-
dong.w.xie
2009-09-29 15:01
#144
Rev.: 2322
-
122 lines of code changed in 9 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+8 -32),
LogGenerator.java (+3 -3),
OperatorsGenerator.java (+4 -8),
SubstitutionModelGenerator.java (+30 -15)
-
src/dr/app/beauti/options:
BeautiOptions.java (+11 -11),
Operator.java (+5),
PartitionOptions.java (+4),
PartitionSubstitutionModel.java (+57 -6),
SubstitutionModelOptions.java (del)
-
dong.w.xie
2009-09-29 09:41
#143
Rev.: 2321
-
14 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
Generator.java (+14 -12)
-
rambaut
2009-09-29 00:47
#142
Rev.: 2320
-
13 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+13 -5)
-
rambaut
2009-09-29 00:29
#141
Rev.: 2319
-
31 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+31)
-
rambaut
2009-09-29 00:25
#140
Rev.: 2318
-
157 lines of code changed in 6 files:
-
build_BEAST_MCMC.xml (+22 -21)
-
release/Mac/scripts:
beast (+27),
beauti (+27),
loganalyser (+27),
logcombiner (+27),
treeannotator (+27)
-
rambaut
2009-09-29 00:05
#139
Rev.: 2317
-
5830 lines of code changed in 71 files:
-
release:
BEAST_launch4j.xml (del),
BEAUTi_launch4j.xml (del),
LogAnalyser_launch4j.xml (del),
LogCombiner_launch4j.xml (del),
README.txt (del),
TreeAnnotator_launch4j.xml (del),
VERSION HISTORY.txt (del)
-
release/Linux/lib:
libNucleotideLikelihoodCore.jnilib (new),
libNucleotideLikelihoodCore.so (new)
-
release/Linux/scripts:
beast (+27),
beauti (+27),
loganalyser (+27),
logcombiner (+27),
treeannotator (+27)
-
release/Mac:
jarbundler-2.1.0.jar (new)
-
release/Mac/lib:
libNucleotideLikelihoodCore.jnilib (changed),
libquaqua.jnilib (changed),
libquaqua64.jnilib (changed),
quaqua-filechooser-only.jar (changed),
quaqua.jar (changed)
-
release/Windows:
BEAST_launch4j.xml (+17),
BEAUTi_launch4j.xml (+16),
LogAnalyser_launch4j.xml (+20),
LogCombiner_launch4j.xml (+20),
TreeAnnotator_launch4j.xml (+20)
-
release/Windows/scripts:
beast.cmd (new 5),
beauti.cmd (new 5),
loganalyser.cmd (new 5),
logocombiner.cmd (new 5),
treeannotator.cmd (new 5)
-
release/common:
README.txt (+193),
VERSION HISTORY.txt (+338)
-
release/common/doc:
BEAST14_Manual_6July2007.pdf (new)
-
release/common/icons:
beast.icns (new),
beast.ico (new),
beast.png (new),
beauti.icns (new),
beauti.ico (new),
beauti.png (new),
beautidoc.icns (new),
beautidoc.ico (new),
utility.icns (new),
utility.ico (new),
utility.png (new)
-
release/common/native:
AminoAcidLikelihoodCore.c (new 2405),
AminoAcidLikelihoodCore.h (new 57),
GeneralLikelihoodCore.c (new 266),
GeneralLikelihoodCore.h (new 52),
Makefile (+41),
Makefile.OSX (new 24),
Makefile.OSX.icc (new 14),
Makefile.amd64 (new 12),
Makefile.ia64 (new 12),
Makefile.icc (new 11),
Makefile.linux (new 11),
Makefile.solaris (new 17),
Makefile.sunos (new 11),
NativeMemoryLikelihoodCore.c (new 509),
NativeMemoryLikelihoodCore.h (new 97),
NativeSubstitutionModel.c (new 177),
NativeSubstitutionModel.h (new 45),
NewNativeLikelihoodCore.c (new 713),
NewNativeLikelihoodCore.h (new 117),
NucleotideLikelihoodCore.c (new 330),
NucleotideLikelihoodCore.h (new 61),
compileNativeLinux.sh (+5),
compileNativeMacOSX.sh (+55),
compileNativeWin32.bat (new 4)
-
release/extra_lib:
NucleotideLikelihoodCore.dll (del),
libNucleotideLikelihoodCore.jnilib (del),
libNucleotideLikelihoodCore.so (del)
-
rambaut
2009-09-28 23:40
#138
-
116 lines of code changed in 5 files:
-
build_BEAST_MCMC.xml (+109 -80)
-
release:
icons (del),
jarbundler-2.1.0.jar (del)
-
src/dr/app/beauti/options:
ModelOptions.java (+2 -2),
PartitionTreePrior.java (+5 -5)
-
akaruiws
2009-09-28 20:07
#137
Rev.: 2314
-
1 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
PriorOptions.java (+1 -1)
-
akaruiws
2009-09-28 19:48
#136
Rev.: 2313
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
LinearBiasModel.java (+1 -12)
-
akaruiws
2009-09-28 19:45
#135
Rev.: 2312
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
LinearBiasModel.java (+1 -1)
-
akaruiws
2009-09-28 19:41
#134
Rev.: 2311
-
2 lines of code changed in 1 file:
-
src/dr/inference/model:
Variable.java (+2 -1)
-
akaruiws
2009-09-28 19:35
#133
-
26 lines of code changed in 2 files:
-
src/dr/inference/model:
DuplicatedParameter.java (+4),
Parameter.java (+22)
-
akaruiws
2009-09-28 19:20
#132
-
9 lines of code changed in 2 files:
-
src/dr/inference/model:
CompoundParameter.java (+4),
MaskedParameter.java (+5)
-
dong.w.xie
2009-09-28 17:52
#131
Rev.: 2306
-
14 lines of code changed in 3 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2 -1)
-
src/dr/app/beauti/options:
PartitionClockModel.java (+10 -6),
PriorOptions.java (+2 -4)
-
msuchard
2009-09-28 09:10
#130
Rev.: 2305
-
229 lines of code changed in 13 files:
-
src/dr/app/beagle/evomodel/parsers:
SVSComplexSubstitutionModelParser.java (new 8)
-
src/dr/app/beagle/evomodel/substmodel:
BaseSubstitutionModel.java (+40 -43),
ColtEigenSystem.java (+7 -5),
ComplexColtEigenSystem.java (+20),
ComplexSubstitutionModel.java (+104 -1),
EigenDecomposition.java (+11),
GeneralSubstitutionModel.java (+3 -1),
SVSComplexSubstitutionModel.java (+8)
-
src/dr/app/beast:
beagle_parsers.properties (+2)
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+9 -10),
GeneralSubstitutionModel.java (+3 -1)
-
src/dr/inference/model:
BayesianStochasticSearchVariableSelection.java (+11 -1),
DuplicatedParameter.java (+3 -3)
-
akaruiws
2009-09-27 00:47
#129
Rev.: 2304
-
218 lines of code changed in 1 file:
-
src/dr/evomodel/tree:
MicrosatelliteSamplerTreeModel.java (+218)
-
dong.w.xie
2009-09-25 16:33
#128
Rev.: 2303
-
36 lines of code changed in 8 files:
-
src/dr/app/beauti/enumTypes:
FixRateType.java (+1 -1)
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+1 -1),
TreePriorGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ClockModelOptions.java (+30 -43),
PriorOptions.java (+1 -1)
-
src/dr/app/beauti/treespanel:
PartitionTreeModelPanel.java (+1 -1)
-
dong.w.xie
2009-09-25 12:25
#127
Rev.: 2302
-
3 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+3 -1)
-
dong.w.xie
2009-09-25 12:21
#126
Rev.: 2301
-
14 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -5),
Parameter.java (+1 -1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+11 -7)
-
dong.w.xie
2009-09-25 11:00
#125
Rev.: 2300
-
65 lines of code changed in 3 files:
-
src/dr/app/beauti/options:
Parameter.java (+2 -1),
PartitionClockModel.java (-1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+63 -35)
-
philippe.lemey@gmail.com
2009-09-24 22:51
#124
Rev.: 2299
-
34 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+34 -25)
-
akaruiws
2009-09-24 22:34
#123
Rev.: 2298
-
3 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
TwoPhaseModel.java (+3 -2)
-
akaruiws
2009-09-24 22:01
#122
Rev.: 2297
-
4 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
LinearBiasModel.java (+4 -2)
-
akaruiws
2009-09-24 17:57
#121
Rev.: 2296
-
5 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastParser.java (+5)
-
alexei.drummond
2009-09-24 17:27
#120
Rev.: 2295
-
55 lines of code changed in 1 file:
-
src/dr/util:
Citation.java (+55)
-
akaruiws
2009-09-24 17:11
#119
Rev.: 2294
-
118 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
TwoPhaseModelTest.java (+118)
-
Sibon.Li@gmail.com
2009-09-24 17:02
#118
Rev.: 2293
-
89 lines of code changed in 2 files:
-
src/dr/evomodel/clock:
ACLikelihood.java (+69 -20)
-
src/dr/math:
MathUtils.java (+20 -1)
-
akaruiws
2009-09-24 16:14
#117
Rev.: 2292
-
75 lines of code changed in 1 file:
-
src/dr/evomodelxml:
TwoPhaseModelParser.java (+75)
-
akaruiws
2009-09-24 15:42
#116
Rev.: 2291
-
210 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
TwoPhaseModel.java (+210)
-
akaruiws
2009-09-24 15:32
#115
Rev.: 2290
-
24 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
LinearBiasModel.java (+24 -14)
-
akaruiws
2009-09-24 15:20
#114
Rev.: 2289
-
1 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+1 -1)
-
akaruiws
2009-09-24 14:59
#113
Rev.: 2288
-
7 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
ComplexSubstitutionModel.java (+7 -5)
-
akaruiws
2009-09-24 14:52
#112
Rev.: 2287
-
206 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
LinearBiasTest.java (+206)
-
akaruiws
2009-09-24 14:47
#111
Rev.: 2286
-
102 lines of code changed in 1 file:
-
src/dr/evomodelxml:
LinearBiasModelParser.java (+102)
-
akaruiws
2009-09-24 14:38
#110
Rev.: 2285
-
186 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
LinearBiasModel.java (+186)
-
msuchard
2009-09-24 13:09
#109
Rev.: 2284
-
99 lines of code changed in 3 files:
-
src/dr/inference/distribution:
EmpiricalDistributionLikelihood.java (+90 -8),
SplineInterpolatedLikelihood.java (+2 -2)
-
src/dr/inferencexml:
EmpiricalDistributionLikelihoodParser.java (+7 -2)
-
msuchard
2009-09-24 12:55
#108
Rev.: 2283
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
dong.w.xie
2009-09-24 12:33
#107
Rev.: 2282
-
4 lines of code changed in 5 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+2 -14)
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (-1)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (-1),
TreeDisplayPanel.java (-2),
TreesPanel.java (+2 -4)
-
alexei.drummond
2009-09-24 12:27
#106
Rev.: 2281
-
638 lines of code changed in 2 files:
-
src/dr/evolution/tree:
FlexibleTree.java (+611 -603)
-
src/dr/evomodel/tree:
TreeModel.java (+27 -6)
-
msuchard
2009-09-24 11:52
#105
Rev.: 2280
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
msuchard
2009-09-24 11:46
#104
Rev.: 2279
-
386 lines of code changed in 17 files:
-
src/dr/app/beagle/evomodel/parsers:
ComplexSubstitutionModelParser.java (+83),
GeneralSubstitutionModelParser.java (+1 -1),
SVSComplexSubstitutionModelParser.java (+116),
SVSGeneralSubstitutionModelParser.java (new 2)
-
src/dr/app/beagle/evomodel/sitemodel:
BranchSiteModel.java (+2),
HomogenousBranchSiteModel.java (+8)
-
src/dr/app/beagle/evomodel/substmodel:
BaseSubstitutionModel.java (+19 -4),
ColtEigenSystem.java (-7),
ComplexSubstitutionModel.java (+31),
DefaultEigenSystem.java (+1 -1),
EigenDecomposition.java (+8),
GeneralSubstitutionModel.java (+3 -5),
SVSComplexSubstitutionModel.java (+101),
SVSGeneralSubstitutionModel.java (+2 -2),
SubstitutionModel.java (+5)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+3)
-
src/dr/inference/model:
BayesianStochasticSearchVariableSelection.java (+1 -1)
-
dong.w.xie
2009-09-24 11:43
#103
Rev.: 2278
-
20 lines of code changed in 1 file:
-
akaruiws
2009-09-24 00:44
#102
Rev.: 2277
-
4 lines of code changed in 1 file:
-
src/test/dr/evomodel/substmodel:
AsymQuadTest.java (+4 -5)
-
akaruiws
2009-09-24 00:36
#101
Rev.: 2276
-
25 lines of code changed in 1 file:
-
src/dr/evomodelxml:
AsymQuadModelParser.java (+25 -16)
-
akaruiws
2009-09-24 00:27
#100
Rev.: 2275
-
66 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
AsymmetricQuadraticModel.java (+66 -41)
-
akaruiws
2009-09-24 00:17
#99
Rev.: 2274
-
35 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
