text: 
  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
  