
seed used = 139996849

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b1125.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 276
# site patterns = 83
    8   13    6    2    6    6    2    6   12   31    1    6   12   11    7
    5    4    1    3    4    6    3    1    5    1    4    5    1    4    7
    7    3    3    1    2    1    3    7    1    1    1    7    1    4    4
    1    5    1    1    1    1    1    2    1    1    1    1    3    1    1
    2    1    2    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1

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



Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT 13 12 12 12 13 13 | Ser TCT  1  1  1  1  1  1 | Tyr TAT  3  4  4  4  4  4 | Cys TGT  1  1  1  1  1  1
    TTC  5  6  6  6  5  5 |     TCC  2  2  2  2  2  2 |     TAC  6  5  5  5  5  5 |     TGC  1  1  1  0  1  1
Leu TTA  2  1  1  1  1  1 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  8  8  8  8  6  6 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  6  6  6  6  6  6
--------------------------------------------------------------------------------------------------------------
Leu CTT  3  2  2  2  2  2 | Pro CCT  0  0  0  2  0  0 | His CAT  0  0  0  0  0  0 | Arg CGT  7  6  6  5  5  5
    CTC  8  9  9  8  8  8 |     CCC  2  2  2  1  3  3 |     CAC  2  2  2  2  2  2 |     CGC  3  4  4  5  5  5
    CTA  1  1  1  2  2  2 |     CCA  4  5  5  4  4  4 | Gln CAA  0  0  0  0  0  0 |     CGA  0  0  0  0  0  0
    CTG 33 34 34 34 35 35 |     CCG  9  8  8  8  8  8 |     CAG  2  2  2  2  2  2 |     CGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Ile ATT 14 14 14 15 15 15 | Thr ACT  3  3  3  2  3  3 | Asn AAT  3  3  3  3  3  3 | Ser AGT  3  3  3  3  3  3
    ATC 13 13 13 12 12 12 |     ACC  6  6  6  7  5  5 |     AAC  6  6  6  6  6  6 |     AGC  4  4  4  6  4  4
    ATA  0  0  0  0  1  1 |     ACA  1  2  2  1  3  3 | Lys AAA  5  5  5  5  5  5 | Arg AGA  0  0  0  0  0  0
Met ATG 12 12 12 12 12 12 |     ACG  5  4  4  5  4  4 |     AAG  7  7  7  7  7  7 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  4  4  4  4  4  4 | Ala GCT  2  1  1  1  1  1 | Asp GAT  4  4  4  6  5  5 | Gly GGT  6  6  6  6  6  6
    GTC  7  6  6  6  6  6 |     GCC  6  7  7  7  8  8 |     GAC  5  5  5  4  5  5 |     GGC  7  7  7  7  7  7
    GTA  2  2  2  2  2  2 |     GCA  1  1  1  1  2  2 | Glu GAA  4  4  4  3  3  3 |     GGA  2  1  1  2  1  1
    GTG  9 10 10 10  9  9 |     GCG  7  7  7  7  7  7 |     GAG  2  2  2  2  2  2 |     GGG  1  2  2  1  2  2
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.18182    C:0.26909    A:0.29818    G:0.25091
position  2:    T:0.48727    C:0.18545    A:0.17818    G:0.14909
position  3:    T:0.24364    C:0.30182    A:0.08364    G:0.37091

#2: S2457T         
position  1:    T:0.17818    C:0.27273    A:0.29818    G:0.25091
position  2:    T:0.48727    C:0.18545    A:0.17818    G:0.14909
position  3:    T:0.23273    C:0.30909    A:0.08364    G:0.37455

#3: Shig4337       
position  1:    T:0.17818    C:0.27273    A:0.29818    G:0.25091
position  2:    T:0.48727    C:0.18545    A:0.17818    G:0.14909
position  3:    T:0.23273    C:0.30909    A:0.08364    G:0.37455

#4: CFT073         
position  1:    T:0.17391    C:0.27174    A:0.30435    G:0.25000
position  2:    T:0.48551    C:0.18478    A:0.17754    G:0.15217
position  3:    T:0.24275    C:0.30435    A:0.07971    G:0.37319

#5: O157           
position  1:    T:0.17029    C:0.27536    A:0.30072    G:0.25362
position  2:    T:0.48188    C:0.19203    A:0.17754    G:0.14855
position  3:    T:0.23913    C:0.30435    A:0.09058    G:0.36594

#6: EDL933         
position  1:    T:0.17029    C:0.27536    A:0.30072    G:0.25362
position  2:    T:0.48188    C:0.19203    A:0.17754    G:0.14855
position  3:    T:0.23913    C:0.30435    A:0.09058    G:0.36594

