| blob | d39f62226261dbd6a960923546b5ea92e2d889f2 |
1 CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio
2 Codon frequencies: F3x4
3 Site-class models: PositiveSelection
4 ns = 3 ls = 6
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.
31 #1: test0
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
36 #2: test1
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
41 #3: test2
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.)
81 test0
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
87 check convergence..
88 lnL(ntime: 3 np: 8): -30.819156 +0.000000
89 4..1 4..2 4..3
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).
94 tree length = 0.87997
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)
141 0.001
142 0.001 0.002 0.003
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