/
testSeqGen.xml
89 lines (80 loc) · 5.12 KB
/
testSeqGen.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
<beast version='2.0'
namespace='beast.evolution.alignment:beast.core:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood'>
<data id="alignment" dataType="nucleotide">
<sequence taxon="human">?</sequence>
<sequence taxon="chimp">?</sequence>
<sequence taxon="bonobo">?</sequence>
<sequence taxon="gorilla">?</sequence>
<sequence taxon="orangutan">?</sequence>
<sequence taxon="siamang">?</sequence>
</data>
<tree id='tree' spec='beast.util.TreeParser' newick='((((human:0.02096625515232275,(chimp:0.014857143159686462,bonobo:0.014857143159686462):0.0061091119926362895):0.012862878672687175,gorilla:0.033829133825009926):0.029471223948245952,orangutan:0.06330035777325588):0.0031773962188650223,siamang:0.0664777539921209)' taxa='@alignment'/>
<run spec="beast.app.seqgen.SequenceSimulator" id="seqgen" data='@alignment' tree='@tree' sequencelength='3000'>
<siteModel spec='SiteModel' id="siteModel" gammaCategoryCount='1'>
<!--
<substModel spec='JukesCantor' id='JC69'/>
-->
<substModel spec='HKY' id='hky'>
<parameter name='kappa' id="hky.kappa" value="5.0" lower="0.0"/>
<frequencies id='freqs' spec='Frequencies'>
<data idref='alignment'/>
</frequencies>
</substModel>
<!--
<substModel id="GTR" spec="GTR">
<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.01"/>
<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.2"/>
<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.03"/>
<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.1"/>
<frequencies id="freqs" spec="Frequencies">
<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
</frequencies>
</substModel>
-->
<!--
<substModel id="TN93" spec="GTR">
<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.5"/>
<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.5"/>
<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.5"/>
<frequencies id="freqs" spec="Frequencies">
<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
</frequencies>
</substModel>
-->
<!--
<substModel id="TIM" spec="GTR">
<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.2"/>
<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.5"/>
<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.2"/>
<frequencies id="freqs" spec="Frequencies">
<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
</frequencies>
</substModel>
-->
<!--
<substModel id="new" spec="GTR">
<parameter dimension="1" id="rateAC.alignment" lower="0.0" minordimension="1" name="rateAC" value="0.2"/>
<parameter dimension="1" id="rateAG.alignment" lower="0.0" minordimension="1" name="rateAG" value="5.0"/>
<parameter dimension="1" id="rateAT.alignment" lower="0.0" minordimension="1" name="rateAT" value="0.5"/>
<parameter dimension="1" id="rateCG.alignment" lower="0.0" minordimension="1" name="rateCG" value="0.1"/>
<parameter dimension="1" id="rateCT.alignment" lower="0.0" minordimension="1" name="rateCT" value="1.0"/>
<parameter dimension="1" id="rateGT.alignment" lower="0.0" minordimension="1" name="rateGT" value="0.2"/>
<frequencies id="freqs" spec="Frequencies">
<parameter name='frequencies' value='0.25 0.25 0.25 0.25'/>
</frequencies>
</substModel>
-->
</siteModel>
<branchRateModel id="StrictClock" spec="beast.evolution.branchratemodel.StrictClockModel">
<parameter dimension="1" estimate="false" id="clockRate" minordimension="1" name="clock.rate" value="1.0"/>
</branchRateModel>
</run>
</beast>