
seed used = 140030265

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b4211.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 6  	ls = 286
# site patterns = 90
    4    7    6    6    2    6   12   13    5    4    1    4    1   11    2
    2   12    6    7    1   12    1    6    4    5    4   10    2    1    1
   15    1    5    5    2    5    1   11    3    4    2    2    1    2    2
    1    1    1    4    1    1    1    1    1    3    3    3    1    2    3
    2    1    2    1    8    1    1    1    1    1    1    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1


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

Codon usage in sequences
--------------------------------------------------------------------------------------------------------------
Phe TTT  4  4  4  4  4  4 | Ser TCT  4  4  4  4  5  5 | Tyr TAT  4  4  4  4  4  4 | Cys TGT  0  0  0  0  0  0
    TTC  1  1  1  1  1  1 |     TCC  3  3  3  4  2  2 |     TAC  5  5  5  5  5  5 |     TGC  0  1  1  0  0  0
Leu TTA  2  2  2  2  2  2 |     TCA  1  1  1  1  1  1 | *** TAA  0  0  0  0  0  0 | *** TGA  0  0  0  0  0  0
    TTG  3  3  3  2  3  3 |     TCG  1  1  1  1  1  1 |     TAG  0  0  0  0  0  0 | Trp TGG  2  2  2  2  2  2
--------------------------------------------------------------------------------------------------------------
Leu CTT  4  4  4  4  5  5 | Pro CCT  1  1  1  2  1  1 | His CAT  3  3  3  3  2  2 | Arg CGT  4  4  4  4  4  4
    CTC  3  3  3  4  3  3 |     CCC  1  1  1  0  1  1 |     CAC  5  4  4  4  5  5 |     CGC  2  2  2  3  2  2
    CTA  2  2  2  2  2  2 |     CCA  1  1  1  1  1  1 | Gln CAA  6  5  5  5  5  5 |     CGA  0  0  0  0  0  0
    CTG 17 17 17 17 16 16 |     CCG  4  4  4  5  4  4 |     CAG  6  7  7  6  8  8 |     CGG  1  1  1  1  1  1
--------------------------------------------------------------------------------------------------------------
Ile ATT  6  7  7  8  6  6 | Thr ACT  2  2  2  2  2  2 | Asn AAT  6  6  6  5  6  6 | Ser AGT  1  1  1  2  1  1
    ATC  8  8  8  7  8  8 |     ACC  6  6  6  5  6  6 |     AAC  3  4  4  4  3  3 |     AGC 13 14 14 12 12 12
    ATA  1  1  1  1  1  1 |     ACA  4  4  4  4  5  5 | Lys AAA 12 12 12 12 13 13 | Arg AGA  0  0  0  0  0  0
Met ATG  4  4  4  4  4  4 |     ACG  6  7  7  7  7  7 |     AAG  2  2  2  2  2  2 |     AGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------
Val GTT  9  8  8  8  9  9 | Ala GCT  7  7  7  8  7  7 | Asp GAT 11 11 11 12 11 11 | Gly GGT  6  7  7  7  6  6
    GTC  1  1  1  1  1  1 |     GCC 16 16 16 15 15 15 |     GAC  4  3  3  4  4  4 |     GGC 16 14 14 15 16 16
    GTA  2  2  2  3  2  2 |     GCA 16 15 15 13 15 15 | Glu GAA 11 11 11 12 11 11 |     GGA  3  3  3  2  3  3
    GTG  6  6  6  6  6  6 |     GCG 10 10 10 11 10 10 |     GAG  4  4  4  3  4  4 |     GGG  0  0  0  0  0  0
--------------------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.10490    C:0.20979    A:0.25874    G:0.42657
position  2:    T:0.25524    C:0.29021    A:0.28671    G:0.16783
position  3:    T:0.25175    C:0.30420    A:0.21329    G:0.23077

#2: S2457T         
position  1:    T:0.10839    C:0.20629    A:0.27273    G:0.41259
position  2:    T:0.25524    C:0.29021    A:0.28322    G:0.17133
position  3:    T:0.25524    C:0.30070    A:0.20629    G:0.23776

#3: Shig4337       
position  1:    T:0.10839    C:0.20629    A:0.27273    G:0.41259
position  2:    T:0.25524    C:0.29021    A:0.28322    G:0.17133
position  3:    T:0.25524    C:0.30070    A:0.20629    G:0.23776

#4: CFT073         
position  1:    T:0.10490    C:0.21329    A:0.26224    G:0.41958
position  2:    T:0.25874    C:0.29021    A:0.28322    G:0.16783
position  3:    T:0.26923    C:0.29371    A:0.20280    G:0.23427

#5: O157           
position  1:    T:0.10490    C:0.20979    A:0.26573    G:0.41958
position  2:    T:0.25524    C:0.29021    A:0.29021    G:0.16434
position  3:    T:0.25524    C:0.29371    A:0.21329    G:0.23776

#6: EDL933         
position  1:    T:0.10490    C:0.20979    A:0.26573    G:0.41958
position  2:    T:0.25524    C:0.29021    A:0.29021    G:0.16434
position  3:    T:0.25524    C:0.29371    A:0.21329    G:0.23776

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT      26 | Tyr Y TAT      24 | Cys C TGT       0
      TTC       6 |       TCC      17 |       TAC      30 |       TGC       2
Leu L TTA      12 |       TCA       6 | *** * TAA       0 | *** * TGA       0
      TTG      17 |       TCG       6 |       TAG       0 | Trp W TGG      12
------------------------------------------------------------------------------
Leu L CTT      26 | Pro P CCT       7 | His H CAT      16 | Arg R CGT      24
      CTC      19 |       CCC       5 |       CAC      27 |       CGC      13
      CTA      12 |       CCA       6 | Gln Q CAA      31 |       CGA       0
      CTG     100 |       CCG      25 |       CAG      42 |       CGG       6
------------------------------------------------------------------------------
Ile I ATT      40 | Thr T ACT      12 | Asn N AAT      35 | Ser S AGT       7
      ATC      47 |       ACC      35 |       AAC      21 |       AGC      77
      ATA       6 |       ACA      26 | Lys K AAA      74 | Arg R AGA       0
Met M ATG      24 |       ACG      41 |       AAG      12 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      51 | Ala A GCT      43 | Asp D GAT      67 | Gly G GGT      39
      GTC       6 |       GCC      93 |       GAC      22 |       GGC      91
      GTA      13 |       GCA      89 | Glu E GAA      67 |       GGA      17
      GTG      36 |       GCG      61 |       GAG      23 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.10606    C:0.20921    A:0.26632    G:0.41841
position  2:    T:0.25583    C:0.29021    A:0.28613    G:0.16783
position  3:    T:0.25699    C:0.29779    A:0.20921    G:0.23601

Codon frequencies under model, for use in evolver:
  0.00709534  0.00822158  0.00577602  0.00651613
  0.00804892  0.00932653  0.00655230  0.00739187
  0.00793579  0.00919544  0.00000000  0.00000000
  0.00465480  0.00539366  0.00000000  0.00427482
  0.01399575  0.01621730  0.01139336  0.01285324
  0.01587673  0.01839684  0.01292459  0.01458067
  0.01565356  0.01813825  0.01274292  0.01437572
  0.00918172  0.01063914  0.00747446  0.00843219
  0.01781631  0.02064430  0.01450353  0.01636192
  0.02021076  0.02341882  0.01645275  0.01856090
  0.01992667  0.02308964  0.01622149  0.01830001
  0.01168815  0.01354341  0.00951484  0.01073402
  0.02799150  0.03243459  0.02278673  0.02570648
  0.03175345  0.03679368  0.02584918  0.02916133
  0.03130712  0.03627650  0.02548584  0.02875143
  0.01836344  0.02127827  0.01494892  0.01686438



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               0.6820 (0.0094 0.0138)
Shig4337             0.6820 (0.0094 0.0138)-1.0000 (0.0000 0.0000)
CFT073               0.1078 (0.0110 0.1024) 0.1787 (0.0174 0.0974) 0.1787 (0.0174 0.0974)
O157                 0.2470 (0.0087 0.0350) 0.4559 (0.0182 0.0399) 0.4559 (0.0182 0.0399) 0.1437 (0.0166 0.1157)
EDL933               0.2470 (0.0087 0.0350) 0.4559 (0.0182 0.0399) 0.4559 (0.0182 0.0399) 0.1437 (0.0166 0.1157)-1.0000 (0.0000 0.0000)


TREE #  1:  ((1, (2, 3)), (4, (5, 6)));   MP score: 44
This is a rooted tree.  Please check!
lnL(ntime: 10  np: 15):  -1398.192570     +0.000000
   7..8     8..1     8..9     9..2     9..3     7..10   10..4    10..11   11..5    11..6  
  0.00481  0.00437  0.02897  0.00000  0.00000  0.00273  0.10565  0.03952  0.00000  0.00000  3.51653  0.98364  0.00000  0.14072 13.96704
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.18605

((1: 0.004367, (2: 0.000004, 3: 0.000004): 0.028967): 0.004806, (4: 0.105648, (5: 0.000004, 6: 0.000004): 0.039515): 0.002728);

((K12: 0.004367, (S2457T: 0.000004, Shig4337: 0.000004): 0.028967): 0.004806, (CFT073: 0.105648, (O157: 0.000004, EDL933: 0.000004): 0.039515): 0.002728);

Detailed output identifying parameters

kappa (ts/tv) =  3.51653


dN/dS for site classes (K=3)

p:   0.98364  0.00000  0.01636
w:   0.14072  1.00000 13.96704

dN & dS for each branch

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

   7..8       0.005    266.0    592.0   0.3669   0.0010   0.0028    0.8    0.6
   8..1       0.004    266.0    592.0   0.3669   0.0009   0.0026    0.7    0.6
   8..9       0.029    266.0    592.0   0.3669   0.0063   0.0171    4.6    3.7
   9..2       0.000    266.0    592.0   0.3669   0.0000   0.0000    0.0    0.0
   9..3       0.000    266.0    592.0   0.3669   0.0000   0.0000    0.0    0.0
   7..10      0.003    266.0    592.0   0.3669   0.0006   0.0016    0.4    0.4
  10..4       0.106    266.0    592.0   0.3669   0.0229   0.0625   16.6   13.6
  10..11      0.040    266.0    592.0   0.3669   0.0086   0.0234    6.2    5.1
  11..5       0.000    266.0    592.0   0.3669   0.0000   0.0000    0.0    0.0
  11..6       0.000    266.0    592.0   0.3669   0.0000   0.0000    0.0    0.0


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

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

   109 T      0.997**       13.923
   176 A      0.935         13.065
   269 H      0.999**       13.959


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

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

    42 A      0.529         4.102 +- 3.754
   109 T      0.964*        7.072 +- 2.488
   176 A      0.868         6.472 +- 3.006
   269 H      0.975*        7.129 +- 2.415



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:   0.714  0.264  0.021  0.001  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.011  0.027  0.055  0.090  0.120  0.139  0.147  0.146  0.138  0.127

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 0.002
 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 0.001 0.031
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.011 0.258
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.007 0.090 0.598

sum of density on p0-p1 =   1.000000
