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CODONML (in paml version 4.5, December 2011) ../Alignments/alignment.phylip
Model: several dN/dS ratios for branches for branches
Codon frequency model: F3x4
Site-class models: PositiveSelection
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)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4
lnL(ntime: 7 np: 12): -308.031579 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.013438 0.013431 0.000004 0.027839 1.518252 1.000000 0.000000 0.000001 21.844874
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
tree length = 0.05472
(((1: 0.000004, 2: 0.013438): 0.000004, 3: 0.013431): 0.000004, 4: 0.000004, 5: 0.027839);
(((Homo_sapie: 0.000004, Pan_troglo: 0.013438): 0.000004, Gorilla_go: 0.013431): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.027839);
Detailed output identifying parameters
kappa (ts/tv) = 1.51825
dN/dS (w) for site classes (K=4)
site class 0 1 2a 2b
proportion 1.00000 0.00000 0.00000 0.00000
background w 0.00000 1.00000 0.00000 1.00000
foreground w 0.00000 1.00000 21.84487 21.84487
(note that p[2] is zero)
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positive sites for foreground lineages Prob(w>1):
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: 0.668 0.219 0.073 0.025 0.009 0.003 0.001 0.001 0.000 0.000
w2: 0.267 0.167 0.122 0.096 0.079 0.068 0.059 0.052 0.047 0.043
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 0.001
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.005
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.005 0.016
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.002 0.003 0.007 0.015 0.047
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.002 0.005 0.009 0.021 0.046 0.136
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.006 0.008 0.018 0.028 0.064 0.136 0.396
sum of density on p0-p1 = 1.000000
Time used: 0:16
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