OnePhaseModel.java (+35 -6)
-
akaruiws
2009-09-24 00:03
#98
Rev.: 2273
-
65 lines of code changed in 1 file:
-
src/dr/evomodel/substmodel:
MicrosatelliteModel.java (+65 -34)
-
akaruiws
2009-09-23 23:50
#97
Rev.: 2272
-
19 lines of code changed in 2 files:
-
src/dr/evoxml:
MicrosatellitePatternParser.java (+19 -15)
-
akaruiws
2009-09-23 23:27
#96
Rev.: 2271
-
1 lines of code changed in 1 file:
-
src/dr/evoxml:
MicrosatelliteParser.java (+1 -1)
-
akaruiws
2009-09-23 23:09
#95
Rev.: 2270
-
13 lines of code changed in 1 file:
-
src/dr/evolution/datatype:
Microsatellite.java (+13 -30)
-
dong.w.xie
2009-09-23 15:01
#94
Rev.: 2269
-
4 lines of code changed in 2 files:
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+3 -3),
TreesPanel.java (+1)
-
dong.w.xie
2009-09-23 14:20
#93
Rev.: 2268
-
5 lines of code changed in 1 file:
-
src/dr/xml:
XMLParser.java (+5 -1)
-
dong.w.xie
2009-09-22 15:34
#92
Rev.: 2267
-
20 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastVersion.java (+5 -5)
-
src/dr/app/beauti:
BeautiApp.java (+4 -2)
-
src/dr/app/pathogen:
PathogenApp.java (+9 -3)
-
src/dr/util:
Version.java (+2)
-
dong.w.xie
2009-09-22 14:48
#91
Rev.: 2266
-
14 lines of code changed in 1 file:
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+14)
-
dong.w.xie
2009-09-21 15:49
#90
Rev.: 2265
-
45 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+14 -13),
LogGenerator.java (+31 -29)
-
dong.w.xie
2009-09-21 15:08
#89
Rev.: 2264
-
15 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -2)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+12 -9)
-
dong.w.xie
2009-09-21 12:43
#88
Rev.: 2263
-
22 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+22 -22)
-
dong.w.xie
2009-09-18 15:58
#87
Rev.: 2262
-
348 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastParser.java (+2 -1)
-
src/dr/evomodel/operators:
ImportanceNarrowExchange.java (+346),
ImportnaceNarrowExchange.java (del)
-
dong.w.xie
2009-09-18 15:53
#86
Rev.: 2261
-
106 lines of code changed in 8 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (-1)
-
src/dr/app/beauti/generator:
BranchRatesModelGenerator.java (+40 -40),
LogGenerator.java (+15 -10),
OperatorsGenerator.java (+37 -25),
TreeLikelihoodGenerator.java (+3 -3)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+3 -2)
-
src/dr/app/beauti/options:
ModelOptions.java (+7),
PartitionClockModelTreeModelLink.java (+1 -1)
-
dong.w.xie
2009-09-18 12:45
#85
Rev.: 2260
-
30 lines of code changed in 2 files:
-
src/dr/app/beauti/datapanel:
DataPanel.java (+28 -16)
-
src/dr/app/beauti/options:
BeautiOptions.java (+2 -2)
-
dong.w.xie
2009-09-17 14:08
#84
Rev.: 2259
-
1 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+1 -1)
-
dong.w.xie
2009-09-17 12:12
#83
Rev.: 2258
-
6 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
STARBEASTGenerator.java (+5 -5)
-
src/dr/app/beauti/treespanel:
SpeciesTreesPanel.java (+1 -1),
TreesPanel.java (-5)
-
dong.w.xie
2009-09-17 11:51
#82
Rev.: 2257
-
112 lines of code changed in 4 files:
-
src/dr/app/beauti/enumTypes:
PopulationSizeModelType.java (+45)
-
src/dr/app/beauti/generator:
STARBEASTGenerator.java (+40 -12)
-
src/dr/app/beauti/options:
PartitionTreePrior.java (+9)
-
src/dr/app/beauti/treespanel:
SpeciesTreesPanel.java (+18 -6)
-
jheled
2009-09-17 08:26
#81
Rev.: 2256
-
14 lines of code changed in 5 files:
-
src/dr/app/beagle/evomodel/parsers:
GTRParser.java (-1)
-
src/dr/app/beagle/evomodel/substmodel:
GTR.java (+6 -6)
-
src/dr/evomodel/tree/randomlocalmodel:
RLTVAnalyzer.java (+6 -6)
-
src/dr/inference/model:
MaskedParameter.java (+1 -1)
-
src/dr/math/distributions:
InverseGammaDistribution.java (+1 -5)
-
dong.w.xie
2009-09-16 13:56
#80
Rev.: 2255
-
39 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+39 -25)
-
dong.w.xie
2009-09-16 12:14
#79
Rev.: 2254
-
101 lines of code changed in 5 files:
-
src/dr/app/beast:
BeastParser.java (+1)
-
src/dr/app/beauti/enumTypes:
PriorType.java (+13 -2)
-
src/dr/app/beauti/generator:
ParameterPriorGenerator.java (+18 -9)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+26 -31)
-
src/dr/inferencexml:
PriorParsers.java (+43)
-
jheled
2009-09-16 11:25
#78
Rev.: 2253
-
4 lines of code changed in 1 file:
-
src/dr/math/distributions:
InverseGammaDistribution.java (+4 -1)
-
dong.w.xie
2009-09-16 10:41
#77
Rev.: 2252
-
1 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
Generator.java (-22),
ParameterPriorGenerator.java (+1 -3)
-
msuchard
2009-09-16 03:22
#76
Rev.: 2251
-
4 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+4 -1)
-
dong.w.xie
2009-09-15 17:16
#75
Rev.: 2250
-
57 lines of code changed in 3 files:
-
src/dr/app/beauti/enumTypes:
PriorType.java (+1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+39 -6),
PriorOptionsPanel.java (+17 -4)
-
dong.w.xie
2009-09-15 16:38
#74
Rev.: 2249
-
12 lines of code changed in 2 files:
-
src/dr/app/beauti/options:
Operator.java (+1 -1),
Parameter.java (+11 -3)
-
dong.w.xie
2009-09-15 16:37
#73
Rev.: 2248
-
12 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+7 -6),
LogGenerator.java (+5 -12)
-
dong.w.xie
2009-09-15 11:26
#72
Rev.: 2247
-
461 lines of code changed in 2 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+9 -385),
LogGenerator.java (+452)
-
dong.w.xie
2009-09-15 11:16
#71
Rev.: 2246
-
199 lines of code changed in 3 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+3 -136),
ParameterPriorGenerator.java (+196),
STARBEASTGenerator.java (-2)
-
