
seed used = 140012693

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


CODONML (in paml 3.14, January 2004)    H:\users\mt269\runpaml\NEWdna80\b2778.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models:  PositiveSelection

ns = 3  	ls = 321
# site patterns = 172
    1    1    1    1    1    1    1    2    1    1    1    2    1    1    1
    2    2    1    1    1    1    1    1    1    1    1    1    1    1    3
    3    1    1    1    1    1    1    2    1    7    2    1    1    1    1
    1    1    7    2    1    1    6    2    2    1    5    1    1    1    1
    5    1    1    1    1    1    1    1    1    5    1    1    2    1    1
    1    1    4    8    1    1    2   13    2    5    5    3    2    7    5
    2    3    4    1    1    1    2    2    2    2    3    2    3    2    1
    1    1    3    1    1    1    1    1    1    1    1    1    6    1    1
    1    2    2    1    1    4    1    3    1    1    3    1    7    5    1
    3    1    1    1    1    1    1    1    1    1    1    1    1    1    1
   14    1    1    1    1    1    1    1    2    1    1    1    2    1    1
    1    1    1    2    2    1    1

K12                                  TTA CCG ATG CCG CCG TCA ATT TAT TTA TCC AGA TTT AAT GAG AAA ATA ATG CGC TTC CTA TTC ACT TTC GTA TGT TCC TTT GTT GCA GCC CAA CCA ACT ATT GTC CCA CAA TTA CAG CAA GTT ACG GAT CTT ACG AGT AGC TTA AAC TCA CAA GAA AAG AAA GAA CTG ACG CAC GAA TCT ATT TTC AAT AAT ACC CAA GTG ATT GCC GTA ATT CCC ACA ACC AAA GAC GAG TAT GCT ACA AGA GTT TTT GAC AAT TGG CGT GGA GAT AAA GGG ATA ATC GTT TCG CGC ACT GTC CGC CAG GGT AAG ACC GGA GAT AGC AAC ATG CCC GCA CAA GAG CTA AAC TTG AAC CTC TCA CAC CCG ACT CCT AGT GCG TCT TCC AGT CAT TAT TAC GCA GTG TTC GGC AGT TGT CGC TGT AGT GGA GTC GCA ATC TAT CTT TTA ATT ACT ATA TTT --- TGT GTA CTT AGA TCT AGA AGC TCC GCT GAT AGC GGC GGA TTT AGC GGC GGG GGT TCT GGA GCA 
Shig4337                             ..G GA. TCA TTA ..C --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... .G. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ..T ... ... T.. ... ... ... ..T ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... T.. .T. ... ... ... ... ... ... G.. ... ... A.. ... ... .C. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... C.. ... ... .C. ... ... ... --- ... ... ... ... ... ... ... ... ... AG. --- --- --- --- --- --- --- --- --- --- ... 
CFT073                               ... ATC T.T ATT .TA --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ... ... ..G TGG ..C CTT CC. .GG CTT ... ..G .A. .T. GC. ..G ..G G.. C.G .GC ... ..G ..C ... A.. ..T G.. .CG ... .G. A.T TCT ... C.A C.. TC. ... ..A ..G C.G GA. ... ACA C.. ..A ..A .GG .C. G.C ..T ... G.A ..G T.C .T. GG. ... ..T ... ... ... ..G ... ... ... ... ... ... ... ... ... ... ... ... A.. ... ..T ... ... ... ... ... ... ... ..C A.. ... .T. ... ... ..C A.. ... T.. .T. ... ... ... ... ... T.. T.. ... ... ... ... ... ... ... ..C ... ... ... ... ... .A. ... ..G .T. ..C A.T ..T A.. G.. ... ... A.. .C. G.. ..C A.. --- ..G ..C .CA .A. ..A ... G.. ..T .G. AG. G.. ... ... ... ... ..A ..T ... ... ..C ..G 



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

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

#1: K12            
position  1:    T:0.27362    C:0.16612    A:0.27687    G:0.28339
position  2:    T:0.32248    C:0.22801    A:0.26384    G:0.18567
position  3:    T:0.35179    C:0.22476    A:0.28990    G:0.13355

#2: Shig4337       
position  1:    T:0.26766    C:0.17100    A:0.27509    G:0.28625
position  2:    T:0.31599    C:0.24164    A:0.27509    G:0.16729
position  3:    T:0.36059    C:0.21190    A:0.29740    G:0.13011

#3: CFT073         
position  1:    T:0.26389    C:0.18056    A:0.25000    G:0.30556
position  2:    T:0.31597    C:0.23264    A:0.24306    G:0.20833
position  3:    T:0.36458    C:0.22917    A:0.24306    G:0.16319

