| blob | 63ded125ce07ab9a03a1314f0c6266b543c92c3b |
2 seed used = 785596301
5 Data set 1
6 3 141
8 all_s57600 CTC TTC CAC ACC TCC CAC TCC CCC CCC CTC CAC TCC TTC TTC ACC TCC CCT TCC CCC TCC CTC CTT CCC TCC CCC ACC CTC TTC CTT TTC CCC TTC CAC TCC CCC TTC CTC CGC CTC CCC TCC CTC CCC CCC CAC CAC CCC
9 all_s56012 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CTC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC
10 all_c11513 CTC CTC CTC ACC TCC CAC TCC CCC CCC TTC CAC TCC TTC TTC ACC CCC CCC TCC CCC CCC CTC CTC CCC TCC CCC ACC CCC TTC CTC TTC CCC TTC CAC TCC TCC TTC CTC CGC CTC TCC TCC CTC CCC CCC CAC CAC CCC
14 Printing out site pattern counts
17 11 93 P
19 all_s57600 ACC CAC CAC CAC CAC CCC CCC CCC CCC CCC CCC CCT CGC CTC CTC CTC CTC CTC CTC CTT CTT TCC TCC TCC TCC TCC TCC TCC TTC TTC TTC
20 all_s56012 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... ... ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ...
21 all_c11513 ... ... ... ... .T. ... ... ... ... ... T.. ..C ... .C. ... ... ... ... T.. ..C ..C C.. C.. ... ... ... ... ... C.. ... ...
23 3 3 1 1 1 1 5 1 1 1 2 1 1 1 1
24 2 1 1 1 1 1 1 1 1 1 3 1 1 1 5
25 1
27 CODONML (in paml version 4.4, January 2010) /scratch/davepaml17/cluster45_fake.phy
28 Model: One dN/dS ratio for branches Global clock
29 Codon frequency model: F3x4
30 ns = 3 ls = 47
32 Codon usage in sequences
33 --------------------------------------------------------------------------------------------------------------
34 Phe TTT 0 0 0 1 0 0 | Ser TCT 0 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 0 | Cys TGT 0 0 0 0 0 0
35 TTC 7 7 7 7 9 7 | TCC 9 10 8 10 8 9 | TAC 0 0 0 0 0 0 | TGC 0 0 0 0 0 0
36 Leu TTA 0 0 0 0 0 0 | TCA 0 0 0 0 0 0 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
37 TTG 0 0 0 0 0 0 | TCG 0 0 0 0 0 0 | TAG 0 0 0 0 0 0 | Trp TGG 0 0 0 0 0 0
38 --------------------------------------------------------------------------------------------------------------
39 Leu CTT 2 1 1 2 1 0 | Pro CCT 1 0 0 0 0 0 | His CAT 0 0 0 0 0 0 | Arg CGT 0 0 0 0 1 0
40 CTC 7 9 4 6 8 10 | CCC 11 11 19 12 13 12 | CAC 6 5 4 5 4 5 | CGC 1 1 1 0 0 1
41 CTA 0 0 0 0 0 0 | CCA 0 0 0 0 0 0 | Gln CAA 0 0 0 0 0 0 | CGA 0 0 0 0 0 0
42 CTG 0 0 0 0 0 0 | CCG 0 0 0 0 0 0 | CAG 0 0 0 0 0 0 | CGG 0 0 0 0 0 0
43 --------------------------------------------------------------------------------------------------------------
44 Ile ATT 0 0 0 0 0 0 | Thr ACT 0 0 0 0 0 0 | Asn AAT 0 0 0 0 0 0 | Ser AGT 0 0 0 0 0 0
