-
Notifications
You must be signed in to change notification settings - Fork 7
/
dengue4_bdsky_equidistant5_treeslicer.xml
243 lines (207 loc) · 37.3 KB
/
dengue4_bdsky_equidistant5_treeslicer.xml
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
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<beast beautitemplate='Standard' beautistatus=''
namespace="beast.core
:beast.evolution.alignment
:beast.evolution.tree.coalescent
:beast.core.util
:beast.core.parameter
:beast.evolution.nuc
:beast.evolution.operators
:beast.evolution.sitemodel
:beast.evolution.substitutionmodel
:beast.evolution.likelihood
:skylinetools.util"
required="BDSKY v1.3.3" version="2.4">
<!--
Dengue example with reproductiveNumber shifts between tMRCA and present and sampling proportion set to 0 before the time of the oldest sample.
-->
<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>
<data id="Dengue4" name="alignment">
<sequence id="seq_D4Brazi82" taxon="D4Brazi82" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGATTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4ElSal83" taxon="D4ElSal83" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCATATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4ElSal94" taxon="D4ElSal94" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATAGCCCAGGGAAAACCAACCTTGGATTTTGAATTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGGAATGGCTGTGGCTTGCTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGATACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGATCTGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTCGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTACACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTATGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGCTCAAGCA"/>
<sequence id="seq_D4Indon76" taxon="D4Indon76" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTAAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTTGTGCATAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTCCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGCAACCAACATAGAGTTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCCTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4Indon77" taxon="D4Indon77" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTAAAAGAGGAACAAGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTAGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTTGTGCATAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGCAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGCTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4Mexico84" taxon="D4Mexico84" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTAGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGCTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCCCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTGTGAAGGTGCTGGAGCTCCCTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCTCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4NewCal81" taxon="D4NewCal81" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCATGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4PRico86" taxon="D4PRico86" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGGGAGCCCTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATCTGGTCCAAATTGAGAACCTTGAGTACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTAATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATCGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGCGTCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGCGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGTATCACTCTGTTTCTGGGCTTCACAGTTCAAGCG"/>
<sequence id="seq_D4Philip56" taxon="D4Philip56" totalcount="4" value="ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTAGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACATATCCAACCATGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGGCAGCAGGAGCAGACACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTATGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATTAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAGGGTGCTGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTAGGGCGCATCATCTCATCTACCCCTTTGGCTGAGTATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACAGTTCACGCA"/>
<sequence id="seq_D4Philip64" taxon="D4Philip64" totalcount="4" value="ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGATACATCCAACCATGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGGCAGCAGGAGCAGATACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATTAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAATATGAGGGTGCTGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTAGGGCGTATCATCTCATCTACCCCTTTGGCTGAGAACACCAACAGTGTAACCAACATAGAATTAGAACCCCCTTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCGGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGTTTCACAGTTCACGCA"/>
<sequence id="seq_D4Philip84" taxon="D4Philip84" totalcount="4" value="ATGCGATGCGTAGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGACTTAGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCAACAAGATGCCCAACGCAAGGAGAACCTTATCTCAAAGAGGAACAAGATCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTCTCATGCTCGGGAAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATATACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCATGGAGTGACAGCCACGATAACCCCTAGGTCACCATCGGTAGAAGTTAAATTACCGGATTATGGAGAATTAACACTTGATTGTGAACCCAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTCTGGATCTGCCTCTACCATGGGCAGCAGGAGCAGATACATCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTGAAATGCAAAGTTCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGGAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTTAAAGTCAAATATGAAGGTGCTGGAGCTCCGTGCAAAGTTCCCATAGAGATAAGAGATGTGAACAGGGAAAAAGTGGTAGGGCGTGTCATCTCATCTACCCCTTTGGCCGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCTTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGAATGGCCATTCTAGGTGAAACAGCCTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATTGGGTTCCTAGTGTTGTGGATTGGCACGAATTCGAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTCATGGGTTTCACAGTTCACGCA"/>
<sequence id="seq_D4SLanka78" taxon="D4SLanka78" totalcount="4" value="ATGCGATGCGTGGGAGTGGGGAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCCTGTCTCAAAGAGGAACAGGATCAACAGTACATCTGCCGGAGAGACGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCCTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTAGTCCGAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTGACACTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGGAAATGAGAAAGAAAACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCATTGGAATCACAAAGAGAGAATGGTGACGTTCAAGGTCCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCAGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATTTGAAGTGCAAAGTTCGCATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAGGGTGCCGGAGCTCCATGTAAAGTTCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGCATCATCTCATCTACCCCTTTTGCTGAGAATACCAACAGTGTGACCAACATAGAATTGGAACCCCCCTTTGGGGATAGCTACATAGTAATAGGTGTAGGAAACAGTGCATTAACACTCCATTGGTTTAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTATTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCAATGTCGTGCATAGCTGTTGGAGGAATTACTTTGTTTCTGGGTTTCACAGTTCATGCA"/>
<sequence id="seq_D4Tahiti79" taxon="D4Tahiti79" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATTTGGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATCCTGATGAAAATGAGAAAGAAGACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACATCAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCGCTGGAGCCACAGAAGTGGACTCCGGTGATGGAAATCACATGTTTGCAGGACATCTCAAGTGCAAAGTCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4Tahiti85" taxon="D4Tahiti85" totalcount="4" value="ATGCGATGCGTAGGAGTAGGAAACAGAGACTTTGTGGAAGGAGTTTCAGGTGGAGCATGGGTCGATTTGGTGCTAGAACATGGAGGATGCGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGACTAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCAATATCAAACATAACTACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTATCTGAAAGAGGAACAGGACCAACAGTACATTTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTGTTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGTTCGGGGAAGATAACAGGCAATCTGGTCCAAATTGAGAACCTTGAATACACAGTGGTCATAACAGTCCACAATGGAGACACCCATGCAGTAGGAAATGACACATCCAATCATGGAGTTACAGCCACGATAACTCCCAGGTCACCATCGGTGGAAGTCAAATTGCCGGACTATGGAGAACTAACACTCGATTGTGAACCCAGGTCTGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACATGGCTCGTGCATAAGCAATGGTTTTTGGATCTGCCTCTTCCATGGACAGCAGGAGCAGACACAACAGAGGTTCACTGGAATTACAAAGAGAGAATGGTGACATTTAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTACTGGGATCTCAGGAAGGAGCCATGCATTCTGCCCTAGCTGGAGCTACAGAAGTGGACTCCGGTGATGGGAATCACATGTTTGCAGGACATCTCAAGTGCAAAATCCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGTTCAGGAAAGTTTTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTGAAAGTCAAGTATGAAGGTGCTGGAGCTCCGTGTAAAGTCCCCATAGAGATAAGAGATGTAAACAAGGAAAAAGTGGTTGGGCGTGTCATCTCATCCACCCCTTTGGCTGAGAATACCAACAGTGTAACCAACATAGAATTAGAACCCCCCTTTGGGGACAGCTACATAGTGATAGGTGTTGGAAACAGCGCATTAACACTCCATTGGTTCAGGAAAGGGAGTTCCATCGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAACGAATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCCGTTGGTGGACTGTTCACATCATTGGGAAAGGCTGTGCACCAGGTTTTTGGAAGTGTGTATACAACCATGTTTGGAGGAGTCTCATGGATGATTAGAATCCTAATTGGGTTCTTAGTGTTGTGGATTGGCACGAACTCAAGGAACACTTCAATGGCTATGACGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCAAGCA"/>
<sequence id="seq_D4Thai63" taxon="D4Thai63" totalcount="4" value="ATGCGATGCGTAGGAGTGGGGAACAGGGACTTTGTGGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCTCAAGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCGATATCAAACATAACCACGGCGACAAGATGTCCAACGCAAGGAGAGCCTTATCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGATGTGGTAGACAGAGGGTGGGGCAATGGCTGTGGCTTACTTGGAAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTGGTTCGAATTGAGAACCTTGAATACACAGTGGTTGTGACAGTCCACAACGGAGACACCCATGCAGTAGGAAATGACATATCCAACCATGGAGTGACAGCCACGATAACTCCCAGGTCACCATCGGTAGAAGTCAAATTACCGGATTATGGAGAATTAACGCTCGATTGTGAACCCAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGGAAATGAGAAAGAAGACGTGGCTTGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACAGCAGAAGTTCATTGGAATTACAAAGAGAGAATGGTGACATTCAAGGTCCCTCATGCTAAGAGACAAGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCTGCCCTCACCGGAGCTACAGAAGTGGATTCCGGTGATGGAAACCACATGTTTGCAGGACATCTTAAGTGCAAGGTTCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGACAAAGAGATGGCAGAAACACAGCATGGGACAACAGTAGTGAAAGTTAAGTATGAAGGCGCTGAAGCTCCATGTAAAATCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTTGTTGGGCGCATCATCTCATCCACTCCTTTGGCTGAAAACACCAACAGCGTGACCAATATAGAATTAGAACCTCCCTTTGGGGACAGCTACATAGTAATAGGTGTTGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAGGGGAGTTCCATTGGCAAGATGTTTGAGTCTACATATAGAGGAGCAAAGCGAATGGCCATTCTAGGTGAAACAGCTTGGGACTTTGGCTCTGTTGGCGGACTGTCTACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGTAGTGTGTACACAACCATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGCTCTTGGTGTTGTGGATTGGCACAAATTCAAGAAACACCTCAATGGCAATGACGTGCATAGCTGTTGGAGGAATCACTCTATTTCTGGGTTTCACAGCTCACGCA"/>
<sequence id="seq_D4Thai78" taxon="D4Thai78" totalcount="4" value="ATGCGATGCGTAGGAGTGGGGAACAGAGACTTTGTAGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCTTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTACCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGACGTGGTAGATAGAGGGTGGGGCAACGGCTGTGGCTTGCTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACAGGCAACTTAGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCTGTAGGAAATGATACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTAACACTTGATTGTGAACCTAGGTCCGGAATTGACTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTCGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCACTGGAATCACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCTATGCATTCAGCCCTCACCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCATATGTTTGCAGGACATCTTAAGTGTAAAGTTCGTATGGAGAAATTGAGGATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGGACAACAGTGGTAAAAGTCAAGTATGAAGGTGCTGGAGCTCCATGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCTACCCCTTTTGCTGAGAATACCAACAGTGTGACCAATATAGAATTGGAACCCCCTTTTGGGGATAGCTACATAGTAATAGGTGTAGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGCTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGCGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTCGGTGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGCAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTGTTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCAATGTCGTGCATAGCTGTTGGAGGAATCACTCTGTTTCTGGGCTTCACAGTTCATGCA"/>