dong.w.xie
2009-09-15 11:04
#70
Rev.: 2245
-
163 lines of code changed in 7 files:
-
src/dr/app/beauti/components:
TipDateSamplingComponentOptions.java (+2 -1)
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+1 -1)
-
src/dr/app/beauti/operatorspanel:
OperatorsPanel.java (+1 -1)
-
src/dr/app/beauti/options:
ModelOptions.java (+54 -40),
Operator.java (+93 -69),
PartitionClockModelTreeModelLink.java (+6 -6),
PartitionTreePrior.java (+6 -7)
-
philippe.lemey@gmail.com
2009-09-15 07:47
#69
Rev.: 2244
-
24 lines of code changed in 1 file:
-
src/dr/app/tools:
TimeSlicer.java (+24 -7)
-
dong.w.xie
2009-09-14 17:09
#68
Rev.: 2243
-
96 lines of code changed in 5 files:
-
src/dr/app/beauti/enumTypes:
TreePriorParameterizationType.java (new 47)
-
src/dr/app/beauti/generator:
TreePriorGenerator.java (+13 -12)
-
src/dr/app/beauti/options:
ModelOptions.java (-8),
PartitionTreePrior.java (+19 -22)
-
src/dr/app/beauti/treespanel:
PartitionTreePriorPanel.java (+17 -17)
-
dong.w.xie
2009-09-14 14:41
#67
Rev.: 2242
-
58 lines of code changed in 5 files:
-
src/dr/app/beauti/options:
PartitionClockModel.java (+1 -20),
PartitionModelOptions.java (new 53),
PartitionSubstitutionModel.java (+3 -21),
PartitionTreeModel.java (+1 -23),
PartitionTreePrior.java (-5)
-
dong.w.xie
2009-09-14 14:15
#66
Rev.: 2241
-
65 lines of code changed in 10 files:
-
src/dr/app/beauti/options:
BeautiOptions.java (-13),
ModelOptions.java (+6 -10),
PartitionClockModel.java (+2 -39),
PartitionClockModelTreeModelLink.java (-24),
PartitionData.java (+5 -28),
PartitionOptions.java (+50 -7),
PartitionSubstitutionModel.java (+1 -39),
PartitionTreeModel.java (-38),
PartitionTreePrior.java (-39)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+1 -15)
-
dong.w.xie
2009-09-14 13:06
#65
Rev.: 2240
-
18 lines of code changed in 6 files:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -48)
-
src/dr/app/beauti/options:
ModelOptions.java (+3 -3),
PartitionClockModel.java (+4 -4),
PartitionOptions.java (+6 -9),
PartitionTreeModel.java (+1 -1),
PriorOptions.java (+2 -2)
-
dong.w.xie
2009-09-14 12:38
#64
Rev.: 2239
-
143 lines of code changed in 8 files:
-
src/dr/app/beauti/components:
SequenceErrorModelComponentOptions.java (+4 -4),
TipDateSamplingComponentOptions.java (+2 -1)
-
src/dr/app/beauti/options:
ModelOptions.java (+28 -31),
Parameter.java (+9 -1),
PartitionClockModelTreeModelLink.java (+17 -16),
PartitionSubstitutionModel.java (+41 -42),
PartitionTreePrior.java (+37 -32),
STARBEASTOptions.java (+5 -5)
-
dong.w.xie
2009-09-11 14:27
#63
-
25 lines of code changed in 4 files:
-
src/dr/app/beauti:
BeautiFrame.java (+11 -7)
-
src/dr/app/beauti/generator:
InitialTreeGenerator.java (+8 -3)
-
src/dr/app/beauti/options:
PartitionSubstitutionModel.java (-1)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+6 -5)
-
dong.w.xie
2009-09-11 11:22
#62
Rev.: 2236
-
0 lines of code changed in 2 files:
-
.classpath (del),
.project (del)
-
msuchard
2009-09-11 09:16
#61
Rev.: 2235
-
17 lines of code changed in 2 files:
-
lib:
beagle.jar (changed)
-
src/dr/app/beagle/evomodel/treelikelihood:
BeagleTreeLikelihood.java (+17 -9)
-
msuchard
2009-09-11 06:47
#60
Rev.: 2234
-
0 lines of code changed in 1 file:
-
lib:
beagle.jar (changed)
-
dong.w.xie
2009-09-10 15:29
#59
Rev.: 2233
-
88 lines of code changed in 8 files:
-
src/dr/app/beauti:
BeautiFrame.java (+6)
-
src/dr/app/beauti/options:
BeautiOptions.java (+5 -4),
ModelOptions.java (+1 -8)
-
src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+13 -11)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+2 -2)
-
src/dr/evoxml:
DateParser.java (+6 -5),
DateUnitsType.java (new 52)
-
src/test/dr/beauti:
BeautiTesterConfig.java (+3 -2)
-
dong.w.xie
2009-09-10 14:46
#58
Rev.: 2232
-
10 lines of code changed in 3 files:
-
src/dr/app/beast:
BeastVersion.java (+5)
-
src/dr/app/beauti/options:
ModelOptions.java (+1 -1)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+4 -2)
-
dong.w.xie
2009-09-09 15:05
#57
Rev.: 2231
-
5 lines of code changed in 1 file:
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+5 -2)
-
dong.w.xie
2009-09-09 14:53
#56
Rev.: 2230
-
91 lines of code changed in 8 files:
-
src/dr/app/beauti/components:
TipDateSamplingComponentOptions.java (+4 -5)
-
src/dr/app/beauti/options:
BeautiOptions.java (+3 -1),
ModelOptions.java (+14 -9),
Parameter.java (+52 -156),
PartitionClockModelTreeModelLink.java (+4 -9),
PartitionOptions.java (+10 -4),
PriorOptions.java (-1)
-
src/dr/app/beauti/priorsPanel:
PriorDialog.java (+4 -2)
-
dong.w.xie
2009-09-09 13:16
#55
Rev.: 2229
-
741 lines of code changed in 17 files:
-
src/dr/app/beauti/components:
TipDateSamplingComponentOptions.java (+1 -1)
-
src/dr/app/beauti/enumTypes:
PriorType.java (+16 -16)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+18 -18),
Generator.java (+3 -3),
InitialTreeGenerator.java (+2 -2)
-
src/dr/app/beauti/options:
ClockModelOptions.java (+4 -4),
Operator_Backup.java (+141),
Parameter.java (+178 -64),
Parameter_Backup.java (+276),
PartitionClockModel.java (+3 -3),
PartitionClockModelTreeModelLink.java (+8 -8),
PartitionTreePrior.java (+3 -3),
PriorOptions.java (+25 -25)
-
src/dr/app/beauti/priorsPanel:
DiscretePriorDialog.java (+6 -6),
PriorDialog.java (+30 -30),
PriorsPanel.java (+1 -1)
-
src/dr/app/beauti/util:
BeautiTemplate.java (+26 -26)
-
dong.w.xie
2009-09-09 11:03
#54
Rev.: 2228
-
4 lines of code changed in 1 file:
-
src/dr/app/beauti/generator:
