Files in sebastianduchene/NELSI
NELSI: Nucleotide EvoLution Simulator
.ipynb_checkpoints/get_ancestor_nodes-checkpoint.ipynb
DESCRIPTION
Ho_et_al_examples/README.Rnw
Ho_et_al_examples/README.html
Ho_et_al_examples/README.md
Ho_et_al_examples/README.md~
Ho_et_al_examples/README.rmd
Ho_et_al_examples/README.rmd~
Ho_et_al_examples/figure/unnamed-chunk-3.png
Ho_et_al_examples/figure/unnamed-chunk-4.png
Ho_et_al_examples/figure/unnamed-chunk-6.png
Ho_et_al_examples/yuletr9.tre
NAMESPACE
R/.Rhistory
R/allnode.times.R
R/annotatedTreeReader.R
R/dist.topo.normalised.R
R/distunlab.R
R/find.monophyletic.R
R/find.sister.R
R/get.ancestor.nodes.branches.R
R/get.branches.age.sorted.R
R/get.clock.data.R
R/get.deepest.br.length.R
R/get.descending.nodes.branches.R
R/get.df.R
R/get.external.branch.length.R
R/get.first.node.height.R
R/get.internal.branch.length.R
R/get.lineage.time.rate.R
R/get.ltt.summary.R
R/get.mrca.R
R/get.oldest.branch.length.R
R/get.ordinates.R
R/get.rate.descendant.pairs.R
R/get.rtt.dist.R
R/get.tree.data.matrix.R
R/intnode.times.R
R/is.polytomy.R
R/make.lsd.dates.R
R/mid.edge.ages.R
R/node.to.tip.dist.R
R/pathnode.R
R/plot.ratesim.R
R/simulate.FLC.R
R/simulate.autocor.kishino.R
R/simulate.autocor.thorne.R
R/simulate.clock.R
R/simulate.dpp.R
R/simulate.rate.R
R/simulate.tdep.ho.R
R/simulate.uncor.exp.R
R/simulate.uncor.gamma.R
R/simulate.uncor.lnorm.R
R/simulate.white.noise.R
R/stemmy.R
R/sum.descending.branches.R
R/testing.R~
R/trann2trdat.R
README.md
Untitled0.ipynb
example_data/hiv_A_env.tree
example_data/tr_example.tree
example_data/tutorial.txt~
experimental/README.md
experimental/Rplot.pdf
experimental/beast_reader.R
experimental/beast_reader.R~
experimental/fig1.pdf
experimental/fig1_2.svg
experimental/figure/unnamed-chunk-11.png
experimental/figure/unnamed-chunk-12.png
experimental/figure/unnamed-chunk-13.png
experimental/figure/unnamed-chunk-17.png
experimental/figure/unnamed-chunk-18.png
experimental/figure/unnamed-chunk-3.png
experimental/figure/unnamed-chunk-5.png
experimental/figure/unnamed-chunk-6.png
experimental/figure/unnamed-chunk-7.png
experimental/figure/unnamed-chunk-8.png
experimental/flcTests/testingCode
experimental/get_tips.R
experimental/nelsi_tutorial_dna.fasta
experimental/nelsi_tutorial_pylogram.tree
experimental/papers_figs.R
experimental/papers_figs.R~
experimental/plot.beast.tree.R
experimental/relaxed_uni.trees
experimental/relaxed_uni.txt
experimental/relaxed_uni_Dicty.trees
experimental/relaxed_uni_Dicty.txt
experimental/simulate.uncor.beta.R
experimental/summ_trees.R
experimental/summ_trees.R~
experimental/tree_summaries.zip
experimental/tree_summaries/relaxed_uni.txt
experimental/tree_summaries/relaxed_uni_Dicty.txt
experimental/tree_summaries/relaxed_uni_names.txt
experimental/tree_summaries/relaxed_uni_names_Dicty.txt
experimental/tut.html
experimental/tut.md
experimental/tutorial-out.docx
experimental/tutorial-out.txt
experimental/tutorial.docx
experimental/tutorial.html
experimental/tutorial.md
experimental/tutorial.rnw
experimental/tutorial.txt
experimental/xml_p88.txt
experimental/xml_p88.txt~
figure/unnamed-chunk-11.png
figure/unnamed-chunk-12.png
figure/unnamed-chunk-13.png
figure/unnamed-chunk-17.png
figure/unnamed-chunk-18.png
figure/unnamed-chunk-3.png
figure/unnamed-chunk-4.png
figure/unnamed-chunk-5.png
figure/unnamed-chunk-6.png
figure/unnamed-chunk-7.png
figure/unnamed-chunk-8.png
figure/unnamed-chunk-9.png
get_ancestor_nodes.ipynb
man/.DS_Store
man/NELSI_0.2-package.Rd
man/allnode.times.Rd
man/annotatedTreeReader.Rd
man/get.clock.data.Rd
man/get.lineage.time.rate.Rd
man/get.rate.descendant.pairs.Rd
man/get.tree.data.matrix.Rd
man/mid.edge.ages.Rd
man/pathnode.Rd
man/plot.ratesim.Rd
man/simulate.autocor.kishino.Rd
man/simulate.autocor.thorne.Rd
man/simulate.clock.Rd
man/simulate.dpp.Rd
man/simulate.rate.Rd
man/simulate.tdep.ho.Rd
man/simulate.uncor.exp.Rd
man/simulate.uncor.gamma.Rd
man/simulate.uncor.lnorm.Rd
man/simulate.white.noise.Rd
man/trann2trdat.Rd
tr.pdf
tutorial/example_data/.DS_Store