<sequence id="seq_D4Thai84" taxon="D4Thai84" totalcount="4" value="ATGCGATGCGTAGGAGTAGGGAACAGAGACTTTGTAGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCCTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTACCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGACGTGGTAGACAGAGGGTGGGGCAACGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACGGGCAACTTAGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCTGTAGGAAATGATACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTAACACTTGATTGTGAACCTAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTCGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCACTGGAATCACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCAGCCCTCGCCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCATATGTTTGCAGGACACTTAAAGTGTAAAGTTCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGAACAACAGTGGTAAAGGTCAAGTATGAAGGCACTGGAGCTCCATGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCTACCCCTTTGGCTGAGAATACCAACAGTGTGACCAATATAGAATTGGAACCTCCTTTTGGGGATAGCTACATAGTGATAGGTGTGGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGCTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGCGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGCAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTGTTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCTATGTCGTGCATAGCTGTTGGAGGAATTACTCTGTTTCTGGGCTTCACAGTTCATGCA"/>
</data>
<!-- Select a slice of the sampling proportion to apply a prior to (can also use ExcludablePrior) -->
<function spec="beast.core.util.Slice" id="samplingProportionSlice" arg="@samplingProportion" index="1" count="1"/>
<!-- Convert heights to dates (unnecessary, for testing and comparison only) -->
<RPNcalculator id="ReSliceDatesRPN" spec="beast.math.statistic.RPNcalculator" expression="1994 ReTreeSlice -">
<parameter idref="ReTreeSlice"/>
</RPNcalculator>
<run id="mcmc" spec="MCMC" chainLength="5000000">
<state id="state" storeEvery="10000000">
<tree id="Tree" name="stateNode">
<trait id="dateTrait" spec="beast.evolution.tree.TraitSet" traitname="date">
D4Brazi82=1982,
D4ElSal83=1983,
D4ElSal94=1994,
D4Indon76=1976,
D4Indon77=1977,
D4Mexico84=1984,
D4NewCal81=1981,
D4Philip64=1964,
D4Philip56=1956,
D4Philip84=1984,
D4PRico86=1986,
D4SLanka78=1978,
D4Tahiti79=1979,
D4Tahiti85=1985,
D4Thai63=1963,
D4Thai78=1978,
D4Thai84=1984
<taxa id="TaxonSet.Dengue4" spec="TaxonSet">
<alignment idref="Dengue4"/>
</taxa>
</trait>
<taxonset idref="TaxonSet.Dengue4"/>
</tree>
<parameter id="kappa" lower="0.0" name="stateNode">2.0</parameter>
<parameter id="freqParameter" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
<parameter id="clockRate" name="stateNode">1.0</parameter>
<parameter id="origin" lower="0.0" name="stateNode" upper="Infinity">100.0</parameter>
<parameter id="samplingProportion" lower="0.0" name="stateNode" upper="1.0">0 0.01</parameter>
<parameter id="becomeUninfectiousRate" lower="0.0" name="stateNode" upper="Infinity">1.0</parameter>
<parameter id="reproductiveNumber" dimension="5" lower="0.0" name="stateNode" upper="Infinity">2.0</parameter>
</state>
<!-- Initial tree -->
<init id="RandomTree" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree" taxa="@Dengue4">
<populationModel id="ConstantPopulation0" spec="ConstantPopulation" popSize="1.0"/>
</init>
<distribution id="posterior" spec="util.CompoundDistribution">
<!-- Begin prior -->
<distribution id="prior" spec="util.CompoundDistribution">
<!-- Treeprior (BDSKY) -->
<distribution id="BirthDeathSkySerial"
spec="beast.evolution.speciation.BirthDeathSkylineModel"
tree="@Tree"
reproductiveNumber="@reproductiveNumber"
becomeUninfectiousRate="@becomeUninfectiousRate"
samplingProportion="@samplingProportion"
origin="@origin">
<birthRateChangeTimes spec="TreeSlicer" id="ReTreeSlice" tree="@Tree" dimension="5" to="tmrca" inclusive="false"/>
<samplingRateChangeTimes spec="TreeSlicer" id="SamplingTreeSlice" tree="@Tree" dimension="2" to="oldestsample" inclusive="true"/>
<reverseTimeArrays spec="BooleanParameter" value="true false true false false"/>
</distribution>
<!-- Treeprior priors -->
<prior id="reproductiveNumberPrior" name="distribution" x="@reproductiveNumber">
<LogNormal name="distr" M="0" S="1" offset="0.0"/>
</prior>
<prior id="becomeUninfectiousRatePrior" name="distribution" x="@becomeUninfectiousRate">
<LogNormal name="distr" M="0" S="1" offset="0.0" meanInRealSpace="false"/>
</prior>
<prior id="samplingProportionPrior" name="distribution" x="@samplingProportionSlice">
<Beta name="distr" alpha="2" beta="10"/>
</prior>
<prior id="originPrior" name="distribution" x="@origin">