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      75 | Ser S TCT       6 | Tyr Y TAT      23 | Cys C TGT       6
      TTC      33 |       TCC      12 |       TAC      31 |       TGC       5
Leu L TTA       7 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      44 |       TCG       6 |       TAG       0 | Trp W TGG      36
------------------------------------------------------------------------------
Leu L CTT      13 | Pro P CCT       2 | His H CAT       0 | Arg R CGT      34
      CTC      50 |       CCC      13 |       CAC      12 |       CGC      26
      CTA       9 |       CCA      26 | Gln Q CAA       0 |       CGA       0
      CTG     205 |       CCG      49 |       CAG      12 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      87 | Thr T ACT      17 | Asn N AAT      18 | Ser S AGT      18
      ATC      75 |       ACC      35 |       AAC      36 |       AGC      26
      ATA       2 |       ACA      12 | Lys K AAA      30 | Arg R AGA       0
Met M ATG      72 |       ACG      26 |       AAG      42 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      24 | Ala A GCT       7 | Asp D GAT      28 | Gly G GGT      36
      GTC      37 |       GCC      43 |       GAC      29 |       GGC      42
      GTA      12 |       GCA       8 | Glu E GAA      21 |       GGA       8
      GTG      57 |       GCG      42 |       GAG      12 |       GGG      10
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.17544    C:0.27284    A:0.30006    G:0.25166
position  2:    T:0.48518    C:0.18754    A:0.17786    G:0.14943
position  3:    T:0.23835    C:0.30551    A:0.08530    G:0.37084

Codon frequencies under model, for use in evolver:
  0.02062823  0.02643974  0.00738219  0.03209418
  0.00797351  0.01021985  0.00285346  0.01240548
  0.00756197  0.00969237  0.00000000  0.00000000
  0.00635308  0.00814291  0.00000000  0.00988437
  0.03208046  0.04111836  0.01148057  0.04991199
  0.01240018  0.01589363  0.00443763  0.01929266
  0.01176017  0.01507331  0.00420859  0.01829691
  0.00988014  0.01266363  0.00353579  0.01537190
  0.03528139  0.04522108  0.01262608  0.05489212
  0.01363745  0.01747947  0.00488041  0.02121765
  0.01293358  0.01657730  0.00462851  0.02012255
  0.01086597  0.01392719  0.00388858  0.01690568
  0.02959085  0.03792735  0.01058962  0.04603855
  0.01143786  0.01466020  0.00409324  0.01779545
  0.01084752  0.01390354  0.00388198  0.01687697
  0.00911339  0.01168087  0.00326139  0.01417895



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
S2457T               0.0000 (0.0000 0.0590)
Shig4337             0.0000 (0.0000 0.0590)-1.0000 (0.0000 0.0000)
CFT073               0.0461 (0.0049 0.1065) 0.0709 (0.0049 0.0692) 0.0709 (0.0049 0.0692)
O157                 0.0726 (0.0066 0.0902) 0.1114 (0.0066 0.0588) 0.1114 (0.0066 0.0588) 0.1033 (0.0090 0.0871)
EDL933               0.0726 (0.0066 0.0902) 0.1114 (0.0066 0.0588) 0.1114 (0.0066 0.0588) 0.1033 (0.0090 0.0871)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1299.751013     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.03986  0.12608  0.03637  0.00000  0.00000  0.00000  0.15784  0.14193  0.00000  0.00000  8.21398  0.99273  0.00000  0.06005 199.51307
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.50210

((1: 0.126079, (2: 0.000004, 3: 0.000004): 0.036369): 0.039865, (4: 0.157835, (5: 0.000004, 6: 0.000004): 0.141934): 0.000000);

((K12: 0.126079, (S2457T: 0.000004, Shig4337: 0.000004): 0.036369): 0.039865, (CFT073: 0.157835, (O157: 0.000004, EDL933: 0.000004): 0.141934): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  8.21398


dN/dS for site classes (K=3)

p:   0.99273  0.00000  0.00727
w:   0.06005  1.00000199.51307

dN & dS for each branch

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

   7..8       0.040    253.8    574.2   1.5096   0.0148   0.0098    2.5    8.5
   8..1       0.126    253.8    574.2   1.5096   0.0469   0.0311    7.9   26.9
   8..9       0.036    253.8    574.2   1.5096   0.0135   0.0090    2.3    7.8
   9..2       0.000    253.8    574.2   1.5096   0.0000   0.0000    0.0    0.0
   9..3       0.000    253.8    574.2   1.5096   0.0000   0.0000    0.0    0.0
   7..10      0.000    253.8    574.2   1.5096   0.0000   0.0000    0.0    0.0
  10..4       0.158    253.8    574.2   1.5096   0.0587   0.0389    9.9   33.7
  10..11      0.142    253.8    574.2   1.5096   0.0528   0.0350    8.9   30.3
  11..5       0.000    253.8    574.2   1.5096   0.0000   0.0000    0.0    0.0
  11..6       0.000    253.8    574.2   1.5096   0.0000   0.0000    0.0    0.0


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

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

   273 *      0.989*        197.369
   275 L      0.984*        196.358


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

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

    69 C      0.503         3.667 +- 3.768
   273 *      0.793         5.748 +- 3.576
   275 L      0.885         6.291 +- 3.251
   276 E      0.545         3.983 +- 3.824



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:   0.979  0.021  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.078  0.071  0.075  0.083  0.092  0.101  0.111  0.120  0.129  0.139

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.032
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.019 0.946

sum of density on p0-p1 =   1.000000