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      49 | Ser S TCT      15 | Tyr Y TAT      18 | Cys C TGT      14
      TTC      27 |       TCC      21 |       TAC       4 |       TGC       1
Leu L TTA      33 |       TCA      24 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       4 |       TAG       0 | Trp W TGG      17
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT       7 | His H CAT      11 | Arg R CGT      10
      CTC       3 |       CCC       5 |       CAC       5 |       CGC      12
      CTA       3 |       CCA       5 | Gln Q CAA      40 |       CGA       0
      CTG      17 |       CCG       7 |       CAG      13 |       CGG       2
------------------------------------------------------------------------------
Ile I ATT      28 | Thr T ACT      18 | Asn N AAT      22 | Ser S AGT      17
      ATC      20 |       ACC      14 |       AAC      10 |       AGC      13
      ATA      14 |       ACA      11 | Lys K AAA      25 | Arg R AGA       8
Met M ATG      12 |       ACG       8 |       AAG      10 |       AGG       1
------------------------------------------------------------------------------
Val V GTT      15 | Ala A GCT      31 | Asp D GAT      29 | Gly G GGT      17
      GTC      13 |       GCC      11 |       GAC       8 |       GGC      25
      GTA      19 |       GCA      17 | Glu E GAA      23 |       GGA      17
      GTG       8 |       GCG       4 |       GAG       7 |       GGG       8
------------------------------------------------------------------------------

(Ambiguity data are not used in the counts.)


Codon position x base (3x4) table, overall

position  1:    T:0.26852    C:0.17245    A:0.26736    G:0.29167
position  2:    T:0.31829    C:0.23380    A:0.26042    G:0.18750
position  3:    T:0.35880    C:0.22222    A:0.27662    G:0.14236

Codon frequencies under model, for use in evolver:
  0.03205024  0.01985047  0.02470970  0.01271671
  0.02354236  0.01458108  0.01815040  0.00934100
  0.02622293  0.01624130  0.00000000  0.00000000
  0.01888051  0.01169373  0.00000000  0.00749130
  0.02058399  0.01274880  0.01586959  0.00816720
  0.01511988  0.00936457  0.01165694  0.00599918
  0.01684145  0.01043083  0.01298421  0.00668225
  0.01212584  0.00751020  0.00934863  0.00481122
  0.03191210  0.01976491  0.02460320  0.01266190
  0.02344089  0.01451823  0.01807217  0.00930074
  0.02610990  0.01617129  0.02012989  0.01035973
  0.01879913  0.01164333  0.01449352  0.00745901
  0.03481320  0.02156172  0.02683985  0.01381298
  0.02557188  0.01583806  0.01971509  0.01014626
  0.02848352  0.01764141  0.02195988  0.01130153
  0.02050814  0.01270181  0.01581111  0.00813710



Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

K12                 
Shig4337             0.6521 (0.0259 0.0397)
CFT073               0.3943 (0.1356 0.3439) 0.4124 (0.1345 0.3261)


TREE #  1:  ((1, 2), 3);   MP score: -1
This is a rooted tree.  Please check!
lnL(ntime:  4  np:  9):  -1844.952010     +0.000000
   4..5     5..1     5..2     4..3  
  1.44085  0.11162  0.18835  1.57281  2.03085  0.56480  0.41814  0.03313 203.48841
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   3.31364

((1: 0.111621, 2: 0.188354): 1.440851, 3: 1.572813);

((K12: 0.111621, Shig4337: 0.188354): 1.440851, CFT073: 1.572813);

Detailed output identifying parameters

kappa (ts/tv) =  2.03085


dN/dS for site classes (K=3)

p:   0.56480  0.41814  0.01706
w:   0.03313  1.00000203.48841

dN & dS for each branch

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

   4..5       1.441    244.3    718.7   3.9084   0.5920   0.1515   37.0  425.5
   5..1       0.112    244.3    718.7   3.9084   0.0459   0.0117    2.9   33.0
   5..2       0.188    244.3    718.7   3.9084   0.0774   0.0198    4.8   55.6
   4..3       1.573    244.3    718.7   3.9084   0.6463   0.1654   40.4  464.5


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

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

     2 P      0.999**       203.386
     3 M      0.998**       203.138
     4 P      1.000**       203.402
    28 V      0.721         147.081


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

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

     2 P      0.997**       9.335 +- 1.411
     3 M      0.987*        9.258 +- 1.626
     4 P      0.980*        9.204 +- 1.757
    28 V      0.837         7.991 +- 3.363
    33 A      0.574         5.708 +- 4.321
    56 Q      0.806         7.716 +- 3.542
    60 E      0.577         5.715 +- 4.295
    69 F      0.675         6.578 +- 4.105
   301 D      0.743         7.188 +- 3.894



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:   0.210  0.380  0.355  0.054  0.001  0.000  0.000  0.000  0.000  0.000
w2:   0.000  0.000  0.002  0.006  0.017  0.041  0.085  0.158  0.268  0.423

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 0.001
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.002 0.042
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.051 0.129
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.124 0.132
 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.004 0.179 0.091
 0.000 0.000 0.000 0.000 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 0.186 0.050

sum of density on p0-p1 =   1.000000
