Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

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.

To cite:

Installation

You can install the latest development version from github using the devtools package:

library(devtools)
install_github( 'emvolz/treedater')

Basic usage

dater( tre, sts, s)

where

  • tre is an ape::phylo phylogeny,
  • sts is a named vector of sample times for each tip in tre
  • s is the length of the genetic sequences used to estimate tre

For a detailed introduction to features available in treedater, see the vignette on analysis of Influena H3N2: vignette('h3n2').

Command line

You can also use treedater from the command line without starting R using the tdcl script:

./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 Rscript or littler.

News

Reference manual

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install.packages("treedater")

0.3.0 by Erik Volz, 8 months ago


Browse source code at https://github.com/cran/treedater


Authors: Erik Volz [aut, cre]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL-2 license


Imports ape

Depends on limSolve

Suggests lubridate, ggplot2, foreach, iterators, mgcv, knitr, rmarkdown, harmonicmeanp


See at CRAN