
seed used = 139995089

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b0941.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 327
# site patterns = 93
    3    9    3    3    6    3    7    9    6    7    1    9    2    4    7
    9    2    5    4    2    2    9    1    6    4    3    1    3    9    5
    9   10   11    6    1    1    7    2    1    2    6    7    2   10    5
    2    4    6    3    5    4    3    4    2    3    8    4    1    1    1
    1    8    3    1    5    1    1    3    1    1    1    1    1    1    1
    1    2    1    1    2    1    1    1    1    2    1    2    1    1    1
    1    1    1

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

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

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

#1: K12            
position  1:    T:0.20795    C:0.16208    A:0.25994    G:0.37003
position  2:    T:0.26606    C:0.25688    A:0.26300    G:0.21407
position  3:    T:0.32722    C:0.25076    A:0.22018    G:0.20183

#2: S2457T         
position  1:    T:0.20183    C:0.17431    A:0.25382    G:0.37003
position  2:    T:0.27523    C:0.25076    A:0.26606    G:0.20795
position  3:    T:0.33945    C:0.24771    A:0.21101    G:0.20183

#3: Shig4337       
position  1:    T:0.20183    C:0.17431    A:0.25382    G:0.37003
position  2:    T:0.27523    C:0.25076    A:0.26606    G:0.20795
position  3:    T:0.33945    C:0.24771    A:0.21101    G:0.20183

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      24 | Ser S TCT       9 | Tyr Y TAT      28 | Cys C TGT      12
      TTC      11 |       TCC      15 |       TAC       9 |       TGC      18
Leu L TTA      32 |       TCA      15 | *** * TAA       0 | *** * TGA       0
      TTG       6 |       TCG       6 |       TAG       0 | Trp W TGG      15
------------------------------------------------------------------------------
Leu L CTT      12 | Pro P CCT      25 | His H CAT       9 | Arg R CGT       9
      CTC       3 |       CCC      11 |       CAC       2 |       CGC       2
      CTA      10 |       CCA       1 | Gln Q CAA       6 |       CGA      13
      CTG      20 |       CCG      17 |       CAG      27 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      28 | Thr T ACT      16 | Asn N AAT      31 | Ser S AGT      12
      ATC      13 |       ACC      11 |       AAC      27 |       AGC      16
      ATA       9 |       ACA      16 | Lys K AAA      28 | Arg R AGA       6
Met M ATG       9 |       ACG      21 |       AAG       5 |       AGG       3
------------------------------------------------------------------------------
Val V GTT      33 | Ala A GCT      19 | Asp D GAT      35 | Gly G GGT      27
      GTC      28 |       GCC      22 |       GAC      21 |       GGC      35
      GTA       8 |       GCA      25 | Glu E GAA      28 |       GGA      13
      GTG      21 |       GCG      19 |       GAG       4 |       GGG      25
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.20387    C:0.17023    A:0.25586    G:0.37003
position  2:    T:0.27217    C:0.25280    A:0.26504    G:0.20999
position  3:    T:0.33537    C:0.24873    A:0.21407    G:0.20183

Codon frequencies under model, for use in evolver:
  0.01921729  0.01425233  0.01226635  0.01156542
  0.01784976  0.01323812  0.01139347  0.01074241
  0.01871346  0.01387868  0.00000000  0.00000000
  0.01482682  0.01099618  0.00000000  0.00892313
  0.01604643  0.01190070  0.01024240  0.00965712
  0.01490455  0.01105383  0.00951354  0.00896991
  0.01562574  0.01158870  0.00997388  0.00940394
  0.01238040  0.00918181  0.00790238  0.00745082
  0.02411769  0.01788668  0.01539427  0.01451460
  0.02240145  0.01661384  0.01429880  0.01348173
  0.02348540  0.01741774  0.01499068  0.01413407
  0.01860766  0.01380021  0.01187723  0.01119853
  0.03487938  0.02586799  0.02226343  0.02099124
  0.03239732  0.02402719  0.02067914  0.01949748
  0.03396493  0.02518980  0.02167975  0.02044090
  0.02691068  0.01995807  0.01717703  0.01619548



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               0.1007 (0.0165 0.1636)
Shig4337             0.1007 (0.0165 0.1636)-1.0000 (0.0000 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 43
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1530.903509     +0.000000
   4..1     4..5     5..2     5..3  
  0.28531  0.00000  0.00000  0.00000  3.05244  0.98726  0.00011  0.06721 39.96475
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.28532

(1: 0.285314, (2: 0.000004, 3: 0.000004): 0.000000);

(K12: 0.285314, (S2457T: 0.000004, Shig4337: 0.000004): 0.000000);

Detailed output identifying parameters

kappa (ts/tv) =  3.05244


dN/dS for site classes (K=3)

p:   0.98726  0.00011  0.01264
w:   0.06721  1.00000 39.96475

dN & dS for each branch

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

   4..1       0.285    281.5    699.5   0.5714   0.0783   0.1370   38.5   54.7
   4..5       0.000    281.5    699.5   0.5714   0.0000   0.0000    0.0    0.0
   5..2       0.000    281.5    699.5   0.5714   0.0000   0.0000    0.0    0.0
   5..3       0.000    281.5    699.5   0.5714   0.0000   0.0000    0.0    0.0


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

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

   139 G      0.518         20.738
   326 A      1.000**       39.946
   327 R      0.984*        39.323


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

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

    11 S      0.503         3.858 +- 3.844
   139 G      0.548         4.215 +- 3.899
   280 T      0.556         4.263 +- 3.892
   326 A      0.956*        6.988 +- 2.733
   327 R      0.921         6.769 +- 2.915



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:   0.991  0.009  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.028  0.046  0.067  0.086  0.102  0.115  0.126  0.136  0.144  0.151

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 0.023
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.015 0.961

sum of density on p0-p1 =   1.000000