BeastGenerator.java (+4 -5)
-
jheled
2009-09-09 08:26
#53
Rev.: 2227
-
103 lines of code changed in 35 files:
-
src/dr/app/treestat:
TaxonSetsPanel.java (+1 -1)
-
src/dr/app/treestat/statistics:
DeltaStatistic.java (new)
-
src/dr/evolution/colouring:
TwoColourSampler.java (+11 -11)
-
src/dr/evolution/io:
NewickImporter.java (+1 -1)
-
src/dr/evolution/util:
Taxon.java (+1 -1)
-
src/dr/evolution/wrightfisher:
Population.java (+7 -7)
-
src/dr/evomodel/arg:
ARGModel.java (+16 -16),
ARGTraceAnalysis.java (+1 -1)
-
src/dr/evomodel/arg/coalescent:
VeryOldCoalescentLikelihood.java (+12 -14)
-
src/dr/evomodel/coalescent:
AbstractCoalescentLikelihood.java (+1 -1)
-
src/dr/evomodel/continuous:
ContinuousLikelihood.java (+2 -2),
RootTraitMLE.java (+3 -3)
-
src/dr/evomodel/sitemodel:
SampleStateAndCategoryModel.java (+11 -11),
SampleStateModel.java (+1 -1)
-
src/dr/evomodel/treelikelihood:
AdvancedTreeLikelihood.java (new)
-
src/dr/gui/chart:
ScatterPlot.java (+4 -3)
-
src/dr/gui/graph:
DefaultGraphModel.java (+4 -4)
-
src/dr/gui/tree:
JTreeDisplay.java (+1 -1)
-
src/dr/inference/markovchain:
Profiler.java (new)
-
src/dr/inference/model:
DuplicatedParameter.java (+1 -1),
MaskedParameter.java (+1 -1)
-
src/dr/inference/operators:
ScaleOperator.java (+2 -2)
-
src/dr/math/functionEval:
PolynomialFunction.java (new)
-
src/dr/xml:
AttributeParser.java (new)
-
dong.w.xie
2009-09-08 15:48
#52
Rev.: 2226
-
2 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+2)
-
jheled
2009-09-08 13:28
#51
Rev.: 2225
-
153 lines of code changed in 6 files:
-
src/dr/inference/model:
ParameterChooser.java (new),
ValuesPool.java (new),
Variable.java (+35 -2)
-
src/dr/inference/operators:
SelectorOperator.java (+109 -94)
-
jheled
2009-09-08 11:29
#50
Rev.: 2224
-
61 lines of code changed in 22 files:
-
src/dr/app/tracer/traces:
JIntervalsChart.java (+6 -4),
JTraceChart.java (+5 -5)
-
src/dr/evolution/sequence:
Sequence.java (+1 -1),
Sequences.java (+2 -2)
-
src/dr/evolution/tree:
FlexibleNode.java (+1 -1),
FlexibleTree.java (+10 -8),
SimpleNode.java (+1 -1),
SimpleTree.java (+4 -2)
-
src/dr/evolution/util:
Taxon.java (+2 -5)
-
src/dr/evomodel/arg:
ARGModel.java (+1 -1),
ARGTree.java (+7 -6)
-
src/dr/evomodel/speciation:
SpeciesTreeModel.java (+1 -1)
-
src/dr/evomodel/tree:
TreeModel.java (+1 -1)
-
src/dr/gui/graph:
DefaultVertex.java (+5 -5)
-
src/dr/gui/tree:
SquareTreePainter.java (+12 -12)
-
src/dr/util:
Attributable.java (+2 -2)
-
dong.w.xie
2009-09-08 10:44
#49
Rev.: 2223
-
47 lines of code changed in 5 files:
-
src/dr/app/beauti:
BeautiFrame.java (+11 -4)
-
src/dr/app/beauti/generator:
BeastGenerator.java (+2 -2)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+17 -26),
BeastImporter.java (+14 -11)
-
src/dr/app/oldbeauti:
BeastGenerator.java (+3 -3)
-
jheled
2009-09-08 06:42
#48
Rev.: 2222
-
266 lines of code changed in 8 files:
-
src/dr/inference/model:
ParameterChooser.java (+25 -4),
ParameterChooserParser.java (+5),
ValuesPool.java (+63 -11),
ValuesPoolParser.java (new),
Variable.java (+3 -3)
-
src/dr/inference/operators:
SelectorOperator.java (+160 -26)
-
jheled
2009-09-08 06:36
#47
Rev.: 2221
-
8 lines of code changed in 2 files:
-
src/dr/inferencexml:
PriorParsers.java (+7 -7)
-
src/dr/math/distributions:
LogNormalDistribution.java (+1 -1)
-
dong.w.xie
2009-09-07 17:30
#46
Rev.: 2220
-
906 lines of code changed in 3 files:
-
src/dr/app/beauti:
BeautiFrame.java (+452 -439)
-
src/dr/app/beauti/options:
BeautiOptions.java (+8 -19)
-
src/dr/app/beauti/util:
BEAUTiImporter.java (+446)
-
dong.w.xie
2009-09-07 15:50
#45
Rev.: 2219
-
10 lines of code changed in 2 files:
-
src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+10 -18)
-
src/dr/app/beauti/options:
PartitionOptions.java (-1)
-
jheled
2009-09-07 14:23
#44
Rev.: 2218
-
82 lines of code changed in 16 files:
-
src/dr/app/beauti/taxonsetspanel:
TaxaPanel.java (+4 -6)
-
src/dr/app/tools:
LogCombinerDialog.java (+6 -6)
-
src/dr/app/treestat/statistics:
GammaStatistic.java (+8 -6)
-
src/dr/evolution/alignment:
Defects.java (new)
-
src/dr/evolution/colouring:
DefaultBranchColouring.java (+17 -17)
-
src/dr/evolution/io:
NexusImporter.java (+14 -17)
-
src/dr/evolution/util:
Taxa.java (+7 -5),
Taxon.java (+3 -3)
-
src/dr/evomodel/tree:
TreeModel.java (+1 -1)
-
src/dr/gui/tree:
JTreeDisplay.java (+2 -2)
-
src/dr/inference/model:
CompoundParameter.java (+3 -3),
DesignMatrix.java (+1 -1),
MatrixParameter.java (+1 -1)
-
jheled
2009-09-07 14:23
#43
Rev.: 2217
-
3 lines of code changed in 2 files:
-
src/dr/evolution/tree:
CladeMetric.java (+3 -7)
-
dong.w.xie
2009-09-07 13:48
#42
Rev.: 2216
-
1 lines of code changed in 1 file:
-
src/dr/inference/model:
ValuesPoolParser.java (+1 -1)
-
dong.w.xie
2009-09-07 13:44
#41
Rev.: 2215
-
57 lines of code changed in 11 files:
-
src/dr/app/beauti/generator:
OperatorsGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
BeautiOptions.java (+1 -22),
ModelOptions.java (-3),
PartitionClockModel.java (+5),
PartitionClockModelTreeModelLink.java (+5),
PartitionData.java (+5),
PartitionOptions.java (+3),
PartitionSubstitutionModel.java (+5),
PartitionTreeModel.java (+4),
PartitionTreePrior.java (+5),
SubstitutionModelOptions.java (new 23)
-
jheled
2009-09-07 13:30
#40
Rev.: 2214
-
14 lines of code changed in 2 files:
-
src/dr/inference/distribution:
DistributionLikelihood.java (+7 -3),
EmpiricalDistributionLikelihood.java (+7 -4)
-
jheled
2009-09-07 13:29
#39
Rev.: 2213
-
