
seed used = 139994921

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0933.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 255
# site patterns = 106
    6    4    1    4    5   15    3    7    6    1    2    7    3    4    1
    3    6    4    1    9    8    1    1    1    8    8    7    4    3    3
   11    3    1    2    1    1    1    1    4    3    1    2    1    1    1
    1    4    1    4    2    1    4    4    1    1    1    1    3    1    2
    4    1    1    1    2    1    1    1    2    1    1    1    2    1    1
    1    1    1    1    1    1    1    1    2    1    1    1    1    1    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1

1       
K12                   ATG AAT ACT GCT CGT CTG AAC CAG GGC ACG CCA TTG CTC GCA GTA AGC AAA CAT TAC GCG GAA ATC GTC CAA GAT TTA ATT CCG GGT TTT GTG CGC GGT GGC AGT ACC CGC GCA ACG ACC GCA GAT ACA GAA GAA GAC CGA CTA TGG TCG GTT GGG CTT GCC GCA CGA GCG TTG GTA GGA GAG GCA CCT GCC TCT CAG CGA AGA CCG GGA GGG GCG GAC GCC TCA CAG GAG CAC GGC GTA CTG GTA GCG CGG CTG GGT ACA ATC CCC CGT CGA GTG GCG GAG GTG CAA CAA GGT GAA ACT CGC CTG AGA AAA CAG GGG 
S2457T                ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... .A. ..C ... ... ... ... ... ... ..T ..T ... ..G ... ... ... ... ... ... ..G ..G ... ... .C. ... ... ..C ... ... ... ... ..T ... ... ..T ... ..A ... ... ... ... C.. ... ... ... ... ... ..A ... T.. A.. ... ... ... ... ... ... ... ..A ..A ... .GG ..G C.T CAA .TG A.T C.G CGT ..T ..T 
Shig4337              ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... .A. ..C ... ... ... ... ... ... ..T ..T ... ..G ... ... ... ... ... ... ..G ..G ... ... .C. ... ... ..C ... ... ... ... ..T ... ... ..T ... ..A ... ... ... ... C.. ... ... ... ... ... ..A ... T.. A.. ... ... ... ... ... ... ... ..A ..A ... .GG ..G C.T CAA .TG A.T C.G CGT ..T ..T 
CFT073                ... ... ..G ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..C ... ... ..T ... ... ... ... ... ..C ... ..G ..T ..T ... ..G ... ... ... ... ... ..G ..G .AG ..T C.. ... ... ... ..G ... ... ... ..A ..T ..G ..A ..T ..T ... ... ..T ..G .T. A.. ... ..T ..T T.. ..G ... ... T.. ... ..G ... ... ..C ..G ..A ..A ..A ... ..G ... ..G C.C CAA .CG A.T C.. CGT ..T ..T 
O157                  ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..G ... ... ... ... ... ..C ... ... ... ... ... ... ... ..T ..T ... ..T ... ... ... ... ... ..T ... ... ... ..A ... T.. ... ..G ..T ... ..C ..G ... ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... 
EDL933                ... ... ... ... ... ... ... ... ... ..A ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ..G ..G ... ... ... ... ... ..C ... ... ... ... ... ... ... ..T ..T ... ..T ... ... ... ... ... ..T ... ... ... ..A ... T.. ... ..G ..T ... ..C ..G ... ... ..A ... ... ..G ... ... ... ... ... ... ... ... ... 

