simSeqfromSp {phybase} | R Documentation |
The function simulates sequences from a species tree.
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")
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" |
The function writes sequences into a file.
Liang Liu lliu@oeb.harvard.edu
Felsenstein, J. The Newick tree format. http://evolution.genetics.washington.edu/phylip/newicktree.html
write.subtree
, read.tree.string
#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)