1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
|
Supplemental results for CODEML (seqf: algn treef: tree)
dN/dS (w) for site classes (K=4)
site class 0 1 2a 2b
proportion 0.93813 0.06187 0.00000 0.00000
background w 0.06076 1.00000 0.06076 1.00000
foreground w 0.06076 1.00000 1.00000 1.00000
Naive Empirical Bayes (NEB) probabilities for 4 classes
(amino acids refer to 1st sequence: Gorilla_gorilla)
1 M 0.96921 0.03079 0.00000 0.00000 ( 1)
2 A 0.94915 0.05085 0.00000 0.00000 ( 1)
3 R 0.97797 0.02203 0.00000 0.00000 ( 1)
4 Y 0.97934 0.02066 0.00000 0.00000 ( 1)
5 R 0.97239 0.02761 0.00000 0.00000 ( 1)
6 C 0.98905 0.01095 0.00000 0.00000 ( 1)
7 C 0.98333 0.01667 0.00000 0.00000 ( 1)
8 R 0.98115 0.01885 0.00000 0.00000 ( 1)
9 S 0.98512 0.01488 0.00000 0.00000 ( 1)
10 Q 0.98131 0.01869 0.00000 0.00000 ( 1)
11 S 0.98512 0.01488 0.00000 0.00000 ( 1)
12 R 0.96886 0.03114 0.00000 0.00000 ( 1)
13 S 0.98512 0.01488 0.00000 0.00000 ( 1)
14 R 0.97239 0.02761 0.00000 0.00000 ( 1)
15 C 0.97638 0.02362 0.00000 0.00000 ( 1)
16 Y 0.97524 0.02476 0.00000 0.00000 ( 1)
17 R 0.97723 0.02277 0.00000 0.00000 ( 1)
18 Q 0.98131 0.01869 0.00000 0.00000 ( 1)
19 S 0.76818 0.23182 0.00000 0.00000 ( 1)
20 R 0.96995 0.03005 0.00000 0.00000 ( 1)
21 S 0.98512 0.01488 0.00000 0.00000 ( 1)
22 R 0.97474 0.02526 0.00000 0.00000 ( 1)
23 C 0.97078 0.02922 0.00000 0.00000 ( 1)
24 Y 0.74652 0.25348 0.00000 0.00000 ( 1)
25 R 0.97723 0.02277 0.00000 0.00000 ( 1)
26 Q 0.98071 0.01929 0.00000 0.00000 ( 1)
27 R 0.97549 0.02451 0.00000 0.00000 ( 1)
28 Q 0.97521 0.02479 0.00000 0.00000 ( 1)
29 S 0.98512 0.01488 0.00000 0.00000 ( 1)
30 Q 0.97802 0.02198 0.00000 0.00000 ( 1)
31 S 0.97876 0.02124 0.00000 0.00000 ( 1)
32 R 0.96995 0.03005 0.00000 0.00000 ( 1)
33 S 0.78537 0.21463 0.00000 0.00000 ( 1)
34 R 0.72010 0.27990 0.00000 0.00000 ( 1)
35 C 0.97867 0.02133 0.00000 0.00000 ( 1)
36 Y 0.97524 0.02476 0.00000 0.00000 ( 1)
37 R 0.97723 0.02277 0.00000 0.00000 ( 1)
38 Q 0.98131 0.01869 0.00000 0.00000 ( 1)
39 S 0.98512 0.01488 0.00000 0.00000 ( 1)
40 Q 0.97812 0.02188 0.00000 0.00000 ( 1)
41 S 0.76818 0.23182 0.00000 0.00000 ( 1)
42 R 0.96995 0.03005 0.00000 0.00000 ( 1)
43 S 0.98512 0.01488 0.00000 0.00000 ( 1)
44 R 0.97474 0.02526 0.00000 0.00000 ( 1)
45 C 0.97078 0.02922 0.00000 0.00000 ( 1)
46 Y 0.97934 0.02066 0.00000 0.00000 ( 1)
47 R 0.97723 0.02277 0.00000 0.00000 ( 1)
48 Q 0.98071 0.01929 0.00000 0.00000 ( 1)
49 R 0.97239 0.02761 0.00000 0.00000 ( 1)
50 Q 0.97521 0.02479 0.00000 0.00000 ( 1)
51 R 0.97239 0.02761 0.00000 0.00000 ( 1)