45 ATC 0 0 0 0 0 0 | ACC 3 3 3 4 3 3 | AAC 0 0 0 0 0 0 | AGC 0 0 0 0 0 0
46 ATA 0 0 0 0 0 0 | ACA 0 0 0 0 0 0 | Lys AAA 0 0 0 0 0 0 | Arg AGA 0 0 0 0 0 0
47 Met ATG 0 0 0 0 0 0 | ACG 0 0 0 0 0 0 | AAG 0 0 0 0 0 0 | AGG 0 0 0 0 0 0
48 --------------------------------------------------------------------------------------------------------------
49 Val GTT 0 0 0 0 0 0 | Ala GCT 0 0 0 0 0 0 | Asp GAT 0 0 0 0 0 0 | Gly GGT 0 0 0 0 0 0
50 GTC 0 0 0 0 0 0 | GCC 0 0 0 0 0 0 | GAC 0 0 0 0 0 0 | GGC 0 0 0 0 0 0
51 GTA 0 0 0 0 0 0 | GCA 0 0 0 0 0 0 | Glu GAA 0 0 0 0 0 0 | GGA 0 0 0 0 0 0
52 GTG 0 0 0 0 0 0 | GCG 0 0 0 0 0 0 | GAG 0 0 0 0 0 0 | GGG 0 0 0 0 0 0
53 --------------------------------------------------------------------------------------------------------------
55 --------------------------------------------------------------------------------------------------
56 Phe TTT 0 0 0 0 0 | Ser TCT 0 0 0 0 0 | Tyr TAT 0 0 0 0 0 | Cys TGT 0 0 0 0 0
57 TTC 7 8 9 7 7 | TCC 9 12 9 10 10 | TAC 0 0 0 0 0 | TGC 0 0 0 0 0
58 Leu TTA 0 0 0 0 0 | TCA 0 0 0 0 0 | *** TAA 0 0 0 0 0 | *** TGA 0 0 0 0 0
59 TTG 0 0 0 0 0 | TCG 0 0 0 0 0 | TAG 0 0 0 0 0 | Trp TGG 0 0 0 0 0
60 --------------------------------------------------------------------------------------------------
61 Leu CTT 0 1 1 1 1 | Pro CCT 0 0 1 0 0 | His CAT 0 0 1 0 0 | Arg CGT 0 0 0 0 0
62 CTC 9 8 6 9 9 | CCC 13 8 11 11 11 | CAC 5 5 5 5 5 | CGC 1 1 0 1 1
63 CTA 0 0 0 0 0 | CCA 0 0 0 0 0 | Gln CAA 0 0 0 0 0 | CGA 0 0 0 0 0
64 CTG 0 0 0 0 0 | CCG 0 0 0 0 0 | CAG 0 0 0 0 0 | CGG 0 0 0 0 0
65 --------------------------------------------------------------------------------------------------
66 Ile ATT 0 0 0 0 0 | Thr ACT 0 0 0 0 0 | Asn AAT 0 0 0 0 0 | Ser AGT 0 0 0 0 0
67 ATC 0 0 0 0 0 | ACC 3 4 4 3 3 | AAC 0 0 0 0 0 | AGC 0 0 0 0 0
68 ATA 0 0 0 0 0 | ACA 0 0 0 0 0 | Lys AAA 0 0 0 0 0 | Arg AGA 0 0 0 0 0
69 Met ATG 0 0 0 0 0 | ACG 0 0 0 0 0 | AAG 0 0 0 0 0 | AGG 0 0 0 0 0
70 --------------------------------------------------------------------------------------------------
71 Val GTT 0 0 0 0 0 | Ala GCT 0 0 0 0 0 | Asp GAT 0 0 0 0 0 | Gly GGT 0 0 0 0 0
72 GTC 0 0 0 0 0 | GCC 0 0 0 0 0 | GAC 0 0 0 0 0 | GGC 0 0 0 0 0
73 GTA 0 0 0 0 0 | GCA 0 0 0 0 0 | Glu GAA 0 0 0 0 0 | GGA 0 0 0 0 0
74 GTG 0 0 0 0 0 | GCG 0 0 0 0 0 | GAG 0 0 0 0 0 | GGG 0 0 0 0 0
75 --------------------------------------------------------------------------------------------------
