
seed used = 139998165

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1287.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 375
# site patterns = 94
    2   16    9   10    5    8    7    6    7   10    8    9    4    7    3
    4    3    1    4    8    6   14    8    3    4    7    5    2    5    5
    7    1    7    4   10    1    1    1    1    4   10    1   10    1    1
    1    6    1    2    1    8    4    9    3    1    4    6    5    5    2
    4    1    1    1    9    3    9    1    3    1    1    1    5    3    1
    2    1    4    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  7  7  7  8  7 | Ser TCT  3  3  3  3  3 | Tyr TAT  9  9  9 10  9 | Cys TGT  5  5  5  6  5
    TTC  4  4  4  4  4 |     TCC  3  5  5  4  3 |     TAC  2  2  2  2  2 |     TGC  3  3  3  3  3
Leu TTA  7  6  6  7  7 |     TCA 10 10 10 10 10 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  6  6  6  6  6 |     TCG  4  4  4  4  4 |     TAG  0  0  0  0  0 | Trp TGG  9  9  9  8  9
--------------------------------------------------------------------------------------------------
Leu CTT 11 11 11 10 11 | Pro CCT  9  9  9  8  9 | His CAT  5  5  5  4  5 | Arg CGT  4  3  3  2  3
    CTC  7  7  7  8  7 |     CCC  5  5  5  6  6 |     CAC  5  5  5  5  5 |     CGC 10 11 11 11 10
    CTA  2  1  1  0  2 |     CCA  0  0  0  1  0 | Gln CAA 10 10 10 10 10 |     CGA  4  5  5  5  4
    CTG 14 16 16 16 15 |     CCG  4  4  4  5  4 |     CAG 12 11 11 10 12 |     CGG  4  4  4  5  5
--------------------------------------------------------------------------------------------------
Ile ATT  9  9  9  9  9 | Thr ACT  3  3  3  3  3 | Asn AAT  9  9  9 10  9 | Ser AGT  4  4  4  4  4
    ATC  8  8  8  8  8 |     ACC 10  9  9  7  8 |     AAC  5  6  6  6  6 |     AGC 11 10 10 10 10
    ATA  5  5  5  4  5 |     ACA  6  6  6  7  6 | Lys AAA  8  7  7  7  8 | Arg AGA  0  0  0  0  0
Met ATG  3  2  2  2  2 |     ACG  8  8  8  7  8 |     AAG  3  3  3  3  2 |     AGG  1  1  1  1  2
--------------------------------------------------------------------------------------------------
Val GTT  6  6  6  7  7 | Ala GCT  8  8  8  8  8 | Asp GAT  7  7  7  6  6 | Gly GGT  3  3  3  3  3
    GTC  4  7  7  6  4 |     GCC 10  8  8  9 11 |     GAC  9  8  8  8  9 |     GGC  7  6  6  6  6
    GTA  2  2  2  3  2 |     GCA  5  6  6  6  5 | Glu GAA 18 17 17 18 19 |     GGA  0  1  1  0  0
    GTG  5  5  5  4  5 |     GCG 10 11 11 11 10 |     GAG  6  7  7  7  6 |     GGG  4  3  3  4  4
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.19200    C:0.28267    A:0.24800    G:0.27733
position  2:    T:0.26667    C:0.26133    A:0.28800    G:0.18400
position  3:    T:0.27200    C:0.27467    A:0.20533    G:0.24800

#2: S2457T         
position  1:    T:0.19467    C:0.28533    A:0.24000    G:0.28000
position  2:    T:0.27200    C:0.26400    A:0.28267    G:0.18133
position  3:    T:0.26933    C:0.27733    A:0.20267    G:0.25067

#3: Shig4337       
position  1:    T:0.19467    C:0.28533    A:0.24000    G:0.28000
position  2:    T:0.27200    C:0.26400    A:0.28267    G:0.18133
position  3:    T:0.26933    C:0.27733    A:0.20267    G:0.25067

