
seed used = 140014277

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2921.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 4  	ls = 298
# site patterns = 95
    9    2   14   11    2    8    2    4   13    4    3    5    7    5    7
    2    4   12   10    6    5    1    1    1    4   11    5   11    2    9
    3    1    8    7    5    1    4    3    4    3    1    5    4    1    5
    2    1    2    1    1    1    3    2    1    2    6    1    1    1    1
    1    1    1    1    1    2    2    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1

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

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

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

#1: K12            
position  1:    T:0.15436    C:0.28188    A:0.30201    G:0.26174
position  2:    T:0.30872    C:0.19799    A:0.33893    G:0.15436
position  3:    T:0.34228    C:0.19799    A:0.21141    G:0.24832

#2: S2457T         
position  1:    T:0.16443    C:0.26846    A:0.31544    G:0.25168
position  2:    T:0.32550    C:0.19799    A:0.32550    G:0.15101
position  3:    T:0.32886    C:0.21141    A:0.20805    G:0.25168

#3: Shig4337       
position  1:    T:0.16443    C:0.26846    A:0.31544    G:0.25168
position  2:    T:0.32550    C:0.19799    A:0.32550    G:0.15101
position  3:    T:0.32886    C:0.21141    A:0.20805    G:0.25168

#4: CFT073         
position  1:    T:0.15436    C:0.28188    A:0.30201    G:0.26174
position  2:    T:0.30872    C:0.19463    A:0.34228    G:0.15436
position  3:    T:0.34228    C:0.19799    A:0.21141    G:0.24832

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      45 | Ser S TCT      12 | Tyr Y TAT      48 | Cys C TGT       4
      TTC      21 |       TCC       4 |       TAC       4 |       TGC       0
Leu L TTA      15 |       TCA      12 | *** * TAA       0 | *** * TGA       0
      TTG       9 |       TCG       8 |       TAG       0 | Trp W TGG       8
------------------------------------------------------------------------------
Leu L CTT      18 | Pro P CCT       4 | His H CAT      28 | Arg R CGT      28
      CTC      12 |       CCC      10 |       CAC       4 |       CGC      20
      CTA      10 |       CCA      16 | Gln Q CAA      33 |       CGA      25
      CTG      46 |       CCG      29 |       CAG      35 |       CGG      10
------------------------------------------------------------------------------
Ile I ATT      66 | Thr T ACT       8 | Asn N AAT      54 | Ser S AGT      13
      ATC      44 |       ACC      23 |       AAC      19 |       AGC      18
      ATA       8 |       ACA       4 | Lys K AAA      32 | Arg R AGA       4
Met M ATG      38 |       ACG      23 |       AAG      10 |       AGG       4
------------------------------------------------------------------------------
Val V GTT      20 | Ala A GCT       9 | Asp D GAT      38 | Gly G GGT       5
      GTC       0 |       GCC      32 |       GAC      12 |       GGC      21
      GTA       4 |       GCA      18 | Glu E GAA      56 |       GGA      13
      GTG      22 |       GCG      23 |       GAG      24 |       GGG       9
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.15940    C:0.27517    A:0.30872    G:0.25671
position  2:    T:0.31711    C:0.19715    A:0.33305    G:0.15268
position  3:    T:0.33557    C:0.20470    A:0.20973    G:0.25000

Codon frequencies under model, for use in evolver:
  0.01747776  0.01066143  0.01092360  0.01302093
  0.01086580  0.00662814  0.00679113  0.00809502
  0.01835627  0.01119732  0.00000000  0.00000000
  0.00841522  0.00513328  0.00000000  0.00626934
  0.03017213  0.01840500  0.01885758  0.02247823
  0.01875780  0.01144226  0.01172363  0.01397456
  0.03168871  0.01933012  0.01980545  0.02360809
  0.01452732  0.00886167  0.00907958  0.01082285
  0.03385165  0.02064951  0.02115728  0.02521948
  0.02104534  0.01283766  0.01315334  0.01567878
  0.03555319  0.02168745  0.02222075  0.02648713
  0.01629894  0.00994236  0.01018684  0.01214271
  0.02814839  0.01717052  0.01759274  0.02097055
  0.01749966  0.01067479  0.01093729  0.01303725
  0.02956325  0.01803358  0.01847703  0.02202462
  0.01355293  0.00826729  0.00847058  0.01009693



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               0.3344 (0.0353 0.1054)
Shig4337             0.3344 (0.0353 0.1054)-1.0000 (0.0000 0.0000)
CFT073               0.0743 (0.0073 0.0983) 0.3386 (0.0414 0.1222) 0.3386 (0.0414 0.1222)


TREE #  1:  ((1, (2, 3)), 4);   MP score: 42
This is a rooted tree.  Please check!
lnL(ntime:  6  np: 11):  -1502.430836     +0.000000
   5..6     6..1     6..7     7..2     7..3     5..4  
  0.03629  0.03322  0.16702  0.00000  0.00000  0.02398  1.21779  0.93224  0.00000  0.00000  6.29360
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.26052

((1: 0.033220, (2: 0.000004, 3: 0.000004): 0.167018): 0.036292, 4: 0.023979);

((K12: 0.033220, (S2457T: 0.000004, Shig4337: 0.000004): 0.167018): 0.036292, CFT073: 0.023979);

Detailed output identifying parameters

kappa (ts/tv) =  1.21779


dN/dS for site classes (K=3)

p:   0.93224  0.00000  0.06776
w:   0.00000  1.00000  6.29360

dN & dS for each branch

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

   5..6       0.036    207.7    686.3   0.4265   0.0092   0.0216    4.5    6.3
   6..1       0.033    207.7    686.3   0.4265   0.0084   0.0198    4.1    5.8
   6..7       0.167    207.7    686.3   0.4265   0.0424   0.0995   20.7   29.1
   7..2       0.000    207.7    686.3   0.4265   0.0000   0.0000    0.0    0.0
   7..3       0.000    207.7    686.3   0.4265   0.0000   0.0000    0.0    0.0
   5..4       0.024    207.7    686.3   0.4265   0.0061   0.0143    3.0    4.2


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

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

    34 P      1.000**       6.294
    94 E      1.000**       6.294
   130 E      1.000**       6.294
   234 A      1.000**       6.294
   285 M      1.000**       6.293
   286 L      1.000**       6.294
   287 Q      1.000**       6.294
   288 H      1.000**       6.294
   289 I      1.000**       6.294
   290 A      1.000**       6.294
   291 E      1.000**       6.294
   292 D      1.000**       6.294
   293 R      1.000**       6.294
   294 D      1.000**       6.294
   296 T      1.000**       6.294
   297 S      1.000**       6.294
   298 H      1.000**       6.294


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

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

   287 Q      0.980*        8.331 +- 1.933
   288 H      0.950*        8.114 +- 2.282
   289 I      0.808         7.000 +- 3.323
   290 A      0.938         8.030 +- 2.409
   292 D      0.895         7.700 +- 2.785
   293 R      0.952*        8.132 +- 2.269
   294 D      0.978*        8.317 +- 1.959
   296 T      0.928         7.950 +- 2.506
   297 S      0.931         7.978 +- 2.478
   298 H      0.803         6.972 +- 3.336



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:   0.994  0.006  0.000  0.000  0.000  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.001  0.005  0.021  0.057  0.111  0.166  0.205  0.220  0.214

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 0.001 0.039
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.143 0.816

sum of density on p0-p1 =   1.000000
