1
CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio
2
Codon frequencies: F3x4
3
Site-class models: PositiveSelection
6
Codon usage in sequences
7
--------------------------------------------------------------------------
8
Phe TTT 1 1 1 | Ser TCT 1 1 0 | Tyr TAT 0 0 0 | Cys TGT 0 0 0
9
TTC 0 0 0 | TCC 0 0 1 | TAC 0 0 0 | TGC 0 0 0
10
Leu TTA 0 0 0 | TCA 0 0 0 | *** TAA 0 0 0 | *** TGA 0 0 0
11
TTG 0 0 0 | TCG 0 0 0 | TAG 0 0 0 | Trp TGG 0 0 0
12
--------------------------------------------------------------------------
13
Leu CTT 0 0 0 | Pro CCT 0 0 0 | His CAT 1 1 1 | Arg CGT 0 0 0
14
CTC 0 0 0 | CCC 0 0 1 | CAC 0 0 0 | CGC 0 0 0
15
CTA 0 0 0 | CCA 1 1 0 | Gln CAA 0 0 0 | CGA 0 0 0
16
CTG 0 0 0 | CCG 0 0 0 | CAG 0 0 0 | CGG 0 0 0
17
--------------------------------------------------------------------------
18
Ile ATT 0 0 0 | Thr ACT 0 0 0 | Asn AAT 0 0 0 | Ser AGT 0 0 0
19
ATC 0 0 0 | ACC 0 0 0 | AAC 0 0 0 | AGC 0 0 0
20
ATA 0 0 0 | ACA 0 0 0 | Lys AAA 0 0 0 | Arg AGA 0 0 0
21
Met ATG 2 1 1 | ACG 0 1 1 | AAG 0 0 0 | AGG 0 0 0
22
--------------------------------------------------------------------------
23
Val GTT 0 0 0 | Ala GCT 0 0 0 | Asp GAT 0 0 0 | Gly GGT 0 0 0
24
GTC 0 0 0 | GCC 0 0 0 | GAC 0 0 0 | GGC 0 0 0
25
GTA 0 0 0 | GCA 0 0 0 | Glu GAA 0 0 0 | GGA 0 0 0
26
GTG 0 0 0 | GCG 0 0 0 | GAG 0 0 0 | GGG 0 0 0
27
--------------------------------------------------------------------------
29
Codon position x base (3x4) table for each sequence.
32
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
33
position 2: T:0.50000 C:0.33333 A:0.16667 G:0.00000
34
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
37
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
38
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
39
position 3: T:0.50000 C:0.00000 A:0.16667 G:0.33333
42
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
43
position 2: T:0.33333 C:0.50000 A:0.16667 G:0.00000
44
position 3: T:0.33333 C:0.33333 A:0.00000 G:0.33333
46
Sums of codon usage counts
47
------------------------------------------------------------------------------
48
Phe F TTT 3 | Ser S TCT 2 | Tyr Y TAT 0 | Cys C TGT 0
49
TTC 0 | TCC 1 | TAC 0 | TGC 0
50
Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
51
TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0
52
------------------------------------------------------------------------------
53
Leu L CTT 0 | Pro P CCT 0 | His H CAT 3 | Arg R CGT 0
54
CTC 0 | CCC 1 | CAC 0 | CGC 0
55
CTA 0 | CCA 2 | Gln Q CAA 0 | CGA 0
56
CTG 0 | CCG 0 | CAG 0 | CGG 0
57
------------------------------------------------------------------------------
58
Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0
59
ATC 0 | ACC 0 | AAC 0 | AGC 0
60
ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0
61
Met M ATG 4 | ACG 2 | AAG 0 | AGG 0
62
------------------------------------------------------------------------------
63
Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
64
GTC 0 | GCC 0 | GAC 0 | GGC 0
65
GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0
66
GTG 0 | GCG 0 | GAG 0 | GGG 0
67
------------------------------------------------------------------------------
70
Codon position x base (3x4) table, overall
72
position 1: T:0.33333 C:0.33333 A:0.33333 G:0.00000
73
position 2: T:0.38889 C:0.44444 A:0.16667 G:0.00000
74
position 3: T:0.44444 C:0.11111 A:0.11111 G:0.33333
77
Nei & Gojobori 1986. dN/dS (dN, dS)
78
(Note: This matrix is not used in later m.l. analysis.
79
Use runmode = -2 for ML pairwise comparison.)
82
test1 -1.0000 (0.0706 0.0000)
83
test2 0.0510 (0.0706 1.3844) 0.0000 (0.0000 0.9745)
86
TREE # 1: (1, 2, 3); MP score: 3
88
lnL(ntime: 3 np: 8): -30.819156 +0.000000
90
0.25573 0.00000 0.62424 5.28487 1.00000 0.00000 0.09213 1.00000
92
Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
96
(1: 0.255727, 2: 0.000004, 3: 0.624239);
98
(test0: 0.255727, test1: 0.000004, test2: 0.624239);
100
Detailed output identifying parameters
102
kappa (ts/tv) = 5.28487
105
dN/dS for site classes (K=3)
107
p: 1.00000 0.00000 0.00000
108
w: 0.09213 1.00000 1.00000
110
dN & dS for each branch
112
branch t N S dN/dS dN dS N*dN S*dS
114
4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
115
4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
116
4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
119
Naive Empirical Bayes (NEB) analysis
120
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
121
Positively selected sites (*: P>95%; **: P>99%)
123
Pr(w>1) post mean +- SE for w
128
The grid (see ternary graph for p0-p1)
130
w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950
131
w2: 1.500 2.500 3.500 4.500 5.500 6.500 7.500 8.500 9.500 10.500
134
Posterior on the grid
136
w0: 0.402 0.260 0.147 0.081 0.045 0.026 0.016 0.010 0.007 0.005
137
w2: 0.138 0.114 0.104 0.098 0.095 0.093 0.091 0.090 0.089 0.088
139
Posterior for p0-p1 (see the ternary graph)
143
0.001 0.001 0.002 0.003 0.006
144
0.000 0.001 0.001 0.002 0.004 0.006 0.010
145
0.000 0.000 0.001 0.001 0.003 0.004 0.007 0.011 0.016
146
0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.008 0.012 0.017 0.025
147
0.000 0.000 0.000 0.001 0.001 0.002 0.004 0.006 0.009 0.013 0.019 0.026 0.036
148
0.000 0.000 0.000 0.000 0.001 0.001 0.003 0.004 0.006 0.009 0.014 0.019 0.027 0.037 0.049
149
0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.014 0.020 0.028 0.037 0.049 0.063
150
0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.002 0.003 0.005 0.007 0.010 0.015 0.020 0.027 0.036 0.046 0.061 0.075
152
sum of density on p0-p1 = 1.000000