
seed used = 140020645

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3487.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 5  	ls = 355
# site patterns = 113
    5   10    3    2    9    3   19   13    6    1   10    4    1   13    1
    1    1    1    4    7    1    3   21    6    3    1    1    5    7    4
    1   14    4   12    6    7    8    5    1    3    1    1    3   13    1
    2   10    1    5    1    1    5    3    1    2    1    1    1    2    1
    1    1    1    1    1    2    1    1    2    1    1    1    1    1    1
    1    1    2    1    1    1    1    1    5    1    3    2    5    1    2
    2    1    3    1    1    1    2    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1

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

Codon usage in sequences
--------------------------------------------------------------------------------------------------
Phe TTT  3  3  3  4  3 | Ser TCT  2  3  3  3  2 | Tyr TAT  3  3  3  3  3 | Cys TGT  0  0  0  0  0
    TTC  4  4  4  3  4 |     TCC  2  1  1  2  2 |     TAC  0  0  0  0  0 |     TGC  0  0  0  0  0
Leu TTA  2  2  2  1  2 |     TCA  1  1  1  1  1 | *** TAA  0  0  0  0  0 | *** TGA  0  0  0  0  0
    TTG  5  4  4  7  5 |     TCG  3  3  3  2  3 |     TAG  0  0  0  0  0 | Trp TGG  6  6  6  6  6
--------------------------------------------------------------------------------------------------
Leu CTT  1  1  1  2  2 | Pro CCT  2  2  2  1  2 | His CAT  3  3  3  3  3 | Arg CGT  8  7  7  9  6
    CTC  4  5  5  2  5 |     CCC  0  0  0  1  0 |     CAC  0  0  0  0  0 |     CGC 12 12 12 12 14
    CTA  0  0  0  0  0 |     CCA  5  5  5  5  5 | Gln CAA 10 10 10 10 10 |     CGA  4  4  4  3  4
    CTG 23 22 22 22 21 |     CCG  7  7  7  7  7 |     CAG 13 14 14 14 14 |     CGG  6  7  7  6  6
--------------------------------------------------------------------------------------------------
Ile ATT  8  7  7  8  7 | Thr ACT  4  4  4  5  3 | Asn AAT  5  5  5  5  5 | Ser AGT  4  5  5  3  3
    ATC  9  9  9  8 10 |     ACC  8  8  8  7  8 |     AAC  0  0  0  0  0 |     AGC  7  6  6  8  8
    ATA  1  1  1  1  1 |     ACA  0  0  0  0  0 | Lys AAA 12 12 12 12 12 | Arg AGA  0  0  0  0  0
Met ATG  5  5  5  5  5 |     ACG  4  4  4  4  5 |     AAG  4  3  3  3  3 |     AGG  1  1  1  1  1
--------------------------------------------------------------------------------------------------
Val GTT  5  6  6  6  6 | Ala GCT 10  8  8 10  8 | Asp GAT 11 10 10 10 11 | Gly GGT  5  4  4  4  4
    GTC 10 12 12 11 10 |     GCC 18 23 23 17 25 |     GAC  8  9  9  9  8 |     GGC  7  7  7  7  8
    GTA  3  1  1  2  2 |     GCA 10  9  9 15  9 | Glu GAA 24 24 24 23 23 |     GGA  1  1  1  2  1
    GTG 14 14 14 14 13 |     GCG 20 19 19 17 16 |     GAG  4  4  4  5  5 |     GGG  4  5  5  4  5
--------------------------------------------------------------------------------------------------

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

#1: K12            
position  1:    T:0.08732    C:0.27606    A:0.20282    G:0.43380
position  2:    T:0.27324    C:0.27042    A:0.27324    G:0.18310
position  3:    T:0.20845    C:0.25070    A:0.20563    G:0.33521

#2: S2457T         
position  1:    T:0.08451    C:0.27887    A:0.19718    G:0.43944
position  2:    T:0.27042    C:0.27324    A:0.27324    G:0.18310
position  3:    T:0.20000    C:0.27042    A:0.19718    G:0.33239

#3: Shig4337       
position  1:    T:0.08451    C:0.27887    A:0.19718    G:0.43944
position  2:    T:0.27042    C:0.27324    A:0.27324    G:0.18310
position  3:    T:0.20000    C:0.27042    A:0.19718    G:0.33239

#4: CFT073         
position  1:    T:0.09014    C:0.27324    A:0.19718    G:0.43944
position  2:    T:0.27042    C:0.27324    A:0.27324    G:0.18310
position  3:    T:0.21408    C:0.24507    A:0.21127    G:0.32958

#5: O157           
position  1:    T:0.08732    C:0.27887    A:0.20000    G:0.43380
position  2:    T:0.27042    C:0.27042    A:0.27324    G:0.18592
position  3:    T:0.19155    C:0.28732    A:0.19718    G:0.32394

