├── .DS_Store ├── DESCRIPTION ├── NAMESPACE ├── R ├── .DS_Store ├── AncCond.R ├── CalcD.R ├── FuzzyMatch.R ├── GetTipRates.R ├── Pfsa.R ├── ReOrderAlignment.R ├── ResSel.R ├── SampleTrees.R ├── SlidingWindow.R ├── SuperMatrix.R ├── WinCalcD.R ├── countTrees.R ├── fix.simmap.R ├── getNe.R ├── make.simmap2.R ├── plot.phyloscaled.R ├── scaleTreeRates.R └── zzz.R ├── README.html ├── README.md ├── data ├── hym.tree.rda ├── mite.trait.RData └── trees.mite.rda ├── inst ├── 1.fasta ├── 3.fasta ├── horn.beetle.csv └── trees.nex ├── man ├── 1.fasta.Rd ├── AncCond.Rd ├── CalcD.Rd ├── FuzzyMatch.Rd ├── GetTipRates.Rd ├── Pfsa.Rd ├── ReOrderAlignment.Rd ├── ResSel.Rd ├── SampleTrees.Rd ├── SlidingWindow.Rd ├── SuperMatrix.Rd ├── WinCalcD.Rd ├── countTrees.Rd ├── evobiR-package.Rd ├── fix.simmap.Rd ├── getNe.Rd ├── horn.beetle.Rd ├── hym.tree.Rd ├── make.simmap2.Rd ├── mite.trait.Rd ├── plot.phyloscaled.Rd ├── scaleTreeRates.Rd ├── trees.mite.Rd └── trees.nex.Rd └── vignettes ├── .DS_Store ├── 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