62 lines of code changed in 12 files:
-
src/dr/evolution/tree:
Tree.java (+1 -1)
-
src/dr/evomodel/indel:
HomologyRecursion.java (+9 -11),
IntMathVec.java (+23 -21),
IstvansProposal.java (new)
-
src/dr/inference/distribution:
AbstractDistributionLikelihood.java (+1 -3)
-
src/dr/inference/operators:
NormalGammaPrecisionGibbsOperator.java (+7 -7),
NormalNormalMeanGibbsOperator.java (+3 -3),
ScaleOperator.java (+5 -5)
-
src/test/dr/evomodel/arg/operators:
ARGAddRemoveOperatorTest.java (+3 -8)
-
jheled
2009-09-07 13:29
#38
Rev.: 2212
-
14 lines of code changed in 6 files:
-
src/dr/gui/chart:
Plot.java (+6 -5)
-
src/dr/inference/distribution:
LogNormalDistributionModel.java (+3 -4)
-
src/dr/inference/model:
StatisticParser.java (new)
-
src/dr/inferencexml:
DistributionLikelihoodParser.java (new 1)
-
src/dr/xml:
XMLDocumentationHandler.java (+3 -3)
-
jheled
2009-09-07 13:28
#37
Rev.: 2211
-
458 lines of code changed in 22 files:
-
src/dr/inference/prior:
AbstractParameterPrior.java (+48 -52),
CompositePrior.java (new),
ContinuousVariablePrior.java (+84 -84),
ExponentialParameterPrior.java (+42 -42),
GammaParameterPrior.java (new),
LogPriorStatistic.java (+19 -19),
NormalParameterPrior.java (+50 -50),
ParameterPrior.java (+17 -17),
Prior.java (new),
SimplePrior.java (new),
UniformParameterPrior.java (new)
-
dong.w.xie
2009-09-07 12:54
#36
Rev.: 2210
-
36 lines of code changed in 1 file:
-
src/dr/app/beauti/mcmcpanel:
MCMCPanel.java (+36 -33)
-
jheled
2009-09-07 08:21
#35
Rev.: 2209
-
419 lines of code changed in 5 files:
-
src/dr/inference/model:
ParameterChooser.java (+71),
ParameterChooserParser.java (+38),
ValuesPool.java (+45),
ValuesPoolParser.java (+47)
-
src/dr/inference/operators:
SelectorOperator.java (+218)
-
jheled
2009-09-07 08:19
#34
Rev.: 2208
-
228 lines of code changed in 8 files:
-
src/dr/app/beagle/evomodel/parsers:
GTRParser.java (+26 -27)
-
src/dr/app/beagle/evomodel/substmodel:
GTR.java (+55 -54)
-
src/dr/evomodel/substmodel:
GTR.java (+81 -80),
HKY.java (+6 -5),
TN93.java (+18 -17)
-
src/dr/evomodelxml:
HKYParser.java (+5 -5)
-
src/dr/inference/model:
Variable.java (+37 -1)
-
jheled
2009-09-07 08:16
#33
Rev.: 2207
-
46 lines of code changed in 31 files:
-
src/dr/evolution/coalescent:
ScaledDemographic.java (new)
-
src/dr/evomodel/coalescent:
BMPriorLikelihood.java (+1 -1),
MultiLociTreeSet.java (+1 -1),
OrnsteinUhlenbeckPriorLikelihood.java (+1 -1)
-
src/dr/evomodel/operators:
TreeNodeSlide.java (+1 -1)
-
src/dr/evomodel/speciation:
BirthDeathGernhard08Model.java (+1 -1),
SpeciesBindings.java (+1 -1),
SpeciesTreeBMPrior.java (+1 -1),
SpeciesTreeModel.java (+1 -1),
SpeciesTreeSimplePrior.java (+1 -1),
TreePartitionCoalescent.java (new 15)
-
src/dr/inference/loggers:
BooleanColumn.java (new),
PercentColumn.java (+1 -1)
-
src/dr/inference/model:
AbstractModelLikelihood.java (+1 -1)
-
src/dr/inference/trace:
LogFileTraceExporter.java (+4 -9)
-
src/dr/util:
FileHelpers.java (+1 -1),
TabularData.java (+7),
Transform.java (+2)
-
src/test/dr/distibutions:
InvGammaTest.java (+1 -1)
-
src/test/dr/evomodel/coalescent:
VDdemographicFunctionTest.java (+1 -1)
-
src/test/dr/evomodel/substmodel:
HKYTest.java (+1 -1),
TN93Test.java (+1 -1)
-
jheled
2009-09-07 08:15
#32
Rev.: 2206
-
5 lines of code changed in 3 files:
-
src/dr/util:
HeapSort.java (new),
MessageLogHandler.java (+3 -4)
-
jheled
2009-09-07 08:15
#31
Rev.: 2205
-
26 lines of code changed in 13 files:
-
src/dr/app/beagle/evomodel/substmodel:
BaseSubstitutionModel.java (-1)
-
src/dr/evomodel/sitemodel:
SiteModel.java (-1)
-
src/dr/evomodelxml:
CSVExporter.java (new 3)
-
src/dr/inference/model:
SumStatistic.java (+9 -11)
-
src/dr/inference/operators:
LogRandomWalkOperator.java (-1)
-
src/dr/stats:
DiscreteStatistics.java (+8 -13)
-
src/dr/util:
Attribute.java (+2 -3),
ComparableDouble.java (+3 -3),
Identifiable.java (-1)
-
src/dr/xml:
Report.java (+1 -1)
-
jheled
2009-09-07 08:12
#30
-
85 lines of code changed in 4 files:
-
src/dr/util:
Assert.java (new),
CollectionHash.java (new)
-
jheled
2009-09-07 08:06
#29
Rev.: 2202
-
6 lines of code changed in 3 files:
-
src/dr/inference/mcmc:
MCMCCriterion.java (new)
-
src/dr/inference/operators:
SimpleOperatorSchedule.java (+4 -2)
-
jheled
2009-09-05 16:35
#28
Rev.: 2201
-
78 lines of code changed in 12 files:
-
src/dr/xml:
AbstractXMLObjectParser.java (+4 -4),
AndRule.java (+13 -4),
AttributeRule.java (+7 -4),
ContentRule.java (+7 -3),
ElementRule.java (+11 -2),
OrRule.java (new),
XMLSyntaxRule.java (new),
XORRule.java (new)
-
jheled
2009-09-05 16:34
#27
Rev.: 2200
-
1 lines of code changed in 1 file:
-
src/dr/inference/trace:
LogFileTraceExporter.java (+1 -1)
-
dong.w.xie
2009-09-04 15:44
#26
Rev.: 2199
-
49 lines of code changed in 4 files:
-
src/dr/app/beast:
development_parsers.properties (+1),
release_parsers.properties (+1)
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+46 -31)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+1 -1)
-
jheled
2009-09-04 10:35
#25
Rev.: 2198
-
2 lines of code changed in 1 file:
-
src/dr/xml:
XMLSyntaxRule.java (+2 -2)
-
dong.w.xie
2009-09-04 10:34
#24
Rev.: 2197
-
60 lines of code changed in 6 files:
-
src/dr/app/beauti/enumTypes:
BinaryModelType.java (new 43)
-
src/dr/app/beauti/generator:
SubstitutionModelGenerator.java (+6 -6),
TreeLikelihoodGenerator.java (+1 -1)
-
src/dr/app/beauti/options:
ModelOptions.java (+2 -2),
PartitionSubstitutionModel.java (+4 -3)
-
src/dr/app/beauti/siteModelsPanel:
PartitionModelPanel.java (+4 -3)
-
dong.w.xie
2009-09-04 10:33
#23
Rev.: 2196
-
6 lines of code changed in 1 file:
-
build_BEAST_MCMC.xml (+6 -6)
-
jheled
2009-09-04 10:29
#22
Rev.: 2195
-
48 lines of code changed in 12 files:
-
src/dr/app/beagle/evomodel/parsers:
CompoundLikelihoodParser.java (+4 -2)
-
src/dr/app/beast:
BeastMain.java (+5 -4)
-
src/dr/evomodel/substmodel:
AbstractNucleotideModel.java (-1),
AbstractSubstitutionModel.java (+8 -1)
-
src/dr/inference/model:
CompoundLikelihood.java (+4 -4),
DefaultModel.java (-3),
PathLikelihood.java (-2)
-
src/dr/inference/prior:
Prior.java (+3 -3)
-
src/dr/inferencexml:
PriorParsers.java (+3 -3)
-
src/dr/xml:
XMLModelFile.java (+21 -22)
-
jheled
2009-09-04 10:29
#21
Rev.: 2194
-
12 lines of code changed in 6 files:
-
src/dr/app/beagle/evomodel/parsers:
FrequencyModelParser.java (+1 -1),
HKYParser.java (+1 -1)
-
src/dr/app/oldbeauti:
BeautiFrame.java (+6 -5)
-
src/dr/app/tools:
AncestralSequenceAnnotator.java (+1 -1)
-
src/dr/inference/model:
DuplicatedParameter.java (+2 -2),
MaskedParameter.java (+1 -1)
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jheled
2009-09-04 10:28
#20
Rev.: 2193
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47 lines of code changed in 1 file:
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src/dr/xml:
AbstractXMLObjectParser.java (+47 -2)
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dong.w.xie
2009-09-03 17:14
#19
Rev.: 2191
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22833 lines of code changed in 36 files:
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doc/Virus Practical Tex:
Alexei Workshop.pdf (new),
Practical_BEAST.aux (new 2),
Practical_BEAST.pdf (new 21003),
Practical_BEAST.tex (new 1827)
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doc/Virus Practical Tex/figures1:
BEAUti_Clock_Model.png (new),
BEAUti_Data.png (new),
BEAUti_MCMC.png (new),
BEAUti_Model.png (new),
BEAUti_Prior.png (new),
BEAUti_Prior1.png (new),
BEAUti_Prior2.png (new),
BEAUti_Subst_Model.png (new),
BEAUti_Taxa.png (new),
BEAUti_Tree.png (new),
FigTree.png (new),
ImportNexus.png (new),
SamplePriorOnly.png (new),
Tracer1.png (new),
Tracer_divergences.png (new),
Tracer_marginalDensity.png (new),
TreeAnnotator1.png (new),
beauti.png (new)
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doc/Virus Practical Tex/figures2:
BEAUTi_Subst_Model.png (new),
Figtree.png (new),
GuessDates.png (new),
Tracer1.png (new),
Tracer2.png (new),
Tracer_density.png (new),
Tracer_relativeRates.png (new),
TreeAnnotator.png (new)
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doc/Virus Practical Tex/figures3:
BEAUTi_Tree.png (new),
Figtree.png (new),
Tracer_BSP.png (new),
Tracer_relativeRates.png (new),
TreeAnnotator.png (new)
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src/dr/app/beast:
BeastVersion.java (+1 -1)
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dong.w.xie
2009-09-03 17:02
#18
Rev.: 2190
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0 lines of code changed in 32 files:
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doc/Virus Practical Tex:
Practical_BEAST.aux (del),
Practical_BEAST.tex (del)
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doc/Virus Practical Tex/figures1:
BEAUti_Data.png (changed),
BEAUti_Model.png (changed),
BEAUti_Prior.png (changed),
BEAUti_Prior1.png (changed),
BEAUti_Prior2.png (changed),
BEAUti_Taxa.png (changed),
FigTree.png (changed),
ImportNexus.png (changed),
SamplePriorOnly.png (changed),
Tracer1.png (changed),
Tracer_divergences.png (changed),
Tracer_marginalDensity.png (changed),
TreeAnnotator1.png (changed),
beauti.png (changed)
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doc/Virus Practical Tex/figures2:
Figtree.png (changed),
GuessDates.png (changed),
Tracer1.png (changed),
Tracer2.png (changed),
Tracer_density.png (changed),
Tracer_relativeRates.png (changed),
TreeAnnotator.png (changed)
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doc/Virus Practical Tex/figures3:
Figtree.png (changed),
Tracer_BSP.png (changed),
Tracer_relativeRates.png (changed),
TreeAnnotator.png (changed)
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examples/beauti1.5/Virus Practical/FPV:
FPV.xml (new),
FPV1.xml (new)
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examples/beauti1.5/Virus Practical/Flu:
Flu.xml (new)
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examples/beauti1.5/Virus Practical/RSVA:
RSVA.xml (new),
RSVA1.xml (new)
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Sibon.Li@gmail.com
2009-09-03 16:05
#17
Rev.: 2189
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16 lines of code changed in 1 file:
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src/dr/app/tools:
NormaliseMeanTreeRate.java (+16 -89)
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Sibon.Li@gmail.com
2009-09-03 15:51
#16
Rev.: 2188
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8 lines of code changed in 1 file:
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src/dr/app/tools:
NexusExporter.java (+8 -5)
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dong.w.xie
2009-09-03 12:12
#15
Rev.: 2186
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983 lines of code changed in 30 files:
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doc/Virus Practical Tex:
Practical_BEAST.aux (+1),
Practical_BEAST.tex (+887)