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  3  3  3  3  3  3 | Ser TCT  2  2  2  2  2  2 | Tyr TAT  0  0  0  0  0  0 | Cys TGT  0  0  0  0  0  0
    TTC  0  0  0  0  0  0 |     TCC  0  0  0  0  0  0 |     TAC  1  1  1  1  1  1 |     TGC  0  0  0  0  0  0
Leu TTA  8  8  8  8  8  8 |     TCA  1  1  1  0  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG 10 11 11  9 11 11 |     TCG  2  2  2  3  2  2 |     TAG  0  0  0  0  0  0 | Trp TGG  4  4  4  4  4  4
--------------------------------------------------------------------------------------------------------------
Leu CTT  4  4  4  4  4  4 | Pro CCT  1  1  1  1  1  1 | His CAT  4  6  6  5  4  4 | Arg CGT  6  8  8  7  5  5
    CTC  3  3  3  3  3  3 |     CCC  1  1  1  1  1  1 |     CAC  1  2  2  2  1  1 |     CGC  5  3  3  5  6  6
    CTA  1  0  0  0  1  1 |     CCA  2  2  2  4  2  2 | Gln CAA  3  3  3  4  2  2 |     CGA  7  5  5  5  5  5
    CTG 18 18 18 20 17 17 |     CCG  6  6  6  5  6  6 |     CAG 10 10 10  9 11 11 |     CGG  2  5  5  3  4  4
--------------------------------------------------------------------------------------------------------------
Ile ATT  7  8  8  8  8  8 | Thr ACT  2  1  1  1  2  2 | Asn AAT  4  4  4  4  4  4 | Ser AGT  1  2  2  1  1  1
    ATC  2  2  2  2  1  1 |     ACC  4  4  4  3  4  4 |     AAC  3  3  3  3  3  3 |     AGC  3  3  3  3  3  3
    ATA  0  0  0  0  0  0 |     ACA  2  3  3  2  2  2 | Lys AAA  7  6  6  6  7  7 | Arg AGA  2  1  1  0  2  2
Met ATG  6  6  6  6  6  6 |     ACG  5  4  4  6  5  5 |     AAG  0  0  0  1  0  0 |     AGG  0  0  0  1  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  1  1  1  2  1  1 | Ala GCT  4  4  4  6  5  5 | Asp GAT 10 12 12 10 12 12 | Gly GGT  6  8  8  8  9  9
    GTC  1  1  1  1  1  1 |     GCC  3  5  5  1  4  4 |     GAC  3  2  2  4  1  1 |     GGC  9  7  7  9  8  8
    GTA  4  5  5  3  4  4 |     GCA  8  8  8  7  6  6 | Glu GAA 11 10 10  9 12 12 |     GGA  3  2  2  2  2  2
    GTG 14 12 12 14 14 14 |     GCG 13 12 12 14 13 13 |     GAG  6  4  4  5  5  5 |     GGG  6  6  6  5  5  5
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.12157    C:0.29020    A:0.18824    G:0.40000
position  2:    T:0.32157    C:0.21961    A:0.24706    G:0.21176
position  3:    T:0.21569    C:0.15294    A:0.23137    G:0.40000

#2: S2457T         
position  1:    T:0.12549    C:0.30196    A:0.18431    G:0.38824
position  2:    T:0.32157    C:0.21961    A:0.24706    G:0.21176
position  3:    T:0.25098    C:0.14510    A:0.21176    G:0.39216

#3: Shig4337       
position  1:    T:0.12549    C:0.30196    A:0.18431    G:0.38824
position  2:    T:0.32157    C:0.21961    A:0.24706    G:0.21176
position  3:    T:0.25098    C:0.14510    A:0.21176    G:0.39216

#4: CFT073         
position  1:    T:0.11765    C:0.30588    A:0.18431    G:0.39216
position  2:    T:0.32549    C:0.21961    A:0.24706    G:0.20784
position  3:    T:0.24314    C:0.14902    A:0.19608    G:0.41176

#5: O157           
position  1:    T:0.12549    C:0.28627    A:0.18824    G:0.40000
position  2:    T:0.32157    C:0.21961    A:0.24706    G:0.21176
position  3:    T:0.23922    C:0.14510    A:0.21176    G:0.40392

#6: EDL933         
position  1:    T:0.12549    C:0.28627    A:0.18824    G:0.40000
position  2:    T:0.32157    C:0.21961    A:0.24706    G:0.21176
position  3:    T:0.23922    C:0.14510    A:0.21176    G:0.40392

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      18 | Ser S TCT      12 | Tyr Y TAT       0 | Cys C TGT       0
      TTC       0 |       TCC       0 |       TAC       6 |       TGC       0
Leu L TTA      48 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG      63 |       TCG      13 |       TAG       0 | Trp W TGG      24
------------------------------------------------------------------------------
Leu L CTT      24 | Pro P CCT       6 | His H CAT      29 | Arg R CGT      39
      CTC      18 |       CCC       6 |       CAC       9 |       CGC      28
      CTA       3 |       CCA      14 | Gln Q CAA      17 |       CGA      32
      CTG     108 |       CCG      35 |       CAG      61 |       CGG      23
------------------------------------------------------------------------------
Ile I ATT      47 | Thr T ACT       9 | Asn N AAT      24 | Ser S AGT       8
      ATC      10 |       ACC      23 |       AAC      18 |       AGC      18
      ATA       0 |       ACA      14 | Lys K AAA      39 | Arg R AGA       8
Met M ATG      36 |       ACG      29 |       AAG       1 |       AGG       1
------------------------------------------------------------------------------
Val V GTT       7 | Ala A GCT      28 | Asp D GAT      68 | Gly G GGT      48
      GTC       6 |       GCC      22 |       GAC      13 |       GGC      48
      GTA      25 |       GCA      43 | Glu E GAA      64 |       GGA      13
      GTG      80 |       GCG      77 |       GAG      29 |       GGG      33
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12353    C:0.29542    A:0.18627    G:0.39477
position  2:    T:0.32222    C:0.21961    A:0.24706    G:0.21111
position  3:    T:0.23987    C:0.14706    A:0.21242    G:0.40065

