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CODONML (in paml 3.15, November 2005)    test.phy   Model: One dN/dS ratio 
Codon frequencies: F3x4
Site-class models: 
ns =   3  ls =   6

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

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

#1: test0          
position  1:    T:0.33333    C:0.33333    A:0.33333    G:0.00000
position  2:    T:0.50000    C:0.33333    A:0.16667    G:0.00000
position  3:    T:0.50000    C:0.00000    A:0.16667    G:0.33333

#2: test1          
position  1:    T:0.33333    C:0.33333    A:0.33333    G:0.00000
position  2:    T:0.33333    C:0.50000    A:0.16667    G:0.00000
position  3:    T:0.50000    C:0.00000    A:0.16667    G:0.33333

#3: test2          
position  1:    T:0.33333    C:0.33333    A:0.33333    G:0.00000
position  2:    T:0.33333    C:0.50000    A:0.16667    G:0.00000
position  3:    T:0.33333    C:0.33333    A:0.00000    G:0.33333

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


Codon position x base (3x4) table, overall

position  1:    T:0.33333    C:0.33333    A:0.33333    G:0.00000
position  2:    T:0.38889    C:0.44444    A:0.16667    G:0.00000
position  3:    T:0.44444    C:0.11111    A:0.11111    G:0.33333


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.)

test0               
test1               -1.0000 (0.0706 0.0000)
test2                0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745)


Model 0: one-ratio


TREE #  1:  (1, 2, 3);   MP score: 3
lnL(ntime:  3  np:  5):    -30.819156     +0.000000
   4..1     4..2     4..3  
  0.25573  0.00000  0.62424  5.28487  0.09213

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.87997

(1: 0.255727, 2: 0.000004, 3: 0.624239);

(test0: 0.255727, test1: 0.000004, test2: 0.624239);

Detailed output identifying parameters

kappa (ts/tv) =  5.28487

omega (dN/dS) =  0.09213

dN & dS for each branch

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

   4..1       0.256     12.9      5.1   0.0921   0.0224   0.2429    0.3    1.2
   4..2       0.000     12.9      5.1   0.0921   0.0000   0.0000    0.0    0.0
   4..3       0.624     12.9      5.1   0.0921   0.0546   0.5930    0.7    3.0

tree length for dN:      0.07702
tree length for dS:      0.83594


Time used:  0:00


Model 1: NearlyNeutral (2 categories)


TREE #  1:  (1, 2, 3);   MP score: 3
lnL(ntime:  3  np:  6):    -30.819157     +0.000000
   4..1     4..2     4..3  
  0.25573  0.00000  0.62424  5.28488  1.00000  0.09213

Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).

tree length =   0.87997

(1: 0.255727, 2: 0.000004, 3: 0.624240);

(test0: 0.255727, test1: 0.000004, test2: 0.624240);

Detailed output identifying parameters

kappa (ts/tv) =  5.28488


dN/dS for site classes (K=2)

p:   1.00000  0.00000
w:   0.09213  1.00000

dN & dS for each branch

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

   4..1       0.256     12.9      5.1   0.0921   0.0224   0.2429    0.3    1.2
   4..2       0.000     12.9      5.1   0.0921   0.0000   0.0000    0.0    0.0
   4..3       0.624     12.9      5.1   0.0921   0.0546   0.5930    0.7    3.0


Naive Empirical Bayes (NEB) analysis
Time used:  0:02