77 Codon position x base (3x4) table for each sequence.
79 #1: all_s57600
80 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
81 position 2: T:0.34043 C:0.51064 A:0.12766 G:0.02128
82 position 3: T:0.06383 C:0.93617 A:0.00000 G:0.00000
83 Average T:0.24823 C:0.68085 A:0.06383 G:0.00709
85 #2: all_s56012
86 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
87 position 2: T:0.36170 C:0.51064 A:0.10638 G:0.02128
88 position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000
89 Average T:0.23404 C:0.70213 A:0.05674 G:0.00709
91 #3: all_c11513
92 position 1: T:0.34043 C:0.59574 A:0.06383 G:0.00000
93 position 2: T:0.34043 C:0.53191 A:0.10638 G:0.02128
94 position 3: T:0.00000 C:1.00000 A:0.00000 G:0.00000
95 Average T:0.22695 C:0.70922 A:0.05674 G:0.00709
97 Sums of codon usage counts
98 ------------------------------------------------------------------------------
99 Phe F TTT 1 | Ser S TCT 0 | Tyr Y TAT 0 | Cys C TGT 0
100 TTC 82 | TCC 104 | TAC 0 | TGC 0
101 Leu L TTA 0 | TCA 0 | *** * TAA 0 | *** * TGA 0
102 TTG 0 | TCG 0 | TAG 0 | Trp W TGG 0
103 ------------------------------------------------------------------------------
104 Leu L CTT 11 | Pro P CCT 2 | His H CAT 1 | Arg R CGT 1
105 CTC 85 | CCC 132 | CAC 54 | CGC 8
106 CTA 0 | CCA 0 | Gln Q CAA 0 | CGA 0
107 CTG 0 | CCG 0 | CAG 0 | CGG 0
108 ------------------------------------------------------------------------------
109 Ile I ATT 0 | Thr T ACT 0 | Asn N AAT 0 | Ser S AGT 0
110 ATC 0 | ACC 36 | AAC 0 | AGC 0
111 ATA 0 | ACA 0 | Lys K AAA 0 | Arg R AGA 0
112 Met M ATG 0 | ACG 0 | AAG 0 | AGG 0
113 ------------------------------------------------------------------------------
114 Val V GTT 0 | Ala A GCT 0 | Asp D GAT 0 | Gly G GGT 0
115 GTC 0 | GCC 0 | GAC 0 | GGC 0
116 GTA 0 | GCA 0 | Glu E GAA 0 | GGA 0
117 GTG 0 | GCG 0 | GAG 0 | GGG 0
118 ------------------------------------------------------------------------------
121 Codon position x base (3x4) table, overall
123 position 1: T:0.36170 C:0.56867 A:0.06963 G:0.00000
124 position 2: T:0.34623 C:0.52998 A:0.10638 G:0.01741
125 position 3: T:0.03095 C:0.96905 A:0.00000 G:0.00000
126 Average T:0.24629 C:0.68923 A:0.05867 G:0.00580
128 Codon frequencies under model, for use in evolver (TTT TTC TTA TTG ... GGG):
129 0.00387564 0.12135585 0.00000000 0.00000000
130 0.00593254 0.18576259 0.00000000 0.00000000
131 0.00119084 0.03728811 0.00000000 0.00000000
132 0.00019486 0.00610169 0.00000000 0.00000000
133 0.00609325 0.19079477 0.00000000 0.00000000
134 0.00932709 0.29205456 0.00000000 0.00000000
135 0.00187223 0.05862409 0.00000000 0.00000000
136 0.00030636 0.00959303 0.00000000 0.00000000
137 0.00074611 0.02336262 0.00000000 0.00000000
138 0.00114209 0.03576178 0.00000000 0.00000000
139 0.00022925 0.00717846 0.00000000 0.00000000
140 0.00003751 0.00117466 0.00000000 0.00000000
141 0.00000000 0.00000000 0.00000000 0.00000000
142 0.00000000 0.00000000 0.00000000 0.00000000
143 0.00000000 0.00000000 0.00000000 0.00000000
144 0.00000000 0.00000000 0.00000000 0.00000000
148 Nei & Gojobori 1986. dN/dS (dN, dS)
149 (Note: This matrix is not used in later ML. analysis.
150 Use runmode = -2 for ML pairwise comparison.)
152 all_s57600
153 all_s56012 0.8758 (0.0717 0.0819)
154 all_c11513 1.0080 (0.0826 0.0819) 0.7616 (0.0199 0.0261)
156 pairwise comparison, codon frequencies: F3x4.
159 2 (all_c56012) ... 1 (all_s57600)
160 lnL = -126.880601
161 0.19045 2.92330 0.10941
163 t= 0.1904 S= 5.8 N= 135.2 dN/dS= 0.1094 dN= 0.0476 dS= 0.4353
166 3 (all_c11513) ... 1 (all_c57600)
167 lnL = -142.636697
168 4.21113 0.72684 0.00175
170 t= 4.2111 S= 4.2 N= 136.8 dN/dS= 0.0018 dN= 0.0789 dS=44.9635
173 3 (all_c11513) ... 2 (all_s56012)
174 lnL = -93.410530
175 0.02176 999.00000 0.13702
177 t= 0.0218 S= 0.0 N= 141.0 dN/dS= 0.1370 dN= 0.0073 dS= nan