| blob | 5a8b1201e60bab842313f19e19908f10f3dce091 |
2 P A U P *
3 Portable version 4.0b10 for Unix
4 Mon Aug 4 19:13:12 2014
6 -----------------------------NOTICE-----------------------------
7 This is a beta-test version. Please report any crashes,
8 apparent calculation errors, or other anomalous results.
9 There are no restrictions on publication of results obtained
10 with this version, but you should check the WWW site
11 frequently for bug announcements and/or updated versions.
12 See the README file on the distribution media for details.
13 ----------------------------------------------------------------
15 Processing of file "/share/users/miaolin/DistMCMC/test.nex" begins...
17 Data read in DNA format
19 Data matrix has 8 taxa, 1140 characters
20 Valid character-state symbols: ACGT
21 Missing data identified by '?'
22 Gaps identified by '-'
23 "Equate" macros in effect:
24 R,r ==> {AG}
25 Y,y ==> {CT}
26 M,m ==> {AC}
27 K,k ==> {GT}
28 S,s ==> {CG}
29 W,w ==> {AT}
30 H,h ==> {ACT}
31 B,b ==> {CGT}
32 V,v ==> {ACG}
33 D,d ==> {AGT}
34 N,n ==> {ACGT}
36 Optimality criterion set to distance.
38 Jukes-Cantor distance matrix
40 1 2 3 4 5 6 7
41 1 NC 003426 -
42 2 NC 003427 0.12060 -
43 3 NC 003428 0.11342 0.02316 -
44 4 NC 009331 0.09230 0.09528 0.09130 -
45 5 NC 009968 0.10430 0.09130 0.08932 0.09031 -
46 6 NC 009970 0.11649 0.09230 0.08440 0.09627 0.10027 -
47 7 NC 011117 0.09528 0.09827 0.09627 0.00971 0.09329 0.09927 -
48 8 NC 011118 0.09927 0.10430 0.10228 0.01149 0.09927 0.10329 0.01060
50 Jukes-Cantor distance matrix (continued)
52 8
53 8 NC 011118 -
55 Kimura 2-parameter distance matrix
57 1 2 3 4 5 6 7
58 1 NC 003426 -
59 2 NC 003427 0.12542 -
60 3 NC 003428 0.11763 0.02330 -
61 4 NC 009331 0.09503 0.09830 0.09406 -
62 5 NC 009968 0.10778 0.09398 0.09187 0.09301 -
63 6 NC 009970 0.12073 0.09503 0.08665 0.09919 0.10337 -
64 7 NC 011117 0.09830 0.10160 0.09946 0.00974 0.09627 0.10249 -
65 8 NC 011118 0.10239 0.10788 0.10572 0.01151 0.10249 0.10660 0.01062
67 Kimura 2-parameter distance matrix (continued)
69 8
70 8 NC 011118 -
72 Jukes-Cantor distance matrix
73 Rates assumed to follow gamma distribution with shape parameter = 1
75 1 2 3 4 5 6 7
76 1 NC 003426 -
77 2 NC 003427 0.13084 -
78 3 NC 003428 0.12245 0.02352 -
79 4 NC 009331 0.09821 0.10159 0.09709 -
80 5 NC 009968 0.11190 0.09709 0.09486 0.09598 -
81 6 NC 009970 0.12602 0.09821 0.08933 0.10273 0.10729 -
82 7 NC 011117 0.10159 0.10500 0.10273 0.00977 0.09934 0.10614 -
83 8 NC 011118 0.10614 0.11190 0.10958 0.01158 0.10614 0.11074 0.01068
85 Jukes-Cantor distance matrix (continued)
87 8
88 8 NC 011118 -
90 Jukes-Cantor distance matrix
91 Rates assumed to follow gamma distribution with shape parameter = 0.6
