
seed used = 140018477

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b3296.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 202
# site patterns = 50
    3    9    2   12    1   14    3   18    7    6    3    5    1    3    2
    6    9    3    4    4    3    1    8    4   10    2    6    7    2    3
    3    3    6    4    5    3    3    2    1    1    1    1    1    1    1
    1    1    1    1    1

1       
K12                   TTG GGT CCT AAG CTC CTG AGC CGT GAG GGC ACC GAC TTA TTC CTT TCT GTT CGC GCG ATC GAT TGT AAA ATT GAA CAA GCT CAG CAC CCG TAT GTG AAC TAC GCA GTA ATG GCC ACT CAT AAC AGT AAT CCA ACC TGG ACG TTT GTC TCC 
S2457T                ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... ... ... ... 
Shig4337              ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... CC. ... ... ... ..T ... ... ... ... ... 

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

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

#1: K12            
position  1:    T:0.11881    C:0.27723    A:0.24257    G:0.36139
position  2:    T:0.25743    C:0.17822    A:0.35644    G:0.20792
position  3:    T:0.33663    C:0.22772    A:0.14851    G:0.28713

#2: S2457T         
position  1:    T:0.11881    C:0.27723    A:0.24257    G:0.36139
position  2:    T:0.25743    C:0.17822    A:0.35644    G:0.20792
position  3:    T:0.34158    C:0.22277    A:0.14851    G:0.28713

#3: Shig4337       
position  1:    T:0.11881    C:0.28218    A:0.23762    G:0.36139
position  2:    T:0.25743    C:0.18317    A:0.35149    G:0.20792
position  3:    T:0.34158    C:0.22277    A:0.14851    G:0.28713

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       3 | Ser S TCT      18 | Tyr Y TAT       9 | Cys C TGT       3
      TTC       9 |       TCC       3 |       TAC      12 |       TGC       0
Leu L TTA       3 |       TCA       0 | *** * TAA       0 | *** * TGA       0
      TTG       9 |       TCG       0 |       TAG       0 | Trp W TGG       3
------------------------------------------------------------------------------
Leu L CTT       6 | Pro P CCT       6 | His H CAT       3 | Arg R CGT      54
      CTC       3 |       CCC       1 |       CAC       6 |       CGC       9
      CTA       0 |       CCA       3 | Gln Q CAA       6 |       CGA       0
      CTG      42 |       CCG       9 |       CAG      21 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      12 | Thr T ACT       5 | Asn N AAT       3 | Ser S AGT       3
      ATC      12 |       ACC      10 |       AAC      20 |       AGC       9
      ATA       0 |       ACA       0 | Lys K AAA      24 | Arg R AGA       0
Met M ATG       9 |       ACG       3 |       AAG      36 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      27 | Ala A GCT      18 | Asp D GAT       9 | Gly G GGT      27
      GTC       3 |       GCC       6 |       GAC      15 |       GGC      18
      GTA       9 |       GCA      15 | Glu E GAA      30 |       GGA       0
      GTG       9 |       GCG      12 |       GAG      21 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.11881    C:0.27888    A:0.24092    G:0.36139
position  2:    T:0.25743    C:0.17987    A:0.35479    G:0.20792
position  3:    T:0.33993    C:0.22442    A:0.14851    G:0.28713

Codon frequencies under model, for use in evolver:
  0.01063119  0.00701865  0.00464470  0.00897974
  0.00742820  0.00490406  0.00324533  0.00627431
  0.01465196  0.00967314  0.00000000  0.00000000
  0.00858673  0.00566891  0.00000000  0.00725287
  0.02495377  0.01647433  0.01090213  0.02107746
  0.01743565  0.01151091  0.00761752  0.01472720
  0.03439141  0.02270501  0.01502538  0.02904906
  0.02015497  0.01330619  0.00880557  0.01702410
  0.02155770  0.01423226  0.00941841  0.01820893
  0.01506275  0.00994434  0.00658081  0.01272290
  0.02971093  0.01961498  0.01298050  0.02509564
  0.01741198  0.01149529  0.00760718  0.01470721
  0.03233654  0.02134840  0.01412762  0.02731339
  0.02259412  0.01491651  0.00987122  0.01908436
  0.04456639  0.02942247  0.01947075  0.03764346
  0.02611798  0.01724294  0.01141077  0.02206082



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               0.0000 (0.0000 0.0067)
Shig4337             0.6606 (0.0044 0.0067)-1.0000 (0.0044 0.0000)


TREE #  1:  (1, (2, 3));   MP score: 2
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):   -826.366078     +0.000000
   4..1     4..5     5..2     5..3  
  0.00000  0.00535  0.00000  0.01839  1.76538  0.99462  0.00000  0.00000 228.38527
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.02376

(1: 0.000004, (2: 0.000004, 3: 0.018395): 0.005355);

(K12: 0.000004, (S2457T: 0.000004, Shig4337: 0.018395): 0.005355);

Detailed output identifying parameters

kappa (ts/tv) =  1.76538


dN/dS for site classes (K=3)

p:   0.99462  0.00000  0.00538
w:   0.00000  1.00000228.38527

dN & dS for each branch

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

   4..1       0.000    148.4    457.6   1.2295   0.0000   0.0000    0.0    0.0
   4..5       0.005    148.4    457.6   1.2295   0.0019   0.0015    0.2    0.9
   5..2       0.000    148.4    457.6   1.2295   0.0000   0.0000    0.0    0.0
   5..3       0.018    148.4    457.6   1.2295   0.0064   0.0052    0.8    2.9


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

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

   122 N      1.000**       228.385


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

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

   122 N      0.789         5.022 +- 3.315



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:   0.176  0.149  0.127  0.110  0.096  0.085  0.075  0.067  0.061  0.055
w2:   0.129  0.114  0.104  0.098  0.095  0.093  0.092  0.092  0.092  0.092

Posterior for p0-p1 (see the ternary graph)

 0.015
 0.008 0.014 0.017
 0.004 0.007 0.010 0.016 0.020
 0.003 0.004 0.005 0.008 0.011 0.019 0.022
 0.002 0.002 0.003 0.004 0.006 0.009 0.013 0.021 0.025
 0.001 0.002 0.002 0.003 0.003 0.005 0.007 0.011 0.015 0.025 0.029
 0.001 0.001 0.002 0.002 0.002 0.003 0.004 0.006 0.008 0.012 0.017 0.029 0.033
 0.001 0.001 0.001 0.002 0.002 0.002 0.003 0.004 0.005 0.007 0.009 0.014 0.020 0.034 0.038
 0.001 0.001 0.001 0.001 0.002 0.002 0.002 0.003 0.003 0.004 0.005 0.008 0.010 0.017 0.024 0.039 0.044
 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.002 0.003 0.004 0.005 0.006 0.009 0.012 0.020 0.028 0.046 0.050

sum of density on p0-p1 =   1.000000
