
seed used = 140008313

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2323.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 406
# site patterns = 90
   17   12    9   15    8    8    8   30   22   13    9    7   15    8    2
   10   10   17    3   10    1    1    1    9    7    3    7    6    2    1
    8    3   10    6    4    3    1    1    1    1    1   10   12    7    1
    1    1    1    1   10    1    5    1    1    2    2    2    1    2    1
    1    1    1    1    4    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    2    1    1    1


1       
K12                   ATG AAA CGT GCA GTG ATT ACT GGC CTG GTT TCC AGC ATC GGT AAT AAC CAG GAA GTC TCT GGA TCA GGG TTC GAG AAG GAT CAC TGG GTA ACC CTC GAC CGC TTT TAT CTT ATC GCT GCG TCT CCG GCT TAC AAC CGC TCC GGC GTG GCG ACC GCC TGC ACC CAT TGT GTA CAA TGC GCT GCA GGT CTG GAC GGC GTA CAC ACC GGT CCG GTA CGC TGC AAG CCA GAT TCC CAC GGT TCG GAG GCC TCT GCT GGC GTA ACG ACC ACC GAT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..T ... ..T ..G ... ... ... ... ... ..C ..G ... ..A ... ... ... T.. ... ... ... ... ..T ..T C.. ... ... ..T ... ... ... ... ... ..A ..G ..T ..G ... ..T ... AGA 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ..T ... ..T ..G ... ... ... ... ... ..C ..G ... ..A ... ... ... T.. ... ... ... ... ..T ..T C.. ... ... ..T ... ... ... ... ... ..A ..G ..T ..G ... ..T ... AGA 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ..A ..T ..C ... ... ... ... ... ... ... ..T ... ... ... ... ..G ..C ... ... ... ... ... ..G ..G ... ... ..T ... ... ... ..C ... ..G ... ... ... ... ..C ..T ..T ... ... ..A ..A ..A ... ... ... ... ..A ..T ... 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ..T ..T ..T ..T ... ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ..T ... ..G ... ..G ..C ..C ... ..T ..T C.. ... ... ... ... ..C ... ... ... ... ... ... ... ... ..T ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  4  4 | Ser TCT 12 12 12 11 13 | Tyr TAT  3  3  3  3  3 | Cys TGT  2  4  4  2  3
    TTC  9  9  9  9  9 |     TCC 11 10 10 11 10 |     TAC  7  8  8  7  7 |     TGC  4  2  2  4  3
Leu TTA  0  0  0  0  0 |     TCA  1  2  2  2  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  0  0  0  0  0 |     TCG  1  1  1  1  1 |     TAG  0  0  0  0  0 | Trp TGG  2  2  2  2  2
--------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  1  1 | Pro CCT  0  0  0  0  0 | His CAT  2  2  2  1  2 | Arg CGT  9 10 10  9 11
    CTC  3  3  3  3  3 |     CCC  0  0  0  0  1 |     CAC  8  7  7  9  8 |     CGC  8  7  7  8  6
    CTA  0  1  1  0  0 |     CCA  1  1  1  1  1 | Gln CAA  1  1  1  1  1 |     CGA  0  0  0  0  0
    CTG 23 22 22 23 23 |     CCG 11 11 11 11 10 |     CAG 10 11 11 10 11 |     CGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Ile ATT  8  8  8  9  8 | Thr ACT  8 10 10  9  9 | Asn AAT  2  2  2  2  3 | Ser AGT  0  0  0  0  0
    ATC 16 16 16 15 16 |     ACC 13 10 10 10 10 |     AAC 11 11 11 11 10 |     AGC  7  7  7  7  7
    ATA  0  1  1  0  0 |     ACA  0  0  0  1  0 | Lys AAA 12 12 12 12 12 | Arg AGA  0  1  1  0  0
Met ATG 17 17 17 17 17 |     ACG  2  3  3  3  4 |     AAG  4  3  3  4  3 |     AGG  0  0  0  0  0
--------------------------------------------------------------------------------------------------
Val GTT 13 13 13 14 13 | Ala GCT 15 13 13 15 14 | Asp GAT  9  8  8  8 10 | Gly GGT 11 13 13 13 10
    GTC  3  3  3  3  3 |     GCC  6  7  7  5  6 |     GAC 11 11 11 12 10 |     GGC 36 34 34 33 37
    GTA  6  4  4  5  5 |     GCA 16 15 15 17 17 | Glu GAA 17 17 17 18 17 |     GGA  1  1  1  1  1
    GTG  9 10 10  9 10 |     GCG 11 13 13 11 11 |     GAG  8  8  8  7  8 |     GGG  1  1  1  2  1
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.13793    C:0.18966    A:0.24631    G:0.42611
position  2:    T:0.27586    C:0.26601    A:0.25862    G:0.19951
position  3:    T:0.24384    C:0.37685    A:0.13547    G:0.24384

#2: S2457T         
position  1:    T:0.14039    C:0.18966    A:0.24877    G:0.42118
position  2:    T:0.27586    C:0.26601    A:0.25616    G:0.20197
position  3:    T:0.25369    C:0.35714    A:0.13793    G:0.25123

#3: Shig4337       
position  1:    T:0.14039    C:0.18966    A:0.24877    G:0.42118
position  2:    T:0.27586    C:0.26601    A:0.25616    G:0.20197
position  3:    T:0.25369    C:0.35714    A:0.13793    G:0.25123

#4: CFT073         
position  1:    T:0.13793    C:0.18966    A:0.24631    G:0.42611
position  2:    T:0.27586    C:0.26601    A:0.25862    G:0.19951
position  3:    T:0.24877    C:0.36207    A:0.14286    G:0.24631

#5: O157           
position  1:    T:0.13793    C:0.19212    A:0.24384    G:0.42611
position  2:    T:0.27586    C:0.26601    A:0.25862    G:0.19951
position  3:    T:0.25616    C:0.35961    A:0.13547    G:0.24877

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      20 | Ser S TCT      60 | Tyr Y TAT      15 | Cys C TGT      15
      TTC      45 |       TCC      52 |       TAC      37 |       TGC      15
Leu L TTA       0 |       TCA       8 | *** * TAA       0 | *** * TGA       0
      TTG       0 |       TCG       5 |       TAG       0 | Trp W TGG      10
------------------------------------------------------------------------------
Leu L CTT       5 | Pro P CCT       0 | His H CAT       9 | Arg R CGT      49
      CTC      15 |       CCC       1 |       CAC      39 |       CGC      36
      CTA       2 |       CCA       5 | Gln Q CAA       5 |       CGA       0
      CTG     113 |       CCG      54 |       CAG      53 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      41 | Thr T ACT      46 | Asn N AAT      11 | Ser S AGT       0
      ATC      79 |       ACC      53 |       AAC      54 |       AGC      35
      ATA       2 |       ACA       1 | Lys K AAA      60 | Arg R AGA       2
Met M ATG      85 |       ACG      15 |       AAG      17 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      66 | Ala A GCT      70 | Asp D GAT      43 | Gly G GGT      60
      GTC      15 |       GCC      31 |       GAC      55 |       GGC     174
      GTA      24 |       GCA      80 | Glu E GAA      86 |       GGA       5
      GTG      48 |       GCG      59 |       GAG      39 |       GGG       6
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.13892    C:0.19015    A:0.24680    G:0.42414
position  2:    T:0.27586    C:0.26601    A:0.25764    G:0.20049
position  3:    T:0.25123    C:0.36256    A:0.13793    G:0.24828

Codon frequencies under model, for use in evolver:
  0.00980074  0.01414382  0.00538080  0.00968544
  0.00945072  0.01363868  0.00518863  0.00933953
  0.00915320  0.01320932  0.00000000  0.00000000
  0.00712304  0.01027953  0.00000000  0.00703924
  0.01341520  0.01935998  0.00736521  0.01325738
  0.01293609  0.01866855  0.00710217  0.01278390
  0.01252884  0.01808084  0.00687858  0.01238144
  0.00974998  0.01407056  0.00535293  0.00963527
  0.01741196  0.02512785  0.00955951  0.01720711
  0.01679011  0.02423043  0.00921810  0.01659257
  0.01626153  0.02346762  0.00892790  0.01607022
  0.01265476  0.01826256  0.00694771  0.01250589
  0.02992355  0.04318379  0.01642862  0.02957151
  0.02885485  0.04164151  0.01584188  0.02851538
  0.02794646  0.04033058  0.01534315  0.02761768
  0.02174801  0.03138536  0.01194008  0.02149215



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               0.1257 (0.0064 0.0511)
Shig4337             0.1257 (0.0064 0.0511)-1.0000 (0.0000 0.0000)
CFT073               0.0000 (0.0000 0.0827) 0.0610 (0.0064 0.1054) 0.0610 (0.0064 0.1054)
O157                 0.0217 (0.0011 0.0506) 0.0774 (0.0053 0.0688) 0.0774 (0.0053 0.0688) 0.0098 (0.0011 0.1124)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 54
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1915.064136     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00243  0.01078  0.04640  0.00000  0.00000  0.00200  0.06270  0.02939  3.84780  0.98781  0.00000  0.00000  6.36895
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.15370

((1: 0.010779, (2: 0.000004, 3: 0.000004): 0.046400): 0.002427, (4: 0.062700, 5: 0.029393): 0.001998);

((K12: 0.010779, (S2457T: 0.000004, Shig4337: 0.000004): 0.046400): 0.002427, (CFT073: 0.062700, O157: 0.029393): 0.001998);

Detailed output identifying parameters

kappa (ts/tv) =  3.84780


dN/dS for site classes (K=3)

p:   0.98781  0.00000  0.01219
w:   0.00000  1.00000  6.36895

dN & dS for each branch

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

   6..7       0.002    357.3    860.7   0.0776   0.0002   0.0023    0.8    0.2
   7..1       0.011    357.3    860.7   0.0776   0.0008   0.0103    3.7    0.7
   7..8       0.046    357.3    860.7   0.0776   0.0034   0.0444   15.9    3.0
   8..2       0.000    357.3    860.7   0.0776   0.0000   0.0000    0.0    0.0
   8..3       0.000    357.3    860.7   0.0776   0.0000   0.0000    0.0    0.0
   6..9       0.002    357.3    860.7   0.0776   0.0001   0.0019    0.7    0.1
   9..4       0.063    357.3    860.7   0.0776   0.0047   0.0600   21.4    4.0
   9..5       0.029    357.3    860.7   0.0776   0.0022   0.0281   10.1    1.9


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

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

    52 V      1.000**       6.369
   252 H      1.000**       6.368
   282 K      1.000**       6.369
   406 D      1.000**       6.369


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

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

   282 K      0.796         3.146 +- 2.347
   406 D      0.868         3.312 +- 2.317



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:   1.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.336  0.224  0.143  0.093  0.063  0.045  0.033  0.026  0.020  0.016

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.999

sum of density on p0-p1 =   1.000000
