
seed used = 140002981

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1819.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 283
# site patterns = 82
    9    5    4    1    4    4    6    4    9    5    1    5   10   11    1
   13   23    3   10    6   14    1    5    5    7    2    7    1    3    5
    1    9    1    5    7    2    1    3    1   14    1    3    4    1    3
    1    2    1    1    1    2    2    2    1    1    1    1    1    1    1
    1    1    1    1    1    2    1    1    1    1    1    1    1    1    1
    1    1    2    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  5  5  5  5  5  5 | Ser TCT  4  3  3  4  4  4 | Tyr TAT  1  1  1  1  1  1 | Cys TGT  1  1  1  1  1  1
    TTC 13 13 13 13 13 13 |     TCC  1  1  1  1  1  1 |     TAC  5  5  5  5  5  5 |     TGC  2  2  2  2  2  2
Leu TTA  2  2  2  3  2  2 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  2  2  2  3  2  2 |     TCG  0  1  1  0  0  0 |     TAG  0  0  0  0  0  0 | Trp TGG  5  5  5  5  5  5
--------------------------------------------------------------------------------------------------------------
Leu CTT  0  2  2  1  0  0 | Pro CCT  1  1  1  1  1  1 | His CAT  1  1  1  1  1  1 | Arg CGT 10 11 11 10 10 10
    CTC  5  5  5  5  5  5 |     CCC  0  0  0  0  0  0 |     CAC  2  1  1  2  2  2 |     CGC  4  3  3  4  4  4
    CTA  1  0  0  0  1  1 |     CCA  3  2  2  3  2  2 | Gln CAA  4  5  5  4  4  4 |     CGA  0  0  0  0  0  0
    CTG 27 26 26 25 27 27 |     CCG  8  9  9  8  9  9 |     CAG  7  7  7  7  7  7 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT  6  5  5  6  6  6 | Thr ACT  7  4  4  6  7  7 | Asn AAT  1  1  1  1  1  1 | Ser AGT  1  1  1  1  1  1
    ATC 14 15 15 14 14 14 |     ACC  7 11 11  8  7  7 |     AAC 10 10 10 10 10 10 |     AGC  2  2  2  2  2  2
    ATA  0  0  0  0  0  0 |     ACA  2  3  3  1  2  2 | Lys AAA 10  9  9 10 10 10 | Arg AGA  0  0  0  0  0  0
Met ATG  9  9  9  9  9  9 |     ACG  2  1  1  3  2  2 |     AAG  1  1  1  1  1  1 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  7  6  6  7  7  7 | Ala GCT  9  9  9  9  9  9 | Asp GAT  4  6  6  5  4  4 | Gly GGT 15 15 15 14 15 15
    GTC  7  5  5  7  7  7 |     GCC  1  1  1  1  1  1 |     GAC  5  3  3  4  5  5 |     GGC 12 11 11 12 12 12
    GTA  7  8  8  7  7  7 |     GCA  7  8  8  8  7  7 | Glu GAA  6  5  5  6  6  6 |     GGA  2  3  3  2  2  2
    GTG  2  4  4  2  2  2 |     GCG  5  4  4  4  5  5 |     GAG  4  4  4  4  4  4 |     GGG  3  4  4  4  3  3
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.14841    C:0.25795    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20495    A:0.21555    G:0.20141
position  3:    T:0.25795    C:0.31802    A:0.15901    G:0.26502

#2: S2457T         
position  1:    T:0.14841    C:0.25795    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20848    A:0.20848    G:0.20495
position  3:    T:0.25442    C:0.31095    A:0.16254    G:0.27208

#3: Shig4337       
position  1:    T:0.14841    C:0.25795    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20848    A:0.20848    G:0.20495
position  3:    T:0.25442    C:0.31095    A:0.16254    G:0.27208

#4: CFT073         
position  1:    T:0.15548    C:0.25088    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20495    A:0.21555    G:0.20141
position  3:    T:0.25795    C:0.31802    A:0.15901    G:0.26502

#5: O157           
position  1:    T:0.14841    C:0.25795    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20495    A:0.21555    G:0.20141
position  3:    T:0.25795    C:0.31802    A:0.15548    G:0.26855

#6: EDL933         
position  1:    T:0.14841    C:0.25795    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20495    A:0.21555    G:0.20141
position  3:    T:0.25795    C:0.31802    A:0.15548    G:0.26855