#4: CFT073         
position  1:    T:0.20000    C:0.28267    A:0.23467    G:0.28267
position  2:    T:0.27200    C:0.26400    A:0.28267    G:0.18133
position  3:    T:0.26933    C:0.27467    A:0.20800    G:0.24800

#5: O157           
position  1:    T:0.19200    C:0.28800    A:0.24000    G:0.28000
position  2:    T:0.26933    C:0.26133    A:0.28800    G:0.18133
position  3:    T:0.26933    C:0.27200    A:0.20800    G:0.25067

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      36 | Ser S TCT      15 | Tyr Y TAT      46 | Cys C TGT      26
      TTC      20 |       TCC      20 |       TAC      10 |       TGC      15
Leu L TTA      33 |       TCA      50 | *** * TAA       0 | *** * TGA       0
      TTG      30 |       TCG      20 |       TAG       0 | Trp W TGG      44
------------------------------------------------------------------------------
Leu L CTT      54 | Pro P CCT      44 | His H CAT      24 | Arg R CGT      15
      CTC      36 |       CCC      27 |       CAC      25 |       CGC      53
      CTA       6 |       CCA       1 | Gln Q CAA      50 |       CGA      23
      CTG      77 |       CCG      21 |       CAG      56 |       CGG      22
------------------------------------------------------------------------------
Ile I ATT      45 | Thr T ACT      15 | Asn N AAT      46 | Ser S AGT      20
      ATC      40 |       ACC      43 |       AAC      29 |       AGC      51
      ATA      24 |       ACA      31 | Lys K AAA      37 | Arg R AGA       0
Met M ATG      11 |       ACG      39 |       AAG      14 |       AGG       6
------------------------------------------------------------------------------
Val V GTT      32 | Ala A GCT      40 | Asp D GAT      33 | Gly G GGT      15
      GTC      28 |       GCC      46 |       GAC      42 |       GGC      31
      GTA      11 |       GCA      28 | Glu E GAA      89 |       GGA       2
      GTG      24 |       GCG      53 |       GAG      33 |       GGG      18
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.19467    C:0.28480    A:0.24053    G:0.28000
position  2:    T:0.27040    C:0.26293    A:0.28480    G:0.18187
position  3:    T:0.26987    C:0.27520    A:0.20533    G:0.24960

Codon frequencies under model, for use in evolver:
  0.01468225  0.01497242  0.01117128  0.01357963
  0.01427683  0.01455898  0.01086280  0.01320465
  0.01546415  0.01576976  0.00000000  0.00000000
  0.00987505  0.01007021  0.00000000  0.00913344
  0.02148034  0.02190485  0.01634374  0.01986719
  0.02088719  0.02129998  0.01589243  0.01931859
  0.02262426  0.02307138  0.01721411  0.02092521
  0.01444733  0.01473285  0.01099253  0.01336235
  0.01814163  0.01850016  0.01380342  0.01677922
  0.01764068  0.01798931  0.01342226  0.01631589
  0.01910776  0.01948538  0.01453851  0.01767279
  0.01220177  0.01244291  0.00928396  0.01128543
  0.02111831  0.02153567  0.01606828  0.01953235
  0.02053516  0.02094099  0.01562458  0.01899300
  0.02224295  0.02268254  0.01692399  0.02057253
  0.01420383  0.01448454  0.01080726  0.01313714



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               0.9887 (0.0179 0.0181)
Shig4337             0.9887 (0.0179 0.0181)-1.0000 (0.0000 0.0000)
CFT073               0.6909 (0.0228 0.0330) 0.3934 (0.0144 0.0365) 0.3934 (0.0144 0.0365)
O157                 0.7643 (0.0083 0.0109) 0.5750 (0.0168 0.0291) 0.5750 (0.0168 0.0291) 0.4575 (0.0168 0.0366)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 47
This is a rooted tree.  Please check!
check convergence..
lnL(ntime:  8  np: 13):  -1824.922706     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00383  0.01213  0.04555  0.00000  0.00000  0.00435  0.06056  0.00938  3.03629  0.86619  0.00000  0.00000  6.53620
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.13581