93 1 2 3 4 5 6 7
94 1 NC 003426 -
95 2 NC 003427 0.13831 -
96 3 NC 003428 0.12900 0.02377 -
97 4 NC 009331 0.10244 0.10611 0.10123 -
98 5 NC 009968 0.11737 0.10123 0.09881 0.10001 -
99 6 NC 009970 0.13296 0.10244 0.09283 0.10735 0.11232 -
100 7 NC 011117 0.10611 0.10983 0.10735 0.00982 0.10366 0.11107 -
101 8 NC 011118 0.11107 0.11737 0.11484 0.01164 0.11107 0.11610 0.01073
103 Jukes-Cantor distance matrix (continued)
105 8
106 8 NC 011118 -
108 Jukes-Cantor distance matrix
109 Rates assumed to follow gamma distribution with shape parameter = 0.2
111 1 2 3 4 5 6 7
112 1 NC 003426 -
113 2 NC 003427 0.18517 -
114 3 NC 003428 0.16951 0.02504 -
115 4 NC 009331 0.12753 0.13310 0.12570 -
116 5 NC 009968 0.15065 0.12570 0.12209 0.12389 -
117 6 NC 009970 0.17611 0.12753 0.11330 0.13499 0.14269 -
118 7 NC 011117 0.13310 0.13881 0.13499 0.01003 0.12937 0.14075 -
119 8 NC 011118 0.14075 0.15065 0.14664 0.01194 0.14075 0.14863 0.01098
121 Jukes-Cantor distance matrix (continued)
123 8
124 8 NC 011118 -
126 Kimura 2-parameter distance matrix
127 Rates assumed to follow gamma distribution with shape parameter = 1
129 1 2 3 4 5 6 7
130 1 NC 003426 -
131 2 NC 003427 0.14194 -
132 3 NC 003428 0.13205 0.02382 -
133 4 NC 009331 0.10430 0.10835 0.10322 -
134 5 NC 009968 0.11976 0.10303 0.10051 0.10195 -
135 6 NC 009970 0.13574 0.10430 0.09428 0.10924 0.11425 -
136 7 NC 011117 0.10835 0.11247 0.10985 0.00982 0.10598 0.11335 -
137 8 NC 011118 0.11314 0.11999 0.11732 0.01162 0.11335 0.11821 0.01072
139 Kimura 2-parameter distance matrix (continued)
141 8
142 8 NC 011118 -
144 Kimura 2-parameter distance matrix
145 Rates assumed to follow gamma distribution with shape parameter = 0.6
147 1 2 3 4 5 6 7
148 1 NC 003426 -
149 2 NC 003427 0.15460 -
150 3 NC 003428 0.14299 0.02417 -
151 4 NC 009331 0.11117 0.11582 0.11000 -
152 5 NC 009968 0.12876 0.10973 0.10688 0.10857 -
153 6 NC 009970 0.14716 0.11117 0.09988 0.11671 0.12237 -
154 7 NC 011117 0.11582 0.12058 0.11759 0.00988 0.11318 0.12147 -
155 8 NC 011118 0.12117 0.12908 0.12601 0.01169 0.12147 0.12691 0.01078
157 Kimura 2-parameter distance matrix (continued)
159 8
160 8 NC 011118 -
162 Kimura 2-parameter distance matrix
163 Rates assumed to follow gamma distribution with shape parameter = 0.2
165 1 2 3 4 5 6 7
166 1 NC 003426 -
167 2 NC 003427 0.24513 -
168 3 NC 003428 0.21941 0.02603 -
169 4 NC 009331 0.15593 0.16509 0.15414 -
170 5 NC 009968 0.18967 0.15326 0.14802 0.15148 -
171 6 NC 009970 0.22745 0.15593 0.13549 0.16600 0.17652 -
172 7 NC 011117 0.16509 0.17469 0.16889 0.01018 0.16047 0.17560 -
173 8 NC 011118 0.17459 0.19077 0.18459 0.01207 0.17560 0.18551 0.01112
175 Kimura 2-parameter distance matrix (continued)
177 8
178 8 NC 011118 -