52 S 0.97540 0.02460 0.00000 0.00000 ( 1)
53 R 0.97551 0.02449 0.00000 0.00000 ( 1)
54 R 0.97239 0.02761 0.00000 0.00000 ( 1)
55 R 0.95266 0.04734 0.00000 0.00000 ( 1)
56 R 0.97797 0.02203 0.00000 0.00000 ( 1)
57 R 0.97187 0.02813 0.00000 0.00000 ( 1)
58 R 0.96616 0.03384 0.00000 0.00000 ( 1)
59 S 0.77337 0.22663 0.00000 0.00000 ( 1)
60 C 0.98905 0.01095 0.00000 0.00000 ( 1)
61 Q 0.98131 0.01869 0.00000 0.00000 ( 1)
62 T 0.95838 0.04162 0.00000 0.00000 ( 1)
63 R 0.96995 0.03005 0.00000 0.00000 ( 1)
64 R 0.97797 0.02203 0.00000 0.00000 ( 1)
65 R 0.97239 0.02761 0.00000 0.00000 ( 1)
66 A 0.94915 0.05085 0.00000 0.00000 ( 1)
67 M 0.96921 0.03079 0.00000 0.00000 ( 1)
68 R 0.97797 0.02203 0.00000 0.00000 ( 1)
69 C 0.98569 0.01431 0.00000 0.00000 ( 1)
70 R 0.98115 0.01885 0.00000 0.00000 ( 1)
71 R 0.98115 0.01885 0.00000 0.00000 ( 1)
72 R 0.97797 0.02203 0.00000 0.00000 ( 1)
73 Y 0.97934 0.02066 0.00000 0.00000 ( 1)
74 R 0.97524 0.02476 0.00000 0.00000 ( 1)
75 L 0.96072 0.03928 0.00000 0.00000 ( 1)
76 R 0.97328 0.02672 0.00000 0.00000 ( 1)
77 R 0.96189 0.03811 0.00000 0.00000 ( 1)
78 R 0.63028 0.36972 0.00000 0.00000 ( 1)
79 R 0.48815 0.51185 0.00000 0.00000 ( 2)
80 P 0.00047 0.99953 0.00000 0.00000 ( 2)
81 Y 0.97211 0.02789 0.00000 0.00000 ( 1)
82 H 0.98099 0.01901 0.00000 0.00000 ( 1)
83 I 0.95719 0.04281 0.00000 0.00000 ( 1)
84 V 0.94612 0.05388 0.00000 0.00000 ( 1)
85 S 0.94623 0.05377 0.00000 0.00000 ( 1)
lnL = -511.919210
Bayes Empirical Bayes (BEB) probabilities for 4 classes (class)
(amino acids refer to 1st sequence: Gorilla_gorilla)
1 M 0.92992 0.04202 0.02666 0.00140 ( 1)
2 A 0.89251 0.06723 0.03729 0.00298 ( 1)
3 R 0.94426 0.03037 0.02437 0.00099 ( 1)
4 Y 0.94908 0.02863 0.02148 0.00081 ( 1)
5 R 0.93423 0.03778 0.02669 0.00129 ( 1)
6 C 0.96697 0.01537 0.01727 0.00039 ( 1)
7 C 0.94935 0.02304 0.02683 0.00077 ( 1)
8 R 0.94993 0.02609 0.02314 0.00083 ( 1)
9 S 0.95796 0.02072 0.02070 0.00061 ( 1)
10 Q 0.95228 0.02595 0.02103 0.00073 ( 1)
11 S 0.95796 0.02072 0.02070 0.00061 ( 1)
12 R 0.92654 0.04232 0.02945 0.00169 ( 1)
13 S 0.95796 0.02072 0.02070 0.00061 ( 1)
14 R 0.93423 0.03778 0.02669 0.00129 ( 1)
15 C 0.93982 0.03245 0.02665 0.00108 ( 1)
16 Y 0.94349 0.03419 0.02135 0.00097 ( 1)
17 R 0.93798 0.03119 0.02965 0.00118 ( 1)
18 Q 0.95228 0.02595 0.02103 0.00073 ( 1)
19 S 0.67821 0.28764 0.02237 0.01178 ( 1)
20 R 0.92829 0.04089 0.02928 0.00154 ( 1)
21 S 0.95796 0.02072 0.02070 0.00061 ( 1)
22 R 0.93929 0.03471 0.02485 0.00116 ( 1)
23 C 0.93229 0.03995 0.02644 0.00133 ( 1)
24 Y 0.66349 0.31280 0.01479 0.00892 ( 1)