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      30 | Ser S TCT      22 | Tyr Y TAT       6 | Cys C TGT       6
      TTC      78 |       TCC       6 |       TAC      30 |       TGC      12
Leu L TTA      13 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      13 |       TCG       2 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT       5 | Pro P CCT       6 | His H CAT       6 | Arg R CGT      62
      CTC      30 |       CCC       0 |       CAC      10 |       CGC      22
      CTA       3 |       CCA      14 | Gln Q CAA      26 |       CGA       0
      CTG     158 |       CCG      52 |       CAG      42 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      34 | Thr T ACT      35 | Asn N AAT       6 | Ser S AGT       6
      ATC      86 |       ACC      51 |       AAC      60 |       AGC      12
      ATA       0 |       ACA      13 | Lys K AAA      58 | Arg R AGA       0
Met M ATG      54 |       ACG      11 |       AAG       6 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      40 | Ala A GCT      54 | Asp D GAT      29 | Gly G GGT      89
      GTC      38 |       GCC       6 |       GAC      25 |       GGC      70
      GTA      44 |       GCA      45 | Glu E GAA      34 |       GGA      14
      GTG      16 |       GCG      27 |       GAG      24 |       GGG      21
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.14959    C:0.25677    A:0.25442    G:0.33922
position  2:    T:0.37809    C:0.20612    A:0.21319    G:0.20259
position  3:    T:0.25677    C:0.31567    A:0.15901    G:0.26855

Codon frequencies under model, for use in evolver:
  0.01479557  0.01818905  0.00916239  0.01547426
  0.00806612  0.00991615  0.00499507  0.00843612
  0.00834267  0.01025613  0.00000000  0.00000000
  0.00792784  0.00974615  0.00000000  0.00829150
  0.02539711  0.03122214  0.01572757  0.02656212
  0.01384578  0.01702142  0.00857422  0.01448091
  0.01432049  0.01760501  0.00886819  0.01497739
  0.01360842  0.01672962  0.00842723  0.01423266
  0.02516411  0.03093570  0.01558328  0.02631843
  0.01371875  0.01686526  0.00849556  0.01434805
  0.01418911  0.01744349  0.00878683  0.01483999
  0.01348357  0.01657614  0.00834992  0.01410209
  0.03355215  0.04124760  0.02077771  0.03509124
  0.01829167  0.02248701  0.01132741  0.01913074
  0.01891881  0.02325799  0.01171578  0.01978665
  0.01797810  0.02210152  0.01113323  0.01880278



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               0.1534 (0.0169 0.1100)
Shig4337             0.1534 (0.0169 0.1100)-1.0000 (0.0000 0.0000)
CFT073               0.0000 (0.0000 0.0570) 0.1392 (0.0169 0.1211) 0.1392 (0.0169 0.1211)
O157                 0.0000 (0.0000 0.0046) 0.1610 (0.0169 0.1048) 0.1610 (0.0169 0.1048) 0.0000 (0.0000 0.0521)
EDL933               0.0000 (0.0000 0.0046) 0.1610 (0.0169 0.1048) 0.1610 (0.0169 0.1048) 0.0000 (0.0000 0.0521)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 36
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1348.606908     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00000  0.00365  0.15006  0.00000  0.00000  0.00000  0.04259  0.00000  0.00000  0.00000  2.32295  0.97639  0.00000  0.00000 11.01087
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.19633

((1: 0.003653, (2: 0.000004, 3: 0.000004): 0.150065): 0.000000, (4: 0.042591, (5: 0.000004, 6: 0.000004): 0.000000): 0.000000);

((K12: 0.003653, (S2457T: 0.000004, Shig4337: 0.000004): 0.150065): 0.000000, (CFT073: 0.042591, (O157: 0.000004, EDL933: 0.000004): 0.000000): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  2.32295


dN/dS for site classes (K=3)

p:   0.97639  0.00000  0.02361
w:   0.00000  1.00000 11.01087

dN & dS for each branch

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

   7..8       0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
   8..1       0.004    251.9    597.1   0.2600   0.0007   0.0025    0.6    0.4
   8..9       0.150    251.9    597.1   0.2600   0.0271   0.1043   26.3   16.2
   9..2       0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
   9..3       0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
   7..10      0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
  10..4       0.043    251.9    597.1   0.2600   0.0077   0.0296    7.5    4.6
  10..11      0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
  11..5       0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0
  11..6       0.000    251.9    597.1   0.2600   0.0000   0.0000    0.0    0.0


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

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

   218 R      1.000**       11.011
   221 D      1.000**       11.011
   223 T      1.000**       11.011
   225 K      1.000**       11.011
   226 E      1.000**       11.011
   227 H      1.000**       11.010


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

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

   218 R      0.946         7.645 +- 2.529
   221 D      0.684         5.638 +- 3.864
   223 T      0.981*        7.882 +- 2.215
   225 K      0.571         4.804 +- 4.103
   226 E      0.985*        7.904 +- 2.179



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:   0.998  0.002  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.002  0.010  0.028  0.055  0.087  0.120  0.148  0.171  0.186  0.193

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 0.005
 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 0.003 0.992

sum of density on p0-p1 =   1.000000
