| blob | 2594bf149833d4365a7bec9c65b9bd67f2338915 |
1 CODONML (in paml 3.15, November 2005) test.phy Model: One dN/dS ratio
2 Codon frequencies: F3x4
3 Site-class models:
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 Model 0: one-ratio
89 TREE # 1: (1, 2, 3); MP score: 3
90 lnL(ntime: 3 np: 5): -30.819156 +0.000000
91 4..1 4..2 4..3
92 0.25573 0.00000 0.62424 5.28487 0.09213
94 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
96 tree length = 0.87997
98 (1: 0.255727, 2: 0.000004, 3: 0.624239);
100 (test0: 0.255727, test1: 0.000004, test2: 0.624239);
102 Detailed output identifying parameters
104 kappa (ts/tv) = 5.28487
106 omega (dN/dS) = 0.09213
108 dN & dS for each branch
110 branch t N S dN/dS dN dS N*dN S*dS
112 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
113 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
114 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
116 tree length for dN: 0.07702
117 tree length for dS: 0.83594
120 Time used: 0:00
123 Model 1: NearlyNeutral (2 categories)
126 TREE # 1: (1, 2, 3); MP score: 3
127 lnL(ntime: 3 np: 6): -30.819157 +0.000000
128 4..1 4..2 4..3
129 0.25573 0.00000 0.62424 5.28488 1.00000 0.09213
131 Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site).
133 tree length = 0.87997
135 (1: 0.255727, 2: 0.000004, 3: 0.624240);
137 (test0: 0.255727, test1: 0.000004, test2: 0.624240);
139 Detailed output identifying parameters
141 kappa (ts/tv) = 5.28488
144 dN/dS for site classes (K=2)
146 p: 1.00000 0.00000
147 w: 0.09213 1.00000
149 dN & dS for each branch
151 branch t N S dN/dS dN dS N*dN S*dS
153 4..1 0.256 12.9 5.1 0.0921 0.0224 0.2429 0.3 1.2
154 4..2 0.000 12.9 5.1 0.0921 0.0000 0.0000 0.0 0.0
155 4..3 0.624 12.9 5.1 0.0921 0.0546 0.5930 0.7 3.0
158 Naive Empirical Bayes (NEB) analysis
159 Time used: 0:02