<Uniform id="Uniform.3" name="distr" upper="500" lower="0"/>
</prior>
<!-- Site model priors -->
<prior id="KappaPrior" name="distribution" x="@kappa">
<LogNormal name="distr" M="1" S="1.25" offset="0.0"/>
</prior>
<!-- Clock model priors -->
<prior id="ClockPrior" name="distribution" x="@clockRate">
<Uniform id="Uniform.0" name="distr" upper="Infinity"/>
</prior>
</distribution>
<!-- End prior -->
<!-- Begin likelihood -->
<distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
<!-- Alignment likelihood -->
<distribution id="treeLikelihood.Dengue4" spec="ThreadedTreeLikelihood" data="@Dengue4" tree="@Tree">
<siteModel id="SiteModel" spec="SiteModel">
<parameter id="mutationRate" estimate="false" name="mutationRate">1.0</parameter>
<parameter id="gammaShape" estimate="false" name="shape">1.0</parameter>
<parameter id="proportionInvariant" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="hky" spec="HKY" kappa="@kappa">
<frequencies id="estimatedFreqs" spec="Frequencies" frequencies="@freqParameter"/>
</substModel>
</siteModel>
<branchRateModel id="StrictClock" spec="beast.evolution.branchratemodel.StrictClockModel" clock.rate="@clockRate"/>
</distribution>
</distribution>
<!-- End likelihood -->
</distribution>
<!-- Begin operators -->
<!-- Site model operators -->
<operator id="KappaScaler" spec="ScaleOperator" parameter="@kappa" scaleFactor="0.5" weight="0.1"/>
<operator id="FrequenciesExchanger" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
<parameter idref="freqParameter"/>
</operator>
<!-- Clock model operators -->
<operator id="StrictClockRateScaler" spec="ScaleOperator" parameter="@clockRate" scaleFactor="0.75" weight="3.0"/>
<operator id="strictClockUpDownOperator" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
<up idref="clockRate"/>
<down idref="Tree"/>
</operator>
<!-- Tree operators -->
<operator id="BDSKY_serialtreeScaler" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree" weight="3.0"/>
<operator id="BDSKY_serialtreeRootScaler" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree" weight="3.0"/>
<operator id="BDSKY_serialUniformOperator" spec="Uniform" tree="@Tree" weight="30.0"/>
<operator id="BDSKY_serialSubtreeSlide" spec="SubtreeSlide" tree="@Tree" weight="15.0"/>
<operator id="BDSKY_serialnarrow" spec="Exchange" tree="@Tree" weight="15.0"/>
<operator id="BDSKY_serialwide" spec="Exchange" isNarrow="false" tree="@Tree" weight="3.0"/>
<operator id="BDSKY_serialWilsonBalding" spec="WilsonBalding" tree="@Tree" weight="3.0"/>
<!-- BDSKY operators -->
<operator id="becomeUninfectiousRateScaler" spec="ScaleOperator" parameter="@becomeUninfectiousRate" scaleFactor="0.75" weight="2.0"/>
<operator id="samplingScaler" spec="ScaleOperator" parameter="@samplingProportion" scaleFactor="0.75" weight="2.0"/>
<operator id="reproductiveNumberScaler" spec="ScaleOperator" parameter="@reproductiveNumber" scaleFactor="0.75" weight="10.0"/>
<operator id="origScaler" spec="ScaleOperator" parameter="@origin" scaleFactor="0.75" weight="1.0"/>
<operator id="updownBD" spec="UpDownOperator" scaleFactor="0.75" weight="2.0">
<up idref="reproductiveNumber"/>
<down idref="becomeUninfectiousRate"/>
</operator>
<!-- End operators -->
<logger id="tracelog" fileName="dengue4_bdsky_equidistant5_treeslicer.log" logEvery="10000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.Dengue4"/>
<log idref="BirthDeathSkySerial"/>
<log idref="kappa"/>
<log idref="freqParameter"/>
<log idref="clockRate"/>
<log id="TreeHeight" spec="beast.evolution.tree.TreeStatLogger" tree="@Tree" logHeight="true"/>
<log idref="origin"/>
<log idref="becomeUninfectiousRate"/>
<log idref="reproductiveNumber"/>
<log idref="samplingProportion"/>
<log idref="ReTreeSlice"/>
<log idref="ReSliceDatesRPN"/>
<log spec="TreeSliceDateLogger" treeSlice="@ReTreeSlice"/>
<log idref="SamplingTreeSlice"/>
<log spec="TreeSliceDateLogger" treeSlice="@SamplingTreeSlice"/>
</logger>
<logger id="screenlog" logEvery="1000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog" fileName="dengue4_bdsky_equidistant5_treeslicer.trees" logEvery="10000" mode="tree">
<log id="TreeWithMetaDataLogger" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree"/>
</logger>
</run>
</beast>