sim.SeqfromSp: simulate DNA sequences from a species tree

In lliu1871/phybase: Basic functions for phylogenetic analysis

simulate DNA sequences from a species tree

Description

The function simulates sequences from a species tree. The function assumes that seq-gen has been installed

Usage

sim.SeqfromSp(sptree, spname, ntaxasp, ngene, theta=0, noclock=0, 
simsequence=1, murate="Dirichlet",alpha=5, seqlength=100, rate=c(1,1,1,1,1,1), frequency=c(1/4,1/4,1/4,1/4), 
outfile, format="phylip", concat=TRUE)

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
rate	rates
frequency	nucleotide frequency
outfile	the full path of the output file
format	either "phylip" or "nexus"
concat	save the concatenated sequences or save single-gene sequences as different data in the same file

Value

The function writes sequences into a file.

Author(s)

Liang Liu [e-mail]

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