735



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               0.5014 (0.0069 0.0138)
Shig4337             0.5014 (0.0069 0.0138)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 9
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1746.288062     +0.000000
   4..1     4..5     5..2     5..3  
  0.06057  0.02529  0.00000  0.00000  4.40202  0.99707  0.00000  0.40412 999.00000
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.08587

(1: 0.060570, (2: 0.000004, 3: 0.000004): 0.025289);

(K12: 0.060570, (S2457T: 0.000004, Shig4337: 0.000004): 0.025289);

Detailed output identifying parameters

kappa (ts/tv) =  4.40202


dN/dS for site classes (K=3)

p:   0.99707  0.00000  0.00293
w:   0.40412  1.00000999.00000

dN & dS for each branch

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

   4..1       0.061    410.6    864.4   3.3256   0.0261   0.0078    3.2   22.5
   4..5       0.025    410.6    864.4   3.3256   0.0109   0.0033    1.3    9.4
   5..2       0.000    410.6    864.4   3.3256   0.0000   0.0000    0.0    0.0
   5..3       0.000    410.6    864.4   3.3256   0.0000   0.0000    0.0    0.0


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

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

   425 N      1.000**       998.908


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

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

   425 N      0.809         5.432 +- 3.404



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:   0.219  0.185  0.151  0.120  0.094  0.072  0.056  0.043  0.033  0.026
w2:   0.130  0.098  0.089  0.087  0.088  0.092  0.096  0.102  0.107  0.112

Posterior for p0-p1 (see the ternary graph)

 0.011
 0.003 0.007 0.015
 0.001 0.002 0.004 0.010 0.020
 0.001 0.001 0.002 0.003 0.005 0.014 0.027
 0.001 0.001 0.001 0.002 0.002 0.004 0.007 0.019 0.035
 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.005 0.009 0.026 0.045
 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.007 0.013 0.035 0.056
 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.003 0.004 0.005 0.010 0.017 0.047 0.067
 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.002 0.003 0.005 0.007 0.013 0.023 0.060 0.074
 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.001 0.001 0.002 0.002 0.003 0.004 0.006 0.009 0.017 0.030 0.074 0.077

sum of density on p0-p1 =   1.000000