((1: 0.012131, (2: 0.000004, 3: 0.000004): 0.045553): 0.003830, (4: 0.060562, 5: 0.009379): 0.004347);

((K12: 0.012131, (S2457T: 0.000004, Shig4337: 0.000004): 0.045553): 0.003830, (CFT073: 0.060562, O157: 0.009379): 0.004347);

Detailed output identifying parameters

kappa (ts/tv) =  3.03629


dN/dS for site classes (K=3)

p:   0.86619  0.00000  0.13381
w:   0.00000  1.00000  6.53620

dN & dS for each branch

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

   6..7       0.004    331.2    793.8   0.8746   0.0012   0.0014    0.5    1.0
   7..1       0.012    331.2    793.8   0.8746   0.0039   0.0044    1.5    3.1
   7..8       0.046    331.2    793.8   0.8746   0.0146   0.0167    5.5   11.6
   8..2       0.000    331.2    793.8   0.8746   0.0000   0.0000    0.0    0.0
   8..3       0.000    331.2    793.8   0.8746   0.0000   0.0000    0.0    0.0
   6..9       0.004    331.2    793.8   0.8746   0.0014   0.0016    0.5    1.1
   9..4       0.061    331.2    793.8   0.8746   0.0194   0.0221    7.3   15.4
   9..5       0.009    331.2    793.8   0.8746   0.0030   0.0034    1.1    2.4


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

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

    21 T      1.000**       6.536
    46 E      1.000**       6.536
    47 K      1.000**       6.536
    58 D      1.000**       6.536
    66 D      1.000**       6.536
    71 Q      1.000**       6.536
   118 T      1.000**       6.536
   157 A      1.000**       6.536
   158 W      1.000**       6.536
   164 S      1.000**       6.536
   186 H      1.000**       6.536
   195 E      1.000**       6.536
   210 L      1.000**       6.536
   239 I      1.000**       6.536
   252 K      1.000**       6.536
   259 G      1.000**       6.536
   261 T      1.000**       6.536
   283 A      1.000**       6.536
   284 T      1.000**       6.536
   287 D      1.000**       6.536
   297 T      1.000**       6.536
   298 L      1.000**       6.536
   299 M      1.000**       6.536
   308 Q      1.000**       6.536


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

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

    21 T      0.504         4.009 +- 3.669
    46 E      0.883         6.843 +- 2.982
    47 K      0.892         6.910 +- 2.936
    58 D      0.891         6.902 +- 2.942
    71 Q      0.526         4.180 +- 3.698
   118 T      0.902         6.983 +- 2.884
   157 A      0.884         6.851 +- 2.977
   158 W      0.542         4.311 +- 3.715
   210 L      0.561         4.456 +- 3.729
   239 I      0.891         6.902 +- 2.942
   252 K      0.508         4.046 +- 3.678
   261 T      0.529         4.206 +- 3.702
   283 A      0.504         4.013 +- 3.671
   284 T      0.533         4.237 +- 3.705
   297 T      0.512         4.073 +- 3.683
   299 M      0.539         4.287 +- 3.713
   308 Q      0.907         7.017 +- 2.858



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:   0.410  0.274  0.163  0.086  0.040  0.017  0.007  0.002  0.001  0.000
w2:   0.005  0.017  0.043  0.078  0.107  0.125  0.140  0.155  0.165  0.166

Posterior for p0-p1 (see the ternary graph)

 0.000
 0.000 0.000 0.001
 0.000 0.000 0.000 0.000 0.002
 0.000 0.000 0.000 0.000 0.000 0.002 0.006
 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.006 0.015
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.020 0.028
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.007 0.053 0.038
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.005 0.023 0.106 0.038
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.004 0.016 0.059 0.156 0.031
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.004 0.011 0.041 0.124 0.166 0.024

sum of density on p0-p1 =   1.000000
