Detection of trait-dependent shifts in the rate of molecular evolution with traitRate (Mayrose & Otto, 2011).
traitRate(phy, seq, x, mainType = "Optimize_Model",
n, charModelParam1 = 0.5, charModelParam2 = 1,
gammaParam = 0.5, seqModelParam1 = 2,
exec = "/Applications/traitRate-1.1/programs/traitRate")a ultrametric phylogenetic tree of class phylo.
a multiple sequence alignment of class DNAbin.
data frame containing a binary character in the first column.
character string giving the type of analysis; two choices are possible: "Optimize_Model" will produce MLE of parameters and "runTraitBootstrap" will perform a parametric bootstrap analysis.
numeric, the number of bootstrap replicates. Will be ignored if mainType = "Optimize_Model".
numeric, giving an initial value for the rate of transitions of character state 0 to 1.
numeric, giving an initial value for the rate of transitions of character state 1 to 0.
numeric, giving an initial value for the alpha parameter of the model of sequence evolution.
numeric, giving an initial value for the kappa parameter of the model of sequence evolution.
character string giving the path to the program directory.
Currently none, but look for the output files in the 'RESULTS' subdirectory in the current working directory.
Mayrose, I. & S.P. Otto. 2011. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol. Biol. Evol. 28: 759-770
read.tree for reading phylogenetic trees, read.fas for reading multiple sequence alignments in FASTA format.