simSeqfromSp: simulate DNA sequences from a species tree

In bomeara/phybase: Basic functions for phylogenetic analysis

Description

The function simulates sequences from a species tree.

Usage

simSeqfromSp(sptree, spname, ntaxasp, ngene, theta=0, noclock=0, 
simsequence=1, murate="Dirichlet",alpha=5, seqlength=100, model=1, 
kappa=2, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4), 
outfile, format="phylip")

Arguments

sptree	A species tree which must be a rooted tree.
spname	species names
ntaxasp	a vector of the number of individuals in each species
ngene	number of genes
theta	population size
noclock	0: clocklike species tree 1: nonclocklike species tree
simsequence	1: simulate sequences and gene trees, 0: simulate gene trees
murate	distribution of mutation rates
alpha	the shape parameter of dirichlet distribution
seqlength	the number of nucleotides along the sequences
model	substitution model
kappa	transition/transversion ratio
rate	rates
frequency	nucleotide frequency
outfile	the full path of the output file
format	either "phylip" or "nexus"

Value

The function writes sequences into a file.

Author(s)

Liang Liu [e-mail]

References

Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html

See Also

write.subtree, read.tree.string

Examples

#read the species tree from a data file
data(sptree)
outfile<-"out.txt"
spname <- paste("S",1:20,sep="")
outgroup <- "S20"
ntaxasp <- rep(2,length(spname))
ntaxasp[length(spname)]<-1
ngene<-2
seqlength<-100
simSeqfromSp(sptree,spname,ntaxasp,noclock=1,ngene=ngene,
seqlength=seqlength,model=1,outfile=outfile)
simSeqfromSp(sptree,spname,ntaxasp,noclock=0,ngene=ngene,simsequence=0,
seqlength=seqlength,model=1,outfile=outfile)

bomeara/phybase documentation built on May 12, 2019, 11:35 p.m.