25 R 0.93798 0.03119 0.02965 0.00118 ( 1)
26 Q 0.95104 0.02676 0.02143 0.00077 ( 1)
27 R 0.93544 0.03352 0.02975 0.00129 ( 1)
28 Q 0.93985 0.03408 0.02498 0.00109 ( 1)
29 S 0.95796 0.02072 0.02070 0.00061 ( 1)
30 Q 0.94683 0.03041 0.02186 0.00090 ( 1)
31 S 0.94315 0.02924 0.02655 0.00105 ( 1)
32 R 0.92829 0.04089 0.02928 0.00154 ( 1)
33 S 0.70349 0.27337 0.01502 0.00812 ( 1)
34 R 0.63397 0.33661 0.01784 0.01158 ( 1)
35 C 0.94711 0.02950 0.02248 0.00091 ( 1)
36 Y 0.94349 0.03419 0.02135 0.00097 ( 1)
37 R 0.93798 0.03119 0.02965 0.00118 ( 1)
38 Q 0.95228 0.02595 0.02103 0.00073 ( 1)
39 S 0.95796 0.02072 0.02070 0.00061 ( 1)
40 Q 0.94348 0.03016 0.02537 0.00100 ( 1)
41 S 0.67821 0.28764 0.02237 0.01178 ( 1)
42 R 0.92829 0.04089 0.02928 0.00154 ( 1)
43 S 0.95796 0.02072 0.02070 0.00061 ( 1)
44 R 0.93929 0.03471 0.02485 0.00116 ( 1)
45 C 0.93229 0.03995 0.02644 0.00133 ( 1)
46 Y 0.94908 0.02863 0.02148 0.00081 ( 1)
47 R 0.93798 0.03119 0.02965 0.00118 ( 1)
48 Q 0.95104 0.02676 0.02143 0.00077 ( 1)
49 R 0.93423 0.03778 0.02669 0.00129 ( 1)
50 Q 0.93985 0.03408 0.02498 0.00109 ( 1)
51 R 0.93423 0.03778 0.02669 0.00129 ( 1)
52 S 0.94075 0.03386 0.02432 0.00107 ( 1)
53 R 0.94204 0.03373 0.02314 0.00108 ( 1)
54 R 0.93423 0.03778 0.02669 0.00129 ( 1)
55 R 0.90035 0.06302 0.03400 0.00263 ( 1)
56 R 0.94426 0.03037 0.02437 0.00099 ( 1)
57 R 0.92956 0.03828 0.03067 0.00149 ( 1)
58 R 0.90393 0.04491 0.04837 0.00279 ( 1)
59 S 0.69102 0.28575 0.01474 0.00849 ( 1)
60 C 0.96697 0.01537 0.01727 0.00039 ( 1)
61 Q 0.95228 0.02595 0.02103 0.00073 ( 1)
62 T 0.90960 0.05584 0.03237 0.00219 ( 1)
63 R 0.92829 0.04089 0.02928 0.00154 ( 1)
64 R 0.94426 0.03037 0.02437 0.00099 ( 1)
65 R 0.93423 0.03778 0.02669 0.00129 ( 1)
66 A 0.89251 0.06723 0.03729 0.00298 ( 1)
67 M 0.92992 0.04202 0.02666 0.00140 ( 1)
68 R 0.94426 0.03037 0.02437 0.00099 ( 1)
69 C 0.96207 0.02001 0.01740 0.00052 ( 1)
70 R 0.94993 0.02609 0.02314 0.00083 ( 1)
71 R 0.94993 0.02609 0.02314 0.00083 ( 1)
72 R 0.94426 0.03037 0.02437 0.00099 ( 1)
73 Y 0.94908 0.02863 0.02148 0.00081 ( 1)
74 R 0.93780 0.03395 0.02708 0.00118 ( 1)
75 L 0.91397 0.05289 0.03114 0.00201 ( 1)
76 R 0.93543 0.03658 0.02673 0.00125 ( 1)
77 R 0.91493 0.05133 0.03174 0.00200 ( 1)
78 R 0.53868 0.40960 0.03013 0.02159 ( 1)
79 R 0.42890 0.53975 0.01203 0.01932 ( 2)
80 P 0.00131 0.63015 0.04520 0.32334 ( 2)
81 Y 0.93289 0.03812 0.02767 0.00133 ( 1)
82 H 0.94481 0.02619 0.02810 0.00090 ( 1)
83 I 0.90475 0.05715 0.03568 0.00242 ( 1)
84 V 0.88645 0.07084 0.03941 0.00329 ( 1)
85 S 0.88711 0.07075 0.03889 0.00325 ( 1)
|