Codon frequencies under model, for use in evolver:
  0.00978502  0.00599899  0.00866521  0.01634392
  0.00666890  0.00408856  0.00590570  0.01113906
  0.00750251  0.00459963  0.00000000  0.00000000
  0.00641088  0.00393037  0.00000000  0.01070809
  0.02340122  0.01434680  0.02072315  0.03908705
  0.01594891  0.00977794  0.01412369  0.02663945
  0.01794252  0.01100018  0.01588915  0.02996938
  0.01533183  0.00939963  0.01357724  0.02560876
  0.01475519  0.00904610  0.01306659  0.02464560
  0.01005628  0.00616529  0.00890542  0.01679700
  0.01131331  0.00693596  0.01001860  0.01889662
  0.00966720  0.00592676  0.00856087  0.01614712
  0.03127066  0.01917138  0.02769200  0.05223137
  0.02131225  0.01306610  0.01887325  0.03559785
  0.02397629  0.01469936  0.02123241  0.04004758
  0.02048767  0.01256056  0.01814303  0.03422055



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               0.2311 (0.0301 0.1301)
Shig4337             0.2311 (0.0301 0.1301)-1.0000 (0.0000 0.0000)
CFT073               0.1062 (0.0264 0.2484) 0.0657 (0.0144 0.2196) 0.0657 (0.0144 0.2196)
O157                 0.0000 (0.0000 0.0931) 0.2304 (0.0300 0.1304) 0.2304 (0.0300 0.1304) 0.1221 (0.0264 0.2159)
EDL933               0.0000 (0.0000 0.0931) 0.2304 (0.0300 0.1304) 0.2304 (0.0300 0.1304) 0.1221 (0.0264 0.2159)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 83
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1436.028237     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.02246  0.04779  0.20696  0.00000  0.00000  0.00393  0.34828  0.02610  0.00000  0.00000  2.44761  0.90298  0.07745  0.00000 24.20371
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.65553

((1: 0.047791, (2: 0.000004, 3: 0.000004): 0.206958): 0.022465, (4: 0.348281, (5: 0.000004, 6: 0.000004): 0.026097): 0.003925);

((K12: 0.047791, (S2457T: 0.000004, Shig4337: 0.000004): 0.206958): 0.022465, (CFT073: 0.348281, (O157: 0.000004, EDL933: 0.000004): 0.026097): 0.003925);

Detailed output identifying parameters

kappa (ts/tv) =  2.44761


dN/dS for site classes (K=3)

p:   0.90298  0.07745  0.01956
w:   0.00000  1.00000 24.20371

dN & dS for each branch

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

   7..8       0.022    228.6    536.4   0.5509   0.0060   0.0109    2.5    3.2
   8..1       0.048    228.6    536.4   0.5509   0.0128   0.0233    5.3    6.9
   8..9       0.207    228.6    536.4   0.5509   0.0555   0.1007   23.0   29.8
   9..2       0.000    228.6    536.4   0.5509   0.0000   0.0000    0.0    0.0
   9..3       0.000    228.6    536.4   0.5509   0.0000   0.0000    0.0    0.0
   7..10      0.004    228.6    536.4   0.5509   0.0011   0.0019    0.4    0.6
  10..4       0.348    228.6    536.4   0.5509   0.0934   0.1695   38.7   50.1
  10..11      0.026    228.6    536.4   0.5509   0.0070   0.0127    2.9    3.8
  11..5       0.000    228.6    536.4   0.5509   0.0000   0.0000    0.0    0.0
  11..6       0.000    228.6    536.4   0.5509   0.0000   0.0000    0.0    0.0


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

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

   246 E      0.960*        23.283
   249 T      1.000**       24.203
   250 R      0.931         22.603
   251 L      0.887         21.574
   253 K      1.000**       24.202


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

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

   246 E      0.993**       9.244 +- 1.461
   249 T      1.000**       9.302 +- 1.291
   250 R      0.949         8.889 +- 2.227
   251 L      0.965*        9.016 +- 1.979
   253 K      1.000**       9.302 +- 1.292



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:   0.000  0.000  0.000  0.003  0.015  0.045  0.098  0.175  0.274  0.389

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 0.006
 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 0.006 0.988

sum of density on p0-p1 =   1.000000
