Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

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Documentation for package ‘treedater’ version 0.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

treedater-package	treedater fits a molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.
boot	Estimate of confidence intervals of molecular clock parameters with user-supplied set of bootstrap trees
dater	Estimate a time-scaled tree and fit a molecular clock
goodnessOfFitPlot	Produce a goodness of fit plot
outlierLineages	Detect lineages with unusually large evolutionary divergence under the fitted treedater model
outlierTips	Detect terminal lineages with unusually large evolutionary divergence under the fitted treedater model
parboot	Estimate of confidence intervals using parametric bootstrap for molecular clock dating.
plot.bootTreedater	Plots lineages through time and confidence intervals estimated by bootstrap.
relaxedClockTest	Use parametric bootstrap to test if relaxed clock offers improved fit to data.
rootToTipRegressionPlot	Plot evolutionary distance from root to sample times and estimated internal node times and regression lines
sampleYearsFromLabels	Compute a vector of numeric sample times from labels in a sequence aligment or phylogeny
treedater	treedater fits a molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry.