
seed used = 140017285

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3088.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 320
# site patterns = 79
   13    3    1    8    9    3    6    7    2   10    1   13    5    5    1
   13   28   12    7    5    1    6    2    3    6   12    8    2    7    5
   17    2    8    5    1    8    1    2    3    5    5    5    1    1    1
    5    1    3    1    3    1    1    1    1    3    1    1    2    4    2
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    1    2    1

1       
K12                   ATG AAT ACT GTC GGC ACG CCG TTG CTA TGG GGA TTC GCT GTT GCC ATT CTG ATC GAC CAG GGG CGT GGG GCA CAT GCC ACC AAA GCG TCG GTG TTA TTT AAC GCC TAT GTG CAA GAA GGT CGC GAT CCA GCA TTT CTC ACA GAG AAA AGC TCT CGC GTG ACT GGC CTA TCG CTG AAG TCA AAG GGA TAC ACA GTA GAA TTC AGC ACT GAC TTC GCG GCG CTG TAC CCA ATT CGG GGT 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ..G ... ... ... ..C ..T ... ..A ... ..G ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..A ... ... ... ... ... ... ..A 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ..G ... ... ... ..C ..T ... ..A ... ..G ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ..A ... ..A ... ... ... ... ..A 
CFT073                ... ... ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ... ... ... ... ... ..A ... ..T ..G ..A T.. ... ... ..A ..T ..T ..G ..G ..G ... ..T ..C ..T ..T ... ..A ... ... ..G ... ... .TA 
O157                  ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..A ... ... ... ... ... ... ..G ..C ... ..G ... ..G ... ..C ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..C ... .T. 
EDL933                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ..A ... ... ... ... ... ... ..G ..C ... ..G ... ..G ... ..C ... ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ..C ... .T. 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  9 10 10 10  9  9 | Ser TCT  1  0  0  1  0  0 | Tyr TAT  8  8  8  9  8  8 | Cys TGT  0  0  0  0  0  0
    TTC 15 14 14 14 15 15 |     TCC  0  1  1  0  1  1 |     TAC  2  2  2  1  2  2 |     TGC  0  0  0  0  0  0
Leu TTA  2  2  2  2  2  2 |     TCA  2  2  2  3  2  2 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  7  7  7  9  7  7 |     TCG  6  6  6  5  6  6 |     TAG  0  0  0  0  0  0 | Trp TGG 10 10 10 10 10 10
--------------------------------------------------------------------------------------------------------------
Leu CTT  0  0  0  0  0  0 | Pro CCT  0  0  0  0  0  0 | His CAT  6  6  6  6  6  6 | Arg CGT  6  7  7  6  6  6
    CTC  5  5  5  5  5  5 |     CCC  0  0  0  0  0  0 |     CAC  0  0  0  0  0  0 |     CGC  6  5  5  6  6  6
    CTA  3  2  3  2  2  2 |     CCA  2  2  2  1  2  2 | Gln CAA  2  2  2  2  2  2 |     CGA  0  0  0  0  0  0
    CTG 31 32 31 30 32 32 |     CCG  6  6  6  7  6  6 |     CAG  5  5  5  5  5  5 |     CGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Ile ATT 14 14 14 14 13 13 | Thr ACT  3  2  2  2  3  3 | Asn AAT  3  3  3  3  3  3 | Ser AGT  0  0  0  1  0  0
    ATC 12 12 12 12 13 13 |     ACC  8  8  8 10  8  8 |     AAC  5  5  5  5  5  5 |     AGC  4  4  4  3  4  4
    ATA  0  0  0  0  0  0 |     ACA  2  2  2  0  1  1 | Lys AAA  3  3  3  4  2  2 | Arg AGA  0  0  0  0  0  0
Met ATG 13 13 13 13 13 13 |     ACG  3  4  4  5  4  4 |     AAG  5  5  5  4  6  6 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  5  5  5  5  6  6 | Ala GCT  5  5  5  5  6  6 | Asp GAT  5  5  5  6  5  5 | Gly GGT  6  5  5  9  5  5
    GTC  8  8  8  8  8  8 |     GCC 14 15 15 13 13 13 |     GAC  8  8  8  7  8  8 |     GGC 12 12 12  9 12 12
    GTA  2  2  2  2  3  3 |     GCA  4  4  4  5  3  3 | Glu GAA  4  4  4  3  4  4 |     GGA  2  3  3  1  3  3
    GTG 19 19 19 20 18 18 |     GCG  9  8  8  8 10 10 |     GAG  3  3  3  4  3  3 |     GGG  3  3  3  3  2  2
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19375    C:0.23125    A:0.23438    G:0.34063
position  2:    T:0.45313    C:0.20313    A:0.18438    G:0.15938
position  3:    T:0.22188    C:0.30938    A:0.08750    G:0.38125

#2: S2457T         
position  1:    T:0.19375    C:0.23125    A:0.23438    G:0.34063
position  2:    T:0.45313    C:0.20313    A:0.18438    G:0.15938
position  3:    T:0.21875    C:0.30938    A:0.08750    G:0.38438

#3: Shig4337       
position  1:    T:0.19375    C:0.23125    A:0.23438    G:0.34063
position  2:    T:0.45313    C:0.20313    A:0.18438    G:0.15938
position  3:    T:0.21875    C:0.30938    A:0.09063    G:0.38125

#4: CFT073         
position  1:    T:0.20000    C:0.22500    A:0.23750    G:0.33750
position  2:    T:0.45625    C:0.20313    A:0.18438    G:0.15625
position  3:    T:0.24063    C:0.29063    A:0.07813    G:0.39063

#5: O157           
position  1:    T:0.19375    C:0.23125    A:0.23438    G:0.34063
position  2:    T:0.45625    C:0.20313    A:0.18438    G:0.15625
position  3:    T:0.21875    C:0.31250    A:0.08125    G:0.38750

#6: EDL933         
position  1:    T:0.19375    C:0.23125    A:0.23438    G:0.34063
position  2:    T:0.45625    C:0.20313    A:0.18438    G:0.15625
position  3:    T:0.21875    C:0.31250    A:0.08125    G:0.38750

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      57 | Ser S TCT       2 | Tyr Y TAT      49 | Cys C TGT       0
      TTC      87 |       TCC       4 |       TAC      11 |       TGC       0
Leu L TTA      12 |       TCA      13 | *** * TAA       0 | *** * TGA       0
      TTG      44 |       TCG      35 |       TAG       0 | Trp W TGG      60
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT      36 | Arg R CGT      38
      CTC      30 |       CCC       0 |       CAC       0 |       CGC      34
      CTA      14 |       CCA      11 | Gln Q CAA      12 |       CGA       0
      CTG     188 |       CCG      37 |       CAG      30 |       CGG      12
------------------------------------------------------------------------------
Ile I ATT      82 | Thr T ACT      15 | Asn N AAT      18 | Ser S AGT       1
      ATC      74 |       ACC      50 |       AAC      30 |       AGC      23
      ATA       0 |       ACA       8 | Lys K AAA      17 | Arg R AGA       0
Met M ATG      78 |       ACG      24 |       AAG      31 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      32 | Ala A GCT      32 | Asp D GAT      31 | Gly G GGT      35
      GTC      48 |       GCC      83 |       GAC      47 |       GGC      69
      GTA      14 |       GCA      23 | Glu E GAA      23 |       GGA      15
      GTG     113 |       GCG      53 |       GAG      19 |       GGG      16
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19479    C:0.23021    A:0.23490    G:0.34010
position  2:    T:0.45469    C:0.20313    A:0.18438    G:0.15781
position  3:    T:0.22292    C:0.30729    A:0.08438    G:0.38542

Codon frequencies under model, for use in evolver:
  0.02013554  0.02775694  0.00762140  0.03481379
  0.00899526  0.01240001  0.00340475  0.01555255
  0.00816493  0.01125539  0.00000000  0.00000000
  0.00698862  0.00963385  0.00000000  0.01208314
  0.02379655  0.03280366  0.00900711  0.04114357
  0.01063076  0.01465455  0.00402379  0.01838029
  0.00964946  0.01330183  0.00365237  0.01668365
  0.00825928  0.01138546  0.00312618  0.01428007
  0.02428110  0.03347160  0.00919051  0.04198133
  0.01084723  0.01495295  0.00410573  0.01875455
  0.00984594  0.01357268  0.00372674  0.01702336
  0.00842746  0.01161729  0.00318983  0.01457084
  0.03515644  0.04846332  0.01330688  0.06078450
  0.01570563  0.02165028  0.00594465  0.02715459
  0.01425588  0.01965179  0.00539592  0.02464801
  0.01220206  0.01682060  0.00461854  0.02109703



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               0.0000 (0.0000 0.0374)
Shig4337             0.0000 (0.0000 0.0417) 0.0000 (0.0000 0.0041)
CFT073               0.0281 (0.0028 0.0999) 0.0246 (0.0028 0.1139) 0.0237 (0.0028 0.1186)
O157                 0.0305 (0.0014 0.0460) 0.0305 (0.0014 0.0460) 0.0279 (0.0014 0.0503) 0.0105 (0.0014 0.1331)
EDL933               0.0305 (0.0014 0.0460) 0.0305 (0.0014 0.0460) 0.0279 (0.0014 0.0503) 0.0105 (0.0014 0.1331)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 42
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1463.345089     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.03450  0.06125  0.00000  0.00768  0.00000  0.28326  0.09079  0.00000  0.00000 16.51882  0.99687  0.00000  0.01150 394.84014
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.47749

((1: 0.034498, (2: 0.000004, 3: 0.007679): 0.061255): 0.000000, (4: 0.283259, (5: 0.000004, 6: 0.000004): 0.090790): 0.000000);

((K12: 0.034498, (S2457T: 0.000004, Shig4337: 0.007679): 0.061255): 0.000000, (CFT073: 0.283259, (O157: 0.000004, EDL933: 0.000004): 0.090790): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) = 16.51882


dN/dS for site classes (K=3)

p:   0.99687  0.00000  0.00313
w:   0.01150  1.00000394.84014

dN & dS for each branch

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

   7..8       0.000    295.8    664.2   1.2486   0.0000   0.0000    0.0    0.0
   8..1       0.034    295.8    664.2   1.2486   0.0123   0.0098    2.9    8.1
   8..9       0.061    295.8    664.2   1.2486   0.0218   0.0174    5.2   14.4
   9..2       0.000    295.8    664.2   1.2486   0.0000   0.0000    0.0    0.0
   9..3       0.008    295.8    664.2   1.2486   0.0027   0.0022    0.6    1.8
   7..10      0.000    295.8    664.2   1.2486   0.0000   0.0000    0.0    0.0
  10..4       0.283    295.8    664.2   1.2486   0.1006   0.0806   23.8   66.8
  10..11      0.091    295.8    664.2   1.2486   0.0322   0.0258    7.6   21.4
  11..5       0.000    295.8    664.2   1.2486   0.0000   0.0000    0.0    0.0
  11..6       0.000    295.8    664.2   1.2486   0.0000   0.0000    0.0    0.0


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

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

   320 G      1.000**       394.840


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

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

   320 G      0.806         3.155 +- 2.509



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:   0.999  0.001  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.410  0.200  0.114  0.073  0.052  0.040  0.033  0.028  0.026  0.024

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 0.002
 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 0.005 0.993

sum of density on p0-p1 =   1.000000
