Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017)
treedater fits a strict or relaxed molecular clock to a phylogenetic tree and estimates evolutionary rates and times of common ancestry. The calendar time of each sample must be specified (possibly with bounds of uncertainty) and the length of the sequences used to estimate the tree.
treedater uses heuristic search to optimise the TMRCAs of a phylogeny and the substitution rate.
An uncorrelated relaxed molecular clock accounts for rate variation between lineages of the phylogeny which is parameterised using a Gamma-Poisson mixture model.
You can install the latest development version from github using the
library(devtools) install_github( 'emvolz/treedater')
dater( tre, sts, s)
stsis a named vector of sample times for each tip in
sis the length of the genetic sequences used to estimate
For a detailed introduction to features available in
treedater, see the vignette on analysis of Influena H3N2:
You can also use treedater from the command line without starting R using the
./tdcl -h Usage: ./tdcl [-[-help|h] [<logical>]] [-[-treefn|t] <character>] [-[-samplefn|s] <character>] [-[-sequenceLength|l] <double>] [-[-output|o] [<character>]] -t <file> : file name of tree in newick format -s <file> : should be a comma-separated-value file with sample times in format <taxon-id,sample-time> and no header -l <length> : the integer length of sequences in alignment used to construct the tree -o <file>: name of file for saving output
Note that you may need to modify the first line of the
tdcl script with the correct path to