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doc/Virus Practical Tex/figures1:
BEAUti_Data.png (changed),
BEAUti_Model.png (new),
BEAUti_Prior.png (new),
BEAUti_Prior1.png (changed),
BEAUti_Prior2.png (changed),
BEAUti_Taxa.png (changed),
FigTree.png (changed),
ImportNexus.png (changed),
SamplePriorOnly.png (changed),
Tracer1.png (changed),
Tracer_divergences.png (changed),
Tracer_marginalDensity.png (changed),
TreeAnnotator1.png (changed),
beauti.png (new)
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doc/Virus Practical Tex/figures2:
Figtree.png (changed),
GuessDates.png (changed),
Tracer1.png (changed),
Tracer2.png (changed),
Tracer_density.png (changed),
Tracer_relativeRates.png (changed),
TreeAnnotator.png (changed)
-
doc/Virus Practical Tex/figures3:
Figtree.png (changed),
Tracer_BSP.png (changed),
Tracer_relativeRates.png (changed),
TreeAnnotator.png (changed)
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examples/beauti1.5/Virus Practical/FPV:
FPV.nex (new 15)
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examples/beauti1.5/Virus Practical/Flu:
Flu.nex (new 33)
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examples/beauti1.5/Virus Practical/RSVA:
RSVA.nex (new 47)
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dong.w.xie
2009-09-03 12:10
#14
Rev.: 2185
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28 lines of code changed in 1 file:
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release:
VERSION HISTORY.txt (new 28)
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alexei.drummond
2009-09-03 11:32
#13
Rev.: 2184
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38 lines of code changed in 2 files:
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release:
README.txt (new 6),
VERSION HISTORY.txt (+32 -5)
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dong.w.xie
2009-09-03 09:50
#12
Rev.: 2182
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1 lines of code changed in 1 file:
-
src/dr/app/beast:
BeastVersion.java (+1 -1)
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Sibon.Li@gmail.com
2009-09-02 17:36
#11
Rev.: 2180
-
10 lines of code changed in 1 file:
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src/dr/evomodel/tree:
TreeLogger.java (+10)
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dong.w.xie
2009-09-02 17:36
#10
Rev.: 2179
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4 lines of code changed in 1 file:
-
src/dr/app/beauti/options:
ClockModelOptions.java (+4)
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Sibon.Li@gmail.com
2009-09-02 17:35
#9
Rev.: 2178
-
71 lines of code changed in 1 file:
-
src/dr/app/tools:
NormaliseMeanTreeRate.java (+71 -73)
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Sibon.Li@gmail.com
2009-09-02 17:34
#8
Rev.: 2177
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19 lines of code changed in 1 file:
-
src/dr/app/tools:
NexusExporter.java (+19 -6)
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dong.w.xie
2009-09-02 16:59
#7
Rev.: 2176
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32 lines of code changed in 3 files:
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src/dr/app/beauti/clockModelsPanel:
ClockModelsPanel.java (+4 -1)
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src/dr/app/beauti/options:
BeautiOptions.java (+1 -1),
ClockModelOptions.java (+27)
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dong.w.xie
2009-09-02 09:54
#6
Rev.: 2175
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1 lines of code changed in 1 file:
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src/dr/app/beast:
BeastVersion.java (+1 -1)
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rambaut
2009-09-01 21:06
#5
Rev.: 2174
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2 lines of code changed in 1 file:
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src/dr/app/beast:
BeastVersion.java (+2 -2)
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dong.w.xie
2009-09-01 16:24
#4
Rev.: 2172
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178 lines of code changed in 10 files:
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src/dr/app/beauti/options:
BeautiOptions.java (-26),
ClockModelOptions.java (+69 -17),
ModelOptions.java (-4),
Parameter.java (+37 -3),
PartitionClockModel.java (+26 -26),
PartitionClockModelTreeModelLink.java (+2 -2),
PartitionOptions.java (+13 -1),
PartitionTreeModel.java (+3 -3),
PriorOptions.java (+18 -4)
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src/dr/app/beauti/tipdatepanel:
TipDatesPanel.java (+10 -6)
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jheled
2009-09-01 09:58
#3
Rev.: 2171
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10 lines of code changed in 1 file:
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src/dr/inference/markovchain:
MarkovChain.java (+10 -4)
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dong.w.xie
2009-09-01 09:22
#2
Rev.: 2170
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64 lines of code changed in 2 files:
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build_BEAST_MCMC.xml (+64 -13)
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release:
jarbundler-2.1.0.jar (new)
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Sibon.Li@gmail.com
2009-09-01 00:21
#1
Rev.: 2169
-
6 lines of code changed in 1 file:
-
src/dr/app/tools:
NormaliseMeanTreeRate.java (+6 -4)