├── .gitignore ├── .travis.yml ├── COPYING ├── README.md ├── examples ├── README.md ├── smoothingpriors │ ├── OUPriorTests.Rmd │ ├── OUPriorTests.html │ ├── OUPriorTests.md │ ├── comparison │ │ └── hcv_bdsky.xml │ ├── figs │ │ ├── ouprior_test1-1.png │ │ ├── ouprior_test2-1.png │ │ ├── ouprior_test3-1.png │ │ ├── ouprior_test4-1.png │ │ └── ouprior_test5-1.png │ ├── ouprior_test1.xml │ ├── ouprior_test2.xml │ ├── ouprior_test3.xml │ ├── ouprior_test4.xml │ └── ouprior_test5.xml └── treeslicer │ ├── comparison │ ├── dengue4_bdsky_csc.xml │ ├── dengue4_bdsky_equidistant5.xml │ ├── dengue4_bdsky_equidistant5_rootcondition.xml │ └── dengue4_bdsky_fixeddates.xml │ ├── dengue4_bdsky_csc_treeslicer.xml │ ├── dengue4_bdsky_csc_treeslicer_joint.xml │ ├── dengue4_bdsky_datestrings_treeslicer.xml │ ├── dengue4_bdsky_equidistant5_treeslicer.xml │ ├── dengue4_bdsky_equidistant5_treeslicer_joint.xml │ └── dengue4_bdsky_fixeddates_treeslicer.xml ├── src ├── beast │ └── evolution │ │ └── speciation │ │ └── BirthDeathSkylineModelTestHelper.java └── skylinetools │ ├── distributions │ ├── BMPrior.java │ └── OUPrior.java │ ├── parameter │ ├── DateParser.java │ └── RealParameterSequence.java │ └── util │ ├── TreeDateLogger.java │ ├── TreeDateSlicer.java │ ├── TreeSliceDateLogger.java │ └── TreeSlicer.java ├── test ├── README.md ├── beast │ └── evolution │ │ └── speciation │ │ └── SkylineTimesTest.java ├── skylinetools │ ├── distributions │ │ └── OUPriorLkTest.java │ ├── parameter │ │ ├── DateParserTest.java │ │ └── RealParameterSequenceTest.java │ └── util │ │ ├── TreeDateSlicerTest.java │ │ └── TreeSlicerTest.java ├── tree.C1.MCC.trim.round.figtree.tree └── tree.C2.MCC.trim.round.figtree.tree └── version.xml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/laduplessis/skylinetools/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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