write.dna: Write sequences to a Nexus file
In bomeara/phybase: Basic functions for phylogenetic analysis

write sequences to a Nexus file.

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)

`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.