
seed used = 1024008133
CODONML (in paml version 4.1, August 2008)  ../Alignments/alignment.phylip
Model: free dN/dS Ratios for branches for branches
Codon frequencies: F3x4
ns =   5  ls =  74

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

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

#1: Homo_sapie     
position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.17568    C:0.20270    A:0.36486    G:0.25676
Average         T:0.20270    C:0.16216    A:0.36937    G:0.26577

#2: Pan_troglo     
position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.16216    C:0.21622    A:0.36486    G:0.25676
Average         T:0.19820    C:0.16667    A:0.36937    G:0.26577

#3: Gorilla_go     
position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.18919    C:0.18919    A:0.36486    G:0.25676
Average         T:0.20721    C:0.15766    A:0.36937    G:0.26577

#4: Pongo_pygm     
position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.17568    C:0.20270    A:0.36486    G:0.25676
Average         T:0.20270    C:0.16216    A:0.36937    G:0.26577

#5: Macaca_mul     
position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.14865    C:0.21622    A:0.37838    G:0.25676
Average         T:0.19369    C:0.16667    A:0.37387    G:0.26577

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT       0 | Ser S TCT       5 | Tyr Y TAT       1 | Cys C TGT      14
      TTC       5 |       TCC       5 |       TAC       4 |       TGC       1
Leu L TTA       0 |       TCA       5 | *** * TAA       0 | *** * TGA       0
      TTG       5 |       TCG       0 |       TAG       0 | Trp W TGG       0
------------------------------------------------------------------------------
Leu L CTT       0 | Pro P CCT       0 | His H CAT       0 | Arg R CGT       0
      CTC      10 |       CCC       5 |       CAC       0 |       CGC       0
      CTA       5 |       CCA      15 | Gln Q CAA       0 |       CGA       5
      CTG      15 |       CCG       0 |       CAG       5 |       CGG       0
------------------------------------------------------------------------------
Ile I ATT      10 | Thr T ACT       0 | Asn N AAT      10 | Ser S AGT       0
      ATC      10 |       ACC       0 |       AAC       0 |       AGC       0
      ATA       0 |       ACA      10 | Lys K AAA      25 | Arg R AGA      10
Met M ATG      15 |       ACG       0 |       AAG      25 |       AGG       0
------------------------------------------------------------------------------
Val V GTT      13 | Ala A GCT       0 | Asp D GAT      10 | Gly G GGT       0
      GTC       1 |       GCC       0 |       GAC      20 |       GGC      15
      GTA      16 |       GCA       0 | Glu E GAA      40 |       GGA       5
      GTG      10 |       GCG       0 |       GAG      20 |       GGG       0
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.12162    C:0.16216    A:0.31081    G:0.40541
position  2:    T:0.31081    C:0.12162    A:0.43243    G:0.13514
position  3:    T:0.17027    C:0.20541    A:0.36757    G:0.25676
Average         T:0.20090    C:0.16306    A:0.37027    G:0.26577

TREE #  1:  (((1, 2), 3), 4, 5);   MP score: 4
check convergence..
lnL(ntime:  7  np: 15):   -308.032209     +0.000000
   6..7     7..8     8..1     8..2     7..3     6..4     6..5  
 0.000000 0.000000 0.000004 0.013437 0.013431 0.000004 0.027837 1.519279 0.988162 1.002397 0.833797 0.000100 0.000100 0.993571 0.000100

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

tree length =   0.05471

(((1: 0.000004, 2: 0.013437): 0.000000, 3: 0.013431): 0.000000, 4: 0.000004, 5: 0.027837);

(((Homo_sapie: 0.000004, Pan_troglo: 0.013437): 0.000000, Gorilla_go: 0.013431): 0.000000, Pongo_pygm: 0.000004, Macaca_mul: 0.027837);

Detailed output identifying parameters

kappa (ts/tv) =  1.51928

w (dN/dS) for branches:  0.98816 1.00240 0.83380 0.00010 0.00010 0.99357 0.00010

dN & dS for each branch

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

   6..7       0.000    167.7     54.3   0.9882   0.0000   0.0000    0.0    0.0
   7..8       0.000    167.7     54.3   1.0024   0.0000   0.0000    0.0    0.0
   8..1       0.000    167.7     54.3   0.8338   0.0000   0.0000    0.0    0.0
   8..2       0.013    167.7     54.3   0.0001   0.0000   0.0183    0.0    1.0
   7..3       0.013    167.7     54.3   0.0001   0.0000   0.0183    0.0    1.0
   6..4       0.000    167.7     54.3   0.9936   0.0000   0.0000    0.0    0.0
   6..5       0.028    167.7     54.3   0.0001   0.0000   0.0379    0.0    2.1

tree length for dN:      0.00001
tree length for dS:      0.07453

dS tree:
(((Homo_sapie: 0.000002, Pan_troglo: 0.018307): 0.000000, Gorilla_go: 0.018298): 0.000000, Pongo_pygm: 0.000001, Macaca_mul: 0.037926);
dN tree:
(((Homo_sapie: 0.000001, Pan_troglo: 0.000002): 0.000000, Gorilla_go: 0.000002): 0.000000, Pongo_pygm: 0.000001, Macaca_mul: 0.000004);

w ratios as labels for TreeView:
(((Homo_sapie'#2' '#0.8338' : 0.000004, Pan_troglo'#3' '#0.0001' : 0.013437)'#1' '#1.0024' : 0.000000, Gorilla_go'#4' '#0.0001' : 0.013431) '#0.9882' : 0.000000, Pongo_pygm'#5' '#0.9936' : 0.000004, Macaca_mul'#6' '#0.0001' : 0.027837);


Time used:  0:07
