write.dna {phybase}R Documentation

Write sequences to a Nexus file

Description

write sequences to a Nexus file.

Usage

write.dna(sequence, name, file = "", format="nexus", program="mrbayes",partition=matrix(0,ncol=2,nrow=1), clock=0, popmupr=0, ngen=1000000,nrun=1,nchain=1,samplefreq=100,taxa=as.vector,burnin=1000,gamma="(3,0.02)", outgroup=1,outfile="",append = FALSE)

Arguments

sequence DNA sequences
name taxa names
file output file
program either mrbayes or best.
format nexus or phylip
partition each partition corresponds a gene or a locus.
clock 1:clock, 0:no clock
popmupr for non-clock species tree model
ngen number of generations
nrun number of runs
nchain number of chains
samplefreq sampling frequency
taxa species names if best is defined
burnin burn in
outgroup the node number of the outgroup
outfile output file
append append or not
gamma parameters in the inverse gamma distribution as the prior of theta.

Author(s)

Liang Liu


[Package phybase version 1.1 Index]