write.dna.seq: Write sequences to a Nexus file

In lliu1871/phybase: Basic functions for phylogenetic analysis

Write sequences to a Nexus file

Description

write sequences to a Nexus file.

Usage

write.dna.seq(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

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.