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      16 | Ser S TCT      13 | Tyr Y TAT      15 | Cys C TGT       0
      TTC      19 |       TCC       8 |       TAC       0 |       TGC       0
Leu L TTA       9 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG      25 |       TCG      14 |       TAG       0 | Trp W TGG      30
------------------------------------------------------------------------------
Leu L CTT       7 | Pro P CCT       9 | His H CAT      15 | Arg R CGT      37
      CTC      21 |       CCC       1 |       CAC       0 |       CGC      62
      CTA       0 |       CCA      25 | Gln Q CAA      50 |       CGA      19
      CTG     110 |       CCG      35 |       CAG      69 |       CGG      32
------------------------------------------------------------------------------
Ile I ATT      37 | Thr T ACT      20 | Asn N AAT      25 | Ser S AGT      20
      ATC      45 |       ACC      39 |       AAC       0 |       AGC      35
      ATA       5 |       ACA       0 | Lys K AAA      60 | Arg R AGA       0
Met M ATG      25 |       ACG      21 |       AAG      16 |       AGG       5
------------------------------------------------------------------------------
Val V GTT      29 | Ala A GCT      44 | Asp D GAT      52 | Gly G GGT      21
      GTC      55 |       GCC     106 |       GAC      43 |       GGC      36
      GTA       9 |       GCA      52 | Glu E GAA     118 |       GGA       6
      GTG      69 |       GCG      91 |       GAG      22 |       GGG      23
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.08676    C:0.27718    A:0.19887    G:0.43718
position  2:    T:0.27099    C:0.27211    A:0.27324    G:0.18366
position  3:    T:0.20282    C:0.26479    A:0.20169    G:0.33070

Codon frequencies under model, for use in evolver:
  0.00484513  0.00632558  0.00481821  0.00790025
  0.00486527  0.00635189  0.00483825  0.00793310
  0.00488542  0.00637819  0.00000000  0.00000000
  0.00328381  0.00428719  0.00000000  0.00535443
  0.01547924  0.02020901  0.01539325  0.02523976
  0.01554361  0.02029304  0.01545725  0.02534471
  0.01560797  0.02037707  0.01552126  0.02544966
  0.01049113  0.01369675  0.01043284  0.01710637
  0.01110604  0.01449955  0.01104434  0.01810902
  0.01115222  0.01455984  0.01109026  0.01818432
  0.01119840  0.01462013  0.01113619  0.01825961
  0.00752717  0.00982714  0.00748535  0.01227347
  0.02441441  0.03187437  0.02427878  0.03980906
  0.02451593  0.03200691  0.02437973  0.03997459
  0.02461745  0.03213944  0.02448068  0.04014011
  0.01654698  0.02160301  0.01645506  0.02698078



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               0.0456 (0.0051 0.1119)
Shig4337             0.0456 (0.0051 0.1119)-1.0000 (0.0000 0.0000)
CFT073               0.0311 (0.0051 0.1640) 0.0000 (0.0000 0.1957) 0.0000 (0.0000 0.1957)
O157                 0.0255 (0.0025 0.0997) 0.0612 (0.0051 0.0834) 0.0612 (0.0051 0.0834) 0.0260 (0.0051 0.1962)


TREE #  1:  ((1, (2, 3)), (4, 5));   MP score: 86
This is a rooted tree.  Please check!
lnL(ntime:  8  np: 13):  -1817.575117     +0.000000
   6..7     7..1     7..8     8..2     8..3     6..9     9..4     9..5  
  0.00187  0.05306  0.05547  0.00000  0.00000  0.00085  0.14200  0.04054  2.79487  0.97660  0.02030  0.00000 20.78484
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.29380

((1: 0.053063, (2: 0.000004, 3: 0.000004): 0.055466): 0.001865, (4: 0.142005, 5: 0.040543): 0.000853);

((K12: 0.053063, (S2457T: 0.000004, Shig4337: 0.000004): 0.055466): 0.001865, (CFT073: 0.142005, O157: 0.040543): 0.000853);

Detailed output identifying parameters

kappa (ts/tv) =  2.79487


dN/dS for site classes (K=3)

p:   0.97660  0.02030  0.00310
w:   0.00000  1.00000 20.78484

dN & dS for each branch

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

   6..7       0.002    332.9    732.1   0.0846   0.0001   0.0017    0.6    0.1
   7..1       0.053    332.9    732.1   0.0846   0.0040   0.0477   15.9    3.0
   7..8       0.055    332.9    732.1   0.0846   0.0042   0.0499   16.6    3.1
   8..2       0.000    332.9    732.1   0.0846   0.0000   0.0000    0.0    0.0
   8..3       0.000    332.9    732.1   0.0846   0.0000   0.0000    0.0    0.0
   6..9       0.001    332.9    732.1   0.0846   0.0001   0.0008    0.3    0.0
   9..4       0.142    332.9    732.1   0.0846   0.0108   0.1277   42.5    7.9
   9..5       0.041    332.9    732.1   0.0846   0.0031   0.0364   12.1    2.3


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

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

    15 L      0.997**       20.733


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

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

    15 L      0.964*        5.382 +- 2.969
    21 I      0.668         3.840 +- 3.103



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:   0.153  0.128  0.110  0.099  0.092  0.088  0.085  0.083  0.081  0.080

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 0.000
 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 1.000

sum of density on p0-p1 =   1.000000
