seed used = 1024020549 CODONML (in paml version 4.4, January 2010) ../Alignments/alignment.phylip Model: One dN/dS ratio for branches Codon frequency model: 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 Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) Homo_sapie Pan_troglo 0.0000 (0.0000 0.0207) Gorilla_go 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421) Pongo_pygm -1.0000 (0.0000 0.0000) 0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0207) Macaca_mul 0.0000 (0.0000 0.0421) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0640) 0.0000 (0.0000 0.0421) pairwise comparison, codon frequencies: F3x4. 2 (Pan_troglo) ... 1 (Homo_sapie) lnL = -291.465693 0.01262 999.00000 0.00100 t= 0.0126 S= 81.4 N= 140.6 dN/dS= 0.0010 dN= 0.0000 dS= 0.0115 3 (Gorilla_go) ... 1 (Homo_sapie) lnL = -290.441129 0.01265 999.00000 0.00100 t= 0.0127 S= 81.7 N= 140.3 dN/dS= 0.0010 dN= 0.0000 dS= 0.0114 3 (Gorilla_go) ... 2 (Pan_troglo) lnL = -296.416525 0.02582 999.00000 0.00100 t= 0.0258 S= 81.5 N= 140.5 dN/dS= 0.0010 dN= 0.0000 dS= 0.0234 4 (Pongo_pygm) ... 1 (Homo_sapie) lnL = -284.119243 0.00001 0.40000 0.00100 t= 0.0000 S= 40.3 N= 181.7 dN/dS= 0.0010 dN= 0.0000 dS= 0.0000 4 (Pongo_pygm) ... 2 (Pan_troglo) lnL = -291.465693 0.01262 999.00000 0.00100 t= 0.0126 S= 81.4 N= 140.6 dN/dS= 0.0010 dN= 0.0000 dS= 0.0115 4 (Pongo_pygm) ... 3 (Gorilla_go) lnL = -290.441129 0.01265 999.00000 0.00100 t= 0.0127 S= 81.7 N= 140.3 dN/dS= 0.0010 dN= 0.0000 dS= 0.0114 5 (Macaca_mul) ... 1 (Homo_sapie) lnL = -293.362778 0.03141 0.40000 0.00100 t= 0.0314 S= 40.0 N= 182.0 dN/dS= 0.0010 dN= 0.0001 dS= 0.0579 5 (Macaca_mul) ... 2 (Pan_troglo) lnL = -299.336634 0.04352 0.94237 0.00100 t= 0.0435 S= 48.1 N= 173.9 dN/dS= 0.0010 dN= 0.0001 dS= 0.0667 5 (Macaca_mul) ... 3 (Gorilla_go) lnL = -298.374374 0.04359 0.93928 0.00100 t= 0.0436 S= 48.4 N= 173.6 dN/dS= 0.0010 dN= 0.0001 dS= 0.0665 5 (Macaca_mul) ... 4 (Pongo_pygm) lnL = -293.362778 0.03141 0.40000 0.00100 t= 0.0314 S= 40.0 N= 182.0 dN/dS= 0.0010 dN= 0.0001 